http://wiki.biouml.org/api.php?action=feedcontributions&user=Lan%40dote.ru&feedformat=atomBioUML platform - User contributions [en]2024-03-29T15:17:05ZUser contributionsMediaWiki 1.20.3http://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2016-06-27T09:08:23Z<p>Lan@dote.ru: /* Try BioUML web edition */</p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* Test server (free) http://ie.biouml.org/bioumlweb/<br />
* Commercial server (free and licensed) http://genexplain-platform.com/bioumlweb/<br />
* '''Server for Colon cancer project''' http://ge.mimomics.it/bioumlweb/<br />
(Colon Cancer Public datasets)<br />
(SysCol project)<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
<br />
=== Examples ===<br />
* [[Metabolic control analysis]]<br />
* [[Quasi-steady-state approximation]]<br />
* [[Sensitivity analysis]]<br />
* [[Flux balance analysis]]<br />
<br />
|}<br />
<br />
<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_server_installationBioUML server installation2015-06-25T09:43:55Z<p>Lan@dote.ru: /* Development installation */</p>
<hr />
<div>This page describes how to install BioUML server provided that you have a CVS access to BioUML sources.<br />
<br />
== Paths ==<br />
The following paths will be referred within this document:<br />
* $SERVER_PATH - path to main BioUML installation folder. Usually it’s /opt/BioUML_Server.<br />
* $CATALINA_HOME - path to tomcat folder.<br />
* $SOURCES - path to BioUML sources<br />
<br />
== Prerequisites ==<br />
* Linux server. Ubuntu preferred.<br />
* Java. Oracle JDK 1.8 or OpenJDK 1.8.<br />
* Apache Tomcat (7+).<br />
aptitude install tomcat7<br />
* Apache Ant.<br />
aptitude install ant<br />
If you see compilation error about org.apache.tools.ant.util.regexp.Jdk14RegexpRegexp, you have to install one of the following:<br />
aptitude install ant-optional<br />
aptitude install ant-apache-regexp<br />
* MySQL (5+):<br />
aptitude install mysql-server<br />
* R (required for some functions such as microarray data normalization) — see [[R installation]] page.<br />
* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)<br />
* Eclipse Java IDE (preferred IDE for development, you may use others as well).<br />
<br />
== BioStore server registration ==<br />
In order to activate user account management server should be registered in BioStore system. For this perform the following steps:<br />
* Register in the BioStore: https://bio-store.org/biostore/ (leave “My first project” fields empty)<br />
* Write an e-mail to us specifying the following information:<br />
** The stable Internet address of your server (host:port). If it’s accessible via local network only, then it’s ok to specify your local address.<br />
** User-friendly server name.<br />
** List of logins (e-mails) registered via BioStore who should become server administrators.<br />
* We will create the server entry and change the permission settings, so you will be able to administer the server.<br />
Further there will be special form for automated server registration via Biostore<br />
<br />
== Development installation ==<br />
For internal development installation you may skip the BioStore integration. Instead write the following in the security.properties file:<br />
<br />
jdbcDriverClass=org.gjt.mm.mysql.Driver<br />
jdbcURL=jdbc:mysql://lachesis:3306/bioumlsupport2<br />
jdbcUser=bioumlsupport2<br />
jdbcPassword=bioumlsupport2<br />
<br />
securityProvider=ru.biosoft.access.security.TestSecurityProvider<br />
products=Server;Import;R;Experimental<br />
<br />
This will bypass the authentication and authorization: every user with any password will have administrative privileges and subscription to the specified products. Change the list of the products if necessary.<br />
<br />
== Getting sources ==<br />
CVS: use the following CVS-root:<br />
:pserver:<username>@cvs.developmentontheedge.com:/usr/cvsroot-biouml (please request an account via e-mail)<br />
<br />
== Deployment prepare ==<br />
Specify $SERVER_PATH in BioUML/src/build.xml:<br />
<property name="SERVER_PATH" value="C:/BioUML_Server_0.9.4" /><br />
Change it to the appropriate value.<br />
<br />
Depending on your Tomcat installation you may need to define DEPLOY_DIR inside “deploy.server” target. Add<br />
<property name="DEPLOY_DIR" value="$CATALINA_HOME/webapps/biouml" /><br />
<br />
=== Subdirectories in $SERVER_PATH ===<br />
The following should be located in $SERVER_PATH:<br />
* preferences.xml: copy $SOURCE/BioUML/preferences_server.xml, edit or remove “Proxy” section and “ServerLink” in “Global”.<br />
* analyses: copy $SOURCE/BioUML/analyses, edit “Galaxy/default.config” if necessary.<br />
* configuration, history, users: will be created automatically during build.<br />
* plugins: create a symlink from $SOURCE/BioUML/plugins to $SERVER_PATH/plugins:<br />
ln -s $SOURCE//BioUML/plugins $SERVER_PATH/plugins<br />
* repo: create the folder and copy contents of BioUML/data_network. New databases will be installed here (it will be discussed later). In security.properties file you should specify your stable server address (the same as registered via BioStore) in “securityProviderServer” field.<br />
* resources: create the folder and copy contents of BioUML/data_resources_network.<br />
<br />
All files in $SERVER_PATH (except plugins directory) must be owned by tomcat user (usually ‘tomcat6’). Use:<br />
chown -R tomcat6.tomcat6 $SERVER_PATH/*<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read $SERVER_PATH/plugins directory.<br />
<br />
=== bioumlsupport2 database ===<br />
* Create database bioumlsupport2. In MySQL console:<br />
create database bioumlsupport2;<br />
grant all on bioumlsupport2.* to `bioumlsupport2`@'localhost' identified by 'bioumlsupport2';<br />
* Import $SOURCE/BioUML/dumps/bioumlsupport2.dump.sql into the newly-created database.<br />
* Add administrative MySQL rights to bioumlsupport2 user (it’s used to create new projects)<br />
grant all privileges on *.* to `bioumlsupport2`@'localhost' with grant option;<br />
grant all privileges on *.* to `bioumlsupport2`@'%' with grant option;<br />
<br />
=== Web files ===<br />
Static web files should be available in $CATALINA_HOME/webapps/bioumlweb. Create a symlink from $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles:<br />
ln -s $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles $CATALINA_HOME/webapps/bioumlweb<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read bioumlweb directory.<br />
<br />
Look into $CATALINA_HOME/webapps/bioumlweb/'''[[defines.js]]''' file. You may need to change some fields there.<br />
<br />
intro.html is the start page. You may edit it as you want.<br />
<br />
=== SimulationEngine workaround ===<br />
Comment following lines in build_bdk.xml:<br />
<nowiki><br />
<!-- copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../server.lcf" /><br />
<copy todir="${TOMCAT_PROJECT_PATH}/../../bin/out"><br />
<fileset dir="${OUTDIR}"><br />
<include name="biouml/plugins/simulation/Model.class" /><br />
<include name="biouml/plugins/simulation/ae/AeModel.class" /><br />
<include name="biouml/plugins/simulation/ae/NewtonSolver.class" /><br />
<include name="biouml/plugins/simulation/java/JavaBaseModel.class" /><br />
<include name="biouml/plugins/simulation/ode/OdeModel.class" /><br />
<include name="ru/biosoft/math/MathRoutines.class" /><br />
</fileset><br />
</copy--></nowiki><br />
<br />
After compilation copy the following files from $SOURCE/BioUML/out to $CATALINA_HOME/out (usually /var/lib/tomcat6/out): <br />
* biouml/plugins/simulation/Model.class<br />
* biouml/plugins/simulation/ae/AeModel.class<br />
* biouml/plugins/simulation/ae/NewtonSolver.class<br />
* biouml/plugins/simulation/java/JavaBaseModel.class<br />
* biouml/plugins/simulation/ode/OdeModel.class<br />
* ru/biosoft/math/MathRoutines.class.<br />
<br />
=== Security properties ===<br />
* Add the following line into policy file ( /usr/lib/jvm/java-8-oracle/jre/lib/security/java.policy or the corresponding file in your Java installation ) grant section:<br />
grant {<br />
permission javax.management.MBeanTrustPermission "register";<br />
};<br />
<br />
=== Logging ===<br />
Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.<br />
<br />
== Compilation ==<br />
Compile in $SOURCE/BioUML/src directory. In general you should not edit build_bdk.xml: use clean CVS version. Some settings should be fixed in build.xml file (see above). To rebuild everything use: <code>ant deploy.server</code>. Make sure that after build biouml.war appears in $CATALINA_HOME/webapps. If not, probably there’s some misconfiguration in build.xml.<br />
<br />
To rebuild most of plugins only (faster): <code>ant plugin.all</code><br />
<br />
Rebuild specific plugin: ant plugin.<name> or ant server.servlets. See build.xml/build_bdk.xml for details.<br />
<br />
Clean: <code>ant clean.</code><br />
<br />
== Launch ==<br />
(Re)start tomcat server to get new changes.<br />
<br />
Open in the browser: http://localhost:8080/bioumlweb/ (address may differ if you changed the tomcat settings)<br />
<br />
== Troubleshooting ==<br />
Eclipse platform caches plugins configuration inside $SERVER_PATH/configuration/org.eclipse.* directories. If you feel that plugins configuration might change or experience strange errors after server restart, try to stop server, remove these directories and start it again. Actually you may remove them every time you restart the server (for example, by adding an appropriate command into server restart script).<br />
<br />
== Logs ==<br />
* Tomcat launch problems in $CATALINA_HOME/logs/catalina.out<br />
* BioUML launch problems in $SERVER_PATH/configuration/*.log (the most recent one)<br />
* BioUML running problems in $CATALINA_HOME/logs/biouml_server.log (though many junk messages are also appear there)<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_server_installationBioUML server installation2015-06-25T09:43:39Z<p>Lan@dote.ru: Development installation</p>
<hr />
<div>This page describes how to install BioUML server provided that you have a CVS access to BioUML sources.<br />
<br />
== Paths ==<br />
The following paths will be referred within this document:<br />
* $SERVER_PATH - path to main BioUML installation folder. Usually it’s /opt/BioUML_Server.<br />
* $CATALINA_HOME - path to tomcat folder.<br />
* $SOURCES - path to BioUML sources<br />
<br />
== Prerequisites ==<br />
* Linux server. Ubuntu preferred.<br />
* Java. Oracle JDK 1.8 or OpenJDK 1.8.<br />
* Apache Tomcat (7+).<br />
aptitude install tomcat7<br />
* Apache Ant.<br />
aptitude install ant<br />
If you see compilation error about org.apache.tools.ant.util.regexp.Jdk14RegexpRegexp, you have to install one of the following:<br />
aptitude install ant-optional<br />
aptitude install ant-apache-regexp<br />
* MySQL (5+):<br />
aptitude install mysql-server<br />
* R (required for some functions such as microarray data normalization) — see [[R installation]] page.<br />
* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)<br />
* Eclipse Java IDE (preferred IDE for development, you may use others as well).<br />
<br />
== BioStore server registration ==<br />
In order to activate user account management server should be registered in BioStore system. For this perform the following steps:<br />
* Register in the BioStore: https://bio-store.org/biostore/ (leave “My first project” fields empty)<br />
* Write an e-mail to us specifying the following information:<br />
** The stable Internet address of your server (host:port). If it’s accessible via local network only, then it’s ok to specify your local address.<br />
** User-friendly server name.<br />
** List of logins (e-mails) registered via BioStore who should become server administrators.<br />
* We will create the server entry and change the permission settings, so you will be able to administer the server.<br />
Further there will be special form for automated server registration via Biostore<br />
<br />
== Development installation ==<br />
For internal development installation you may skip the BioStore integration. Instead write the following in the security.properties file:<br />
<br />
jdbcDriverClass=org.gjt.mm.mysql.Driver<br />
jdbcURL=jdbc:mysql://lachesis:3306/bioumlsupport2<br />
jdbcUser=bioumlsupport2<br />
jdbcPassword=bioumlsupport2<br />
<br />
securityProvider=ru.biosoft.access.security.TestSecurityProvider<br />
products=Server;Import;R;Experimental<br />
<br />
This will bypass the authentication and authorization: every user with any password will have administrative privileges and subscription to the specified products. Change the list of the products if necessary.<br />
<br />
== Getting sources ==<br />
CVS: use the following CVS-root:<br />
:pserver:<username>@cvs.developmentontheedge.com:/usr/cvsroot-biouml (please request an account via e-mail)<br />
<br />
== Deployment prepare ==<br />
Specify $SERVER_PATH in BioUML/src/build.xml:<br />
<property name="SERVER_PATH" value="C:/BioUML_Server_0.9.4" /><br />
Change it to the appropriate value.<br />
<br />
Depending on your Tomcat installation you may need to define DEPLOY_DIR inside “deploy.server” target. Add<br />
<property name="DEPLOY_DIR" value="$CATALINA_HOME/webapps/biouml" /><br />
<br />
=== Subdirectories in $SERVER_PATH ===<br />
The following should be located in $SERVER_PATH:<br />
* preferences.xml: copy $SOURCE/BioUML/preferences_server.xml, edit or remove “Proxy” section and “ServerLink” in “Global”.<br />
* analyses: copy $SOURCE/BioUML/analyses, edit “Galaxy/default.config” if necessary.<br />
* configuration, history, users: will be created automatically during build.<br />
* plugins: create a symlink from $SOURCE/BioUML/plugins to $SERVER_PATH/plugins:<br />
ln -s $SOURCE//BioUML/plugins $SERVER_PATH/plugins<br />
* repo: create the folder and copy contents of BioUML/data_network. New databases will be installed here (it will be discussed later). In security.properties file you should specify your stable server address (the same as registered via BioStore) in “securityProviderServer” field.<br />
* resources: create the folder and copy contents of BioUML/data_resources_network.<br />
<br />
All files in $SERVER_PATH (except plugins directory) must be owned by tomcat user (usually ‘tomcat6’). Use:<br />
chown -R tomcat6.tomcat6 $SERVER_PATH/*<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read $SERVER_PATH/plugins directory.<br />
<br />
=== bioumlsupport2 database ===<br />
* Create database bioumlsupport2. In MySQL console:<br />
create database bioumlsupport2;<br />
grant all on bioumlsupport2.* to `bioumlsupport2`@'localhost' identified by 'bioumlsupport2';<br />
* Import $SOURCE/BioUML/dumps/bioumlsupport2.dump.sql into the newly-created database.<br />
* Add administrative MySQL rights to bioumlsupport2 user (it’s used to create new projects)<br />
grant all privileges on *.* to `bioumlsupport2`@'localhost' with grant option;<br />
grant all privileges on *.* to `bioumlsupport2`@'%' with grant option;<br />
<br />
=== Web files ===<br />
Static web files should be available in $CATALINA_HOME/webapps/bioumlweb. Create a symlink from $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles:<br />
ln -s $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles $CATALINA_HOME/webapps/bioumlweb<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read bioumlweb directory.<br />
<br />
Look into $CATALINA_HOME/webapps/bioumlweb/'''[[defines.js]]''' file. You may need to change some fields there.<br />
<br />
intro.html is the start page. You may edit it as you want.<br />
<br />
=== SimulationEngine workaround ===<br />
Comment following lines in build_bdk.xml:<br />
<nowiki><br />
<!-- copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../server.lcf" /><br />
<copy todir="${TOMCAT_PROJECT_PATH}/../../bin/out"><br />
<fileset dir="${OUTDIR}"><br />
<include name="biouml/plugins/simulation/Model.class" /><br />
<include name="biouml/plugins/simulation/ae/AeModel.class" /><br />
<include name="biouml/plugins/simulation/ae/NewtonSolver.class" /><br />
<include name="biouml/plugins/simulation/java/JavaBaseModel.class" /><br />
<include name="biouml/plugins/simulation/ode/OdeModel.class" /><br />
<include name="ru/biosoft/math/MathRoutines.class" /><br />
</fileset><br />
</copy--></nowiki><br />
<br />
After compilation copy the following files from $SOURCE/BioUML/out to $CATALINA_HOME/out (usually /var/lib/tomcat6/out): <br />
* biouml/plugins/simulation/Model.class<br />
* biouml/plugins/simulation/ae/AeModel.class<br />
* biouml/plugins/simulation/ae/NewtonSolver.class<br />
* biouml/plugins/simulation/java/JavaBaseModel.class<br />
* biouml/plugins/simulation/ode/OdeModel.class<br />
* ru/biosoft/math/MathRoutines.class.<br />
<br />
=== Security properties ===<br />
* Add the following line into policy file ( /usr/lib/jvm/java-8-oracle/jre/lib/security/java.policy or the corresponding file in your Java installation ) grant section:<br />
grant {<br />
permission javax.management.MBeanTrustPermission "register";<br />
};<br />
<br />
=== Logging ===<br />
Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.<br />
<br />
== Compilation ==<br />
Compile in $SOURCE/BioUML/src directory. In general you should not edit build_bdk.xml: use clean CVS version. Some settings should be fixed in build.xml file (see above). To rebuild everything use: <code>ant deploy.server</code>. Make sure that after build biouml.war appears in $CATALINA_HOME/webapps. If not, probably there’s some misconfiguration in build.xml.<br />
<br />
To rebuild most of plugins only (faster): <code>ant plugin.all</code><br />
<br />
Rebuild specific plugin: ant plugin.<name> or ant server.servlets. See build.xml/build_bdk.xml for details.<br />
<br />
Clean: <code>ant clean.</code><br />
<br />
== Launch ==<br />
(Re)start tomcat server to get new changes.<br />
<br />
Open in the browser: http://localhost:8080/bioumlweb/ (address may differ if you changed the tomcat settings)<br />
<br />
== Troubleshooting ==<br />
Eclipse platform caches plugins configuration inside $SERVER_PATH/configuration/org.eclipse.* directories. If you feel that plugins configuration might change or experience strange errors after server restart, try to stop server, remove these directories and start it again. Actually you may remove them every time you restart the server (for example, by adding an appropriate command into server restart script).<br />
<br />
== Logs ==<br />
* Tomcat launch problems in $CATALINA_HOME/logs/catalina.out<br />
* BioUML launch problems in $SERVER_PATH/configuration/*.log (the most recent one)<br />
* BioUML running problems in $CATALINA_HOME/logs/biouml_server.log (though many junk messages are also appear there)<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_server_installationBioUML server installation2015-06-16T08:55:40Z<p>Lan@dote.ru: /* Prerequisites */</p>
<hr />
<div>This page describes how to install BioUML server provided that you have a CVS access to BioUML sources.<br />
<br />
== Paths ==<br />
The following paths will be referred within this document:<br />
* $SERVER_PATH - path to main BioUML installation folder. Usually it’s /opt/BioUML_Server.<br />
* $CATALINA_HOME - path to tomcat folder.<br />
* $SOURCES - path to BioUML sources<br />
<br />
== Prerequisites ==<br />
* Linux server. Ubuntu preferred.<br />
* Java. Oracle JDK 1.8 or OpenJDK 1.8.<br />
* Apache Tomcat (7+).<br />
aptitude install tomcat7<br />
* Apache Ant.<br />
aptitude install ant<br />
If you see compilation error about org.apache.tools.ant.util.regexp.Jdk14RegexpRegexp, you have to install one of the following:<br />
aptitude install ant-optional<br />
aptitude install ant-apache-regexp<br />
* MySQL (5+):<br />
aptitude install mysql-server<br />
* R (required for some functions such as microarray data normalization) — see [[R installation]] page.<br />
* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)<br />
* Eclipse Java IDE (preferred IDE for development, you may use others as well).<br />
<br />
== BioStore server registration ==<br />
In order to activate user account management server should be registered in BioStore system. For this perform the following steps:<br />
* Register in the BioStore: https://bio-store.org/biostore/ (leave “My first project” fields empty)<br />
* Write an e-mail to us specifying the following information:<br />
** The stable Internet address of your server (host:port). If it’s accessible via local network only, then it’s ok to specify your local address.<br />
** User-friendly server name.<br />
** List of logins (e-mails) registered via BioStore who should become server administrators.<br />
* We will create the server entry and change the permission settings, so you will be able to administer the server.<br />
Further there will be special form for automated server registration via Biostore<br />
<br />
== Getting sources ==<br />
CVS: use the following CVS-root:<br />
:pserver:<username>@cvs.developmentontheedge.com:/usr/cvsroot-biouml (please request an account via e-mail)<br />
<br />
== Deployment prepare ==<br />
Specify $SERVER_PATH in BioUML/src/build.xml:<br />
<property name="SERVER_PATH" value="C:/BioUML_Server_0.9.4" /><br />
Change it to the appropriate value.<br />
<br />
Depending on your Tomcat installation you may need to define DEPLOY_DIR inside “deploy.server” target. Add<br />
<property name="DEPLOY_DIR" value="$CATALINA_HOME/webapps/biouml" /><br />
<br />
=== Subdirectories in $SERVER_PATH ===<br />
The following should be located in $SERVER_PATH:<br />
* preferences.xml: copy $SOURCE/BioUML/preferences_server.xml, edit or remove “Proxy” section and “ServerLink” in “Global”.<br />
* analyses: copy $SOURCE/BioUML/analyses, edit “Galaxy/default.config” if necessary.<br />
* configuration, history, users: will be created automatically during build.<br />
* plugins: create a symlink from $SOURCE/BioUML/plugins to $SERVER_PATH/plugins:<br />
ln -s $SOURCE//BioUML/plugins $SERVER_PATH/plugins<br />
* repo: create the folder and copy contents of BioUML/data_network. New databases will be installed here (it will be discussed later). In security.properties file you should specify your stable server address (the same as registered via BioStore) in “securityProviderServer” field.<br />
* resources: create the folder and copy contents of BioUML/data_resources_network.<br />
<br />
All files in $SERVER_PATH (except plugins directory) must be owned by tomcat user (usually ‘tomcat6’). Use:<br />
chown -R tomcat6.tomcat6 $SERVER_PATH/*<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read $SERVER_PATH/plugins directory.<br />
<br />
=== bioumlsupport2 database ===<br />
* Create database bioumlsupport2. In MySQL console:<br />
create database bioumlsupport2;<br />
grant all on bioumlsupport2.* to `bioumlsupport2`@'localhost' identified by 'bioumlsupport2';<br />
* Import $SOURCE/BioUML/dumps/bioumlsupport2.dump.sql into the newly-created database.<br />
* Add administrative MySQL rights to bioumlsupport2 user (it’s used to create new projects)<br />
grant all privileges on *.* to `bioumlsupport2`@'localhost' with grant option;<br />
grant all privileges on *.* to `bioumlsupport2`@'%' with grant option;<br />
<br />
=== Web files ===<br />
Static web files should be available in $CATALINA_HOME/webapps/bioumlweb. Create a symlink from $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles:<br />
ln -s $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles $CATALINA_HOME/webapps/bioumlweb<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read bioumlweb directory.<br />
<br />
Look into $CATALINA_HOME/webapps/bioumlweb/'''[[defines.js]]''' file. You may need to change some fields there.<br />
<br />
intro.html is the start page. You may edit it as you want.<br />
<br />
=== SimulationEngine workaround ===<br />
Comment following lines in build_bdk.xml:<br />
<nowiki><br />
<!-- copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../server.lcf" /><br />
<copy todir="${TOMCAT_PROJECT_PATH}/../../bin/out"><br />
<fileset dir="${OUTDIR}"><br />
<include name="biouml/plugins/simulation/Model.class" /><br />
<include name="biouml/plugins/simulation/ae/AeModel.class" /><br />
<include name="biouml/plugins/simulation/ae/NewtonSolver.class" /><br />
<include name="biouml/plugins/simulation/java/JavaBaseModel.class" /><br />
<include name="biouml/plugins/simulation/ode/OdeModel.class" /><br />
<include name="ru/biosoft/math/MathRoutines.class" /><br />
</fileset><br />
</copy--></nowiki><br />
<br />
After compilation copy the following files from $SOURCE/BioUML/out to $CATALINA_HOME/out (usually /var/lib/tomcat6/out): <br />
* biouml/plugins/simulation/Model.class<br />
* biouml/plugins/simulation/ae/AeModel.class<br />
* biouml/plugins/simulation/ae/NewtonSolver.class<br />
* biouml/plugins/simulation/java/JavaBaseModel.class<br />
* biouml/plugins/simulation/ode/OdeModel.class<br />
* ru/biosoft/math/MathRoutines.class.<br />
<br />
=== Security properties ===<br />
* Add the following line into policy file ( /usr/lib/jvm/java-8-oracle/jre/lib/security/java.policy or the corresponding file in your Java installation ) grant section:<br />
grant {<br />
permission javax.management.MBeanTrustPermission "register";<br />
};<br />
<br />
=== Logging ===<br />
Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.<br />
<br />
== Compilation ==<br />
Compile in $SOURCE/BioUML/src directory. In general you should not edit build_bdk.xml: use clean CVS version. Some settings should be fixed in build.xml file (see above). To rebuild everything use: <code>ant deploy.server</code>. Make sure that after build biouml.war appears in $CATALINA_HOME/webapps. If not, probably there’s some misconfiguration in build.xml.<br />
<br />
To rebuild most of plugins only (faster): <code>ant plugin.all</code><br />
<br />
Rebuild specific plugin: ant plugin.<name> or ant server.servlets. See build.xml/build_bdk.xml for details.<br />
<br />
Clean: <code>ant clean.</code><br />
<br />
== Launch ==<br />
(Re)start tomcat server to get new changes.<br />
<br />
Open in the browser: http://localhost:8080/bioumlweb/ (address may differ if you changed the tomcat settings)<br />
<br />
== Troubleshooting ==<br />
Eclipse platform caches plugins configuration inside $SERVER_PATH/configuration/org.eclipse.* directories. If you feel that plugins configuration might change or experience strange errors after server restart, try to stop server, remove these directories and start it again. Actually you may remove them every time you restart the server (for example, by adding an appropriate command into server restart script).<br />
<br />
== Logs ==<br />
* Tomcat launch problems in $CATALINA_HOME/logs/catalina.out<br />
* BioUML launch problems in $SERVER_PATH/configuration/*.log (the most recent one)<br />
* BioUML running problems in $CATALINA_HOME/logs/biouml_server.log (though many junk messages are also appear there)<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_server_installationBioUML server installation2015-06-16T08:55:21Z<p>Lan@dote.ru: /* Security properties */</p>
<hr />
<div>This page describes how to install BioUML server provided that you have a CVS access to BioUML sources.<br />
<br />
== Paths ==<br />
The following paths will be referred within this document:<br />
* $SERVER_PATH - path to main BioUML installation folder. Usually it’s /opt/BioUML_Server.<br />
* $CATALINA_HOME - path to tomcat folder.<br />
* $SOURCES - path to BioUML sources<br />
<br />
== Prerequisites ==<br />
* Linux server. Ubuntu preferred.<br />
* Java. Oracle JDK 1.7 or OpenJDK 1.7.<br />
* Apache Tomcat (6+).<br />
aptitude install tomcat6<br />
* Apache Ant.<br />
aptitude install ant<br />
If you see compilation error about org.apache.tools.ant.util.regexp.Jdk14RegexpRegexp, you have to install one of the following:<br />
aptitude install ant-optional<br />
aptitude install ant-apache-regexp<br />
* MySQL (5+):<br />
aptitude install mysql-server<br />
* R (required for some functions such as microarray data normalization) — see [[R installation]] page.<br />
* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)<br />
* Eclipse Java IDE (preferred IDE for development, you may use others as well).<br />
<br />
== BioStore server registration ==<br />
In order to activate user account management server should be registered in BioStore system. For this perform the following steps:<br />
* Register in the BioStore: https://bio-store.org/biostore/ (leave “My first project” fields empty)<br />
* Write an e-mail to us specifying the following information:<br />
** The stable Internet address of your server (host:port). If it’s accessible via local network only, then it’s ok to specify your local address.<br />
** User-friendly server name.<br />
** List of logins (e-mails) registered via BioStore who should become server administrators.<br />
* We will create the server entry and change the permission settings, so you will be able to administer the server.<br />
Further there will be special form for automated server registration via Biostore<br />
<br />
== Getting sources ==<br />
CVS: use the following CVS-root:<br />
:pserver:<username>@cvs.developmentontheedge.com:/usr/cvsroot-biouml (please request an account via e-mail)<br />
<br />
== Deployment prepare ==<br />
Specify $SERVER_PATH in BioUML/src/build.xml:<br />
<property name="SERVER_PATH" value="C:/BioUML_Server_0.9.4" /><br />
Change it to the appropriate value.<br />
<br />
Depending on your Tomcat installation you may need to define DEPLOY_DIR inside “deploy.server” target. Add<br />
<property name="DEPLOY_DIR" value="$CATALINA_HOME/webapps/biouml" /><br />
<br />
=== Subdirectories in $SERVER_PATH ===<br />
The following should be located in $SERVER_PATH:<br />
* preferences.xml: copy $SOURCE/BioUML/preferences_server.xml, edit or remove “Proxy” section and “ServerLink” in “Global”.<br />
* analyses: copy $SOURCE/BioUML/analyses, edit “Galaxy/default.config” if necessary.<br />
* configuration, history, users: will be created automatically during build.<br />
* plugins: create a symlink from $SOURCE/BioUML/plugins to $SERVER_PATH/plugins:<br />
ln -s $SOURCE//BioUML/plugins $SERVER_PATH/plugins<br />
* repo: create the folder and copy contents of BioUML/data_network. New databases will be installed here (it will be discussed later). In security.properties file you should specify your stable server address (the same as registered via BioStore) in “securityProviderServer” field.<br />
* resources: create the folder and copy contents of BioUML/data_resources_network.<br />
<br />
All files in $SERVER_PATH (except plugins directory) must be owned by tomcat user (usually ‘tomcat6’). Use:<br />
chown -R tomcat6.tomcat6 $SERVER_PATH/*<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read $SERVER_PATH/plugins directory.<br />
<br />
=== bioumlsupport2 database ===<br />
* Create database bioumlsupport2. In MySQL console:<br />
create database bioumlsupport2;<br />
grant all on bioumlsupport2.* to `bioumlsupport2`@'localhost' identified by 'bioumlsupport2';<br />
* Import $SOURCE/BioUML/dumps/bioumlsupport2.dump.sql into the newly-created database.<br />
* Add administrative MySQL rights to bioumlsupport2 user (it’s used to create new projects)<br />
grant all privileges on *.* to `bioumlsupport2`@'localhost' with grant option;<br />
grant all privileges on *.* to `bioumlsupport2`@'%' with grant option;<br />
<br />
=== Web files ===<br />
Static web files should be available in $CATALINA_HOME/webapps/bioumlweb. Create a symlink from $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles:<br />
ln -s $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles $CATALINA_HOME/webapps/bioumlweb<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read bioumlweb directory.<br />
<br />
Look into $CATALINA_HOME/webapps/bioumlweb/'''[[defines.js]]''' file. You may need to change some fields there.<br />
<br />
intro.html is the start page. You may edit it as you want.<br />
<br />
=== SimulationEngine workaround ===<br />
Comment following lines in build_bdk.xml:<br />
<nowiki><br />
<!-- copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../server.lcf" /><br />
<copy todir="${TOMCAT_PROJECT_PATH}/../../bin/out"><br />
<fileset dir="${OUTDIR}"><br />
<include name="biouml/plugins/simulation/Model.class" /><br />
<include name="biouml/plugins/simulation/ae/AeModel.class" /><br />
<include name="biouml/plugins/simulation/ae/NewtonSolver.class" /><br />
<include name="biouml/plugins/simulation/java/JavaBaseModel.class" /><br />
<include name="biouml/plugins/simulation/ode/OdeModel.class" /><br />
<include name="ru/biosoft/math/MathRoutines.class" /><br />
</fileset><br />
</copy--></nowiki><br />
<br />
After compilation copy the following files from $SOURCE/BioUML/out to $CATALINA_HOME/out (usually /var/lib/tomcat6/out): <br />
* biouml/plugins/simulation/Model.class<br />
* biouml/plugins/simulation/ae/AeModel.class<br />
* biouml/plugins/simulation/ae/NewtonSolver.class<br />
* biouml/plugins/simulation/java/JavaBaseModel.class<br />
* biouml/plugins/simulation/ode/OdeModel.class<br />
* ru/biosoft/math/MathRoutines.class.<br />
<br />
=== Security properties ===<br />
* Add the following line into policy file ( /usr/lib/jvm/java-8-oracle/jre/lib/security/java.policy or the corresponding file in your Java installation ) grant section:<br />
grant {<br />
permission javax.management.MBeanTrustPermission "register";<br />
};<br />
<br />
=== Logging ===<br />
Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.<br />
<br />
== Compilation ==<br />
Compile in $SOURCE/BioUML/src directory. In general you should not edit build_bdk.xml: use clean CVS version. Some settings should be fixed in build.xml file (see above). To rebuild everything use: <code>ant deploy.server</code>. Make sure that after build biouml.war appears in $CATALINA_HOME/webapps. If not, probably there’s some misconfiguration in build.xml.<br />
<br />
To rebuild most of plugins only (faster): <code>ant plugin.all</code><br />
<br />
Rebuild specific plugin: ant plugin.<name> or ant server.servlets. See build.xml/build_bdk.xml for details.<br />
<br />
Clean: <code>ant clean.</code><br />
<br />
== Launch ==<br />
(Re)start tomcat server to get new changes.<br />
<br />
Open in the browser: http://localhost:8080/bioumlweb/ (address may differ if you changed the tomcat settings)<br />
<br />
== Troubleshooting ==<br />
Eclipse platform caches plugins configuration inside $SERVER_PATH/configuration/org.eclipse.* directories. If you feel that plugins configuration might change or experience strange errors after server restart, try to stop server, remove these directories and start it again. Actually you may remove them every time you restart the server (for example, by adding an appropriate command into server restart script).<br />
<br />
== Logs ==<br />
* Tomcat launch problems in $CATALINA_HOME/logs/catalina.out<br />
* BioUML launch problems in $SERVER_PATH/configuration/*.log (the most recent one)<br />
* BioUML running problems in $CATALINA_HOME/logs/biouml_server.log (though many junk messages are also appear there)<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/KeyNodes_hubKeyNodes hub2015-05-22T09:28:06Z<p>Lan@dote.ru: </p>
<hr />
<div>KeyNodes hub is a [[BioHub]] which can be used in [[Regulator search (analysis)|Regulator search]] and [[Effector search (analysis)|Effector search]] analyses as well as several helper analyses. Its main purpose is provide abilities to traverse through gene/molecules network represented as directed weighted graph.<br />
<br />
== Implementation details ==<br />
All the KeyNodes hubs must extends the {{Class|biouml.plugins.keynodes.biohub.KeyNodesHub}} class. If the hub is based on MySQL database, it's better to extend {{Class|biouml.plugins.keynodes.biohub.KeyNodesSqlHub}} class as it provides additional support for handling SQL connection. Both classes are parametrized by type which represents hub node. <br />
<br />
=== Nodes representation ===<br />
Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]]. The {{Method|java.lang.Object.equals(Object)}} and {{Method|java.lang.Object.hashCode()}} methods must be redefined for node type. Nodes with the same string representation must be equal and have the same hashCode.<br />
<br />
To support hub nodes you should override the following methods:<br />
* {{Method|ru.biosoft.access.biohub.BioHubSupport.getSupportedInputTypes()}}: return an array of possible [[reference type]]s which can be converted to internal node type. Usually it's only one type.<br />
* {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getElementConverter()}}: return an {{Class|biouml.plugins.keynodes.graph.ElementConverter}} object which is capable to convert internal nodes from/to {{Class|ru.biosoft.access.biohub.Element}} objects:<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.toNode(Element)}} method should create a hub node object using {{Class|ru.biosoft.access.biohub.Element}}. The toString() method of the resulting node should produce the same string as {{Method|ru.biosoft.access.biohub.Element.getAccession()}}.<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method must create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element (substance/protein/gene/etc.) in the [[repository]].<br />
<br />
=== Edges representation ===<br />
Hub edge must implement the {{Class|biouml.plugins.keynodes.graph.HubEdge}} interface. It has the following methods:<br />
* {{Method|biouml.plugins.keynodes.graph.HubEdge.createElement(KeyNodesHub)}} method must create a new <br />
{{Class|ru.biosoft.access.biohub.Element}} object by existing edge. It must have the full path set, preferably linked to the existing element (reaction/semantic relation) in the [[repository]].<br />
* {{Method|biouml.plugins.keynodes.graph.HubEdge.getRelationType(boolean)}} method must return relation type string (see the constants in {{Class|ru.biosoft.access.biohub.RelationType}} class).<br />
<br />
Additionally a toString() method must return an accession number for given relation.<br />
<br />
To spare memory it's recommended to make both node and edge objects as simple as possible. They should not be linked to each other or to the graph. Also edges should not contain the weight: it might be changed by decorators.<br />
<br />
=== Graph represenation ===<br />
The graph is represented by {{Class|biouml.plugins.keynodes.graph.HubGraph}} interface. It has the following methods:<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.nodes()}} method must return the stream of all nodes in the graph<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.hasNode(N)}} method must return true if given node appears in the graph<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.visitEdges()}} method must call given visitor for all the nodes directly adjacent to supplied start node in either upstream or downstream direction.<br />
<br />
Usually it's unnecessary to implement this interface. Instead you may use a {{Class|biouml.plugins.keynodes.graph.MemoryHubGraph}} implementation. To create it, construct a stream of {{Class|biouml.plugins.keynodes.graph.MemoryHubGraph.HubRelation}} objects which represent single relation from given start node to given end node with given edge object and given weight. After that collect this stream with {{Method|biouml.plugins.keynodes.graph.MemoryHubGraph.toMemoryHub()}} collector.<br />
<br />
=== Graph chaining ===<br />
The graphs can be modified by set of decorators supplied by user during analysis. To support this feature in your hub you should define a hub cache. The easiest way is to store a {{Class|biouml.plugins.keynodes.graph.MemoryHubCache}} instance into hub field and use it when defining {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getHub(TargetOptions, String[])}} method. You must supply a function which will create the base hub (for example, read something from SQL database). The hub cache will take care on caching and chaining with decorators.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/KeyNodes_hubKeyNodes hub2015-05-22T09:16:58Z<p>Lan@dote.ru: </p>
<hr />
<div>KeyNodes hub is a [[BioHub]] which can be used in [[Regulator search (analysis)|Regulator search]] and [[Effector search (analysis)|Effector search]] analyses as well as several helper analyses. Its main purpose is provide abilities to traverse through gene/molecules network represented as directed weighted graph.<br />
<br />
== Implementation details ==<br />
All the KeyNodes hubs must extends the {{Class|biouml.plugins.keynodes.biohub.KeyNodesHub}} class. If the hub is based on MySQL database, it's better to extend {{Class|biouml.plugins.keynodes.biohub.KeyNodesSqlHub}} class as it provides additional support for handling SQL connection. Both classes are parametrized by type which represents hub node. <br />
<br />
=== Nodes representation ===<br />
Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]]. The {{Method|java.lang.Object.equals(Object)}} and {{Method|java.lang.Object.hashCode()}} methods must be redefined for node type. Nodes with the same string representation must be equal and have the same hashCode.<br />
<br />
To support hub nodes you should override the following methods:<br />
* {{Method|ru.biosoft.access.biohub.BioHubSupport.getSupportedInputTypes()}}: return an array of possible [[reference type]]s which can be converted to internal node type. Usually it's only one type.<br />
* {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getElementConverter()}}: return an {{Class|biouml.plugins.keynodes.graph.ElementConverter}} object which is capable to convert internal nodes from/to {{Class|ru.biosoft.access.biohub.Element}} objects:<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.toNode(Element)}} method should create a hub node object using {{Class|ru.biosoft.access.biohub.Element}}. The toString() method of the resulting node should produce the same string as {{Method|ru.biosoft.access.biohub.Element.getAccession()}}.<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method must create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element (substance/protein/gene/etc.) in the [[repository]].<br />
<br />
=== Edges representation ===<br />
Hub edge must implement the {{Class|biouml.plugins.keynodes.graph.HubEdge}} interface. It has the following methods:<br />
* {{Method|biouml.plugins.keynodes.graph.HubEdge.createElement(KeyNodesHub)}} method must create a new <br />
{{Class|ru.biosoft.access.biohub.Element}} object by existing edge. It must have the full path set, preferably linked to the existing element (reaction/semantic relation) in the [[repository]].<br />
* {{Method|biouml.plugins.keynodes.graph.HubEdge.getRelationType(boolean)}} method must return relation type string (see the constants in {{Class|ru.biosoft.access.biohub.RelationType}} class).<br />
<br />
Additionally a toString() method must return an accession number for given relation.<br />
<br />
To spare memory it's recommended to make both node and edge objects as simple as possible. They should not be linked to each other or to the graph.<br />
<br />
=== Graph represenation ===<br />
The graph is represented by {{Class|biouml.plugins.keynodes.graph.HubGraph}} interface. It has the following methods:<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.nodes()}} method must return the stream of all nodes in the graph<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.hasNode(N)}} method must return true if given node appears in the graph<br />
* {{Method|biouml.plugins.keynodes.graph.HubGraph.visitEdges(N, boolean, HubEdgeVisitor<N>)}} method must call given visitor for all the nodes directly adjacent to supplied start node in either upstream or downstream direction.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/KeyNodes_hubKeyNodes hub2015-05-22T09:00:23Z<p>Lan@dote.ru: First draft</p>
<hr />
<div>KeyNodes hub is a [[BioHub]] which can be used in [[Regulator search (analysis)|Regulator search]] and [[Effector search (analysis)|Effector search]] analyses as well as several helper analyses. Its main purpose is provide abilities to traverse through gene/molecules network represented as directed weighted graph.<br />
<br />
== Implementation details ==<br />
All the KeyNodes hubs must extends the {{Class|biouml.plugins.keynodes.biohub.KeyNodesHub}} class. If the hub is based on MySQL database, it's better to extend {{Class|biouml.plugins.keynodes.biohub.KeyNodesSqlHub}} class as it provides additional support for handling SQL connection. Both classes are parametrized by type which represents hub node. <br />
<br />
=== Nodes representation ===<br />
Hub node (molecule or gene) can be represented by any type. Sometimes it's ok to use {{Class|java.lang.Integer}}, {{Class|java.lang.String}}, sometimes it's better to create your own class. The {{Method|java.lang.Object.toString()}} of this class should produce stable accession number for the molecule or gene which belongs to the registered [[reference type]].<br />
<br />
To support hub nodes you should override the following methods:<br />
* {{Method|ru.biosoft.access.biohub.BioHubSupport.getSupportedInputTypes()}}: return an array of possible [[reference type]]s which can be converted to internal node type. Usually it's only one type.<br />
* {{Method|biouml.plugins.keynodes.biohub.KeyNodesHub.getElementConverter()}}: return an {{Class|biouml.plugins.keynodes.graph.ElementConverter}} object which is capable to convert internal nodes from/to {{Class|ru.biosoft.access.biohub.Element}} objects:<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.toNode(Element)}} method should create a hub node object using {{Class|ru.biosoft.access.biohub.Element}}. The toString() method of the resulting node should produce the same string as {{Method|ru.biosoft.access.biohub.Element.getAccession()}}.<br />
** {{Method|biouml.plugins.keynodes.graph.ElementConverter.fromNode(N)}} method should create a new {{Class|ru.biosoft.access.biohub.Element}} object by existing node. It must have the full path set, preferably linked to the existing element in the [[repository]].</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/AcknowledgementsAcknowledgements2015-03-19T06:31:32Z<p>Lan@dote.ru: </p>
<hr />
<div>[[BioUML]] development was supported by:<br />
<br />
* Volkswagen-Stiftung (I/75941)<br />
* INTAS 03-51-5218 (2006-2008)<br />
* RFBR 04-04-49826-a (2004-2007)<br />
* Siberian Branch of the Russian Academy of Sciences (interdisciplinary projects 46 (2006-2008), 17 (2009-2011), 91(2009-2011), 55 (2012-present time) and 58 (2012 - present time)).<br />
* Basic science for medicine project №33 (The Russian Academy of Sciences program) (2011, 2012)<br />
* European Committee grant 037590 "Net2Drug" (2007-2010)<br />
* European Committee grant 37231 "Sysco"(2007-2011)<br />
* European Committee grant 202272 "LipidomicNet" (2008-2012)<br />
<br />
[[BioUML]] is developed in collaboration with:<br />
<br />
* [http://www.kti.nsc.ru Design Technological Institute of Digital Techniques]<br />
* [http://www.iis.nsk.su/ Institute of Informatics Systems]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/AcknowledgementsAcknowledgements2015-03-19T06:31:04Z<p>Lan@dote.ru: </p>
<hr />
<div>[[BioUML]] development was supported by:<br />
<br />
* Volkswagen-Stiftung (I/75941)<br />
* INTAS 03-51-5218 (2006-2008)<br />
* RFBR 04-04-49826-a (2004-2007)<br />
* Siberian Branch of the Russian Academy of Sciences (interdisciplinary projects 46 (2006-2008), 17 (2009-2011), 91(2009-2011), 55 (2012-present time) and 58 (2012 - present time)).<br />
* Basic science for medicine project №33 (The Russian Academy of Sciences program) (2011, 2012)<br />
* European Committee grant 037590 "Net2Drug" (2007-2010)<br />
* European Committee grant 37231 "Sysco"(2007-2011)<br />
* European Committee grant 202272 "LipidomicNet" (2008-2012)<br />
<br />
* [http://www.kti.nsc.ru Design Technological Institute of Digital Techniques]<br />
* [http://www.iis.nsk.su/ Institute of Informatics Systems]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_teamBioUML team2015-03-19T06:29:13Z<p>Lan@dote.ru: </p>
<hr />
<div>'''Project Leader:'''<br />[[User:Fkolpakov@gmail.com]]<br />
<br />
'''Developers:'''<br />
<br />
<u>2015</u><br />
<br />
Institute of Informatics Systems:<br />
<br />
* [[User:Lan@dote.ru]]<br />
<br />
Design Technological Institute of Digital Techniques:<br />
<br />
* [[User:Ivan@dote.ru]]<br />
* [[User:Axec@dote.ru]]<br />
* [[User:Yvkondrat@mail.ru]]<br />
* Nikita Mandrik<br />
* Elena Kutumova<br />
* Sofia Kinsht<br />
<br />
<u>2014</u><br />
<br />
* [[User:Lan@dote.ru]]<br />
* [[User:Ivan@dote.ru]]<br />
* [[User:Axec@dote.ru]]<br />
* [[User:Yvkondrat@mail.ru]]<br />
* Elena Kutumova<br />
* Eseniya Basmanova<br />
* Nikita Mandrik<br />
<br />
<u>2013</u><br />
<br />
* [[User:Lan@dote.ru]]<br />
* [[User:Ivan@dote.ru]]<br />
* [[User:Axec@dote.ru]]<br />
* [[User:Yvkondrat@mail.ru]]<br />
* Alexander Bukharov<br />
* Nikita Mandrik<br />
<br />
<u>2012</u><br />
<br />
* Nikita Tolstyh<br />
* [[User:Lan@dote.ru]]<br />
* [[User:Ivan@dote.ru]]<br />
* [[User:Axec@dote.ru]]<br />
* Elena Kutumova<br />
* [[User:Yvkondrat@mail.ru]]<br />
<br />
<u>2011</u><br />
<br />
* Nikita Tolstyh<br />
* [[User:Lan@dote.ru]]<br />
* [[User:Axec@dote.ru]]<br />
* Elena Kutumova<br />
* Anna Ryabova<br />
* [[User:Yvkondrat@mail.ru]]<br />
* [[User:Ivan@dote.ru]]<br />
* Boris Semisalov<br />
<br />
<u>2010</u><br />
<br />
* Nikita Tolstyh<br />
* [[User:Lan@dote.ru]]<br />
* Alexey Shadrin<br />
* [[User:Axec@dote.ru]]<br />
* Elena Kutumova<br />
* Anna Ryabova<br />
* Tatyana Leonova<br />
<br />
<u>2009</u><br />
<br />
* Nikita Tolstyh<br />
* Elena Kutumova<br />
* [[User:Axec@dote.ru]]<br />
* Alexey Shadrin<br />
* Tatyana Leonova<br />
* Mikhail Puzanov<br />
<br />
<u>2008</u><br />
<br />
* Nikita Tolstyh<br />
* Mikhail Puzanov<br />
* Denis Ryumin<br />
* Tatyana Leonova<br />
* Boris Semisalov<br />
<br />
<u>2007</u><br />
<br />
* Mikhail Puzanov<br />
* Nikita Tolstyh<br />
* Denis Ryumin<br />
* Tatyana Leonova<br />
* Boris Semisalov<br />
* Alexander Magdysyuk<br />
<br />
<u>2004-2005</u><br />
<br />
* Mikhail Puzanov<br />
* Alexander Koshukov<br />
* Vasily Hudyakov<br />
* Artem Shaidukov<br />
<br />
<u>2002-2003</u><br />
<br />
* Igor Tyazhev<br />
* Vlad Zhvaleev<br />
* Oleg Onegov<br />
<br />
'''Annotators of Biopath database '''(codename, http://biopath.biouml.org)'''<nowiki>:</nowiki>'''<br />
<br />
* [[User:Shrus79@gmail.com]]<br />
* Elena Cheremushkina</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Lucene_indexes_creationLucene indexes creation2014-12-11T09:47:33Z<p>Lan@dote.ru: /* Indexes in BioUML server */</p>
<hr />
<div>'''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.<br />
<br />
__TOC__<br />
=== Indexes in BioUML workbench ===<br />
In [[BioUML workbench]] indexes are created automatically when you try to search the corresponding database:<br />
<br />
[[File:Lucene_indexes_creation_workbench.png|400px]]<br />
<br />
An indexes creation window will appear prompting you on which indexes you want to create. Upon pressing Ok button indexes recreation procedure will start. It may time a lot of time depending on the database:<br />
<br />
[[File:Lucene_indexes_creation_workbench_process.png|300px]]<br />
<br />
After it finishes you may use the search.<br />
<br />
=== Indexes in BioUML server ===<br />
Indexes on BioUML server can be created using administrative analysis [[Rebuild search indexes (analysis)|Rebuild search indexes]].<br />
<br />
=== Recreating indexes after the database update ===<br />
When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.<br />
<br />
=== See also ===<br />
* [[Databases installation]]<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Transformer_(extension_point)Transformer (extension point)2014-12-11T09:04:57Z<p>Lan@dote.ru: +name</p>
<hr />
<div>{{Extension point|transformer|ru.biosoft.access|registry=ru.biosoft.access.generic.TransformerRegistry}}<br />
=== Description ===<br />
Transformer classes should be registered if you want transformed items to be compatible with {{Class|ru.biosoft.access.generic.GenericDataCollection}}.<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT transformer><br />
<!ATTLIST transformer<br />
name CDATA #REQUIRED<br />
inputClass CDATA #REQUIRED<br />
outputClass CDATA #REQUIRED<br />
transformerClass CDATA #REQUIRED<br />
><br />
<br />
;name<br />
:Unique human-readable name representing the title of resulting element<br />
;inputClass<br />
:Fully-qualified name of input class accepted by transformer. Currently only {{Class|ru.biosoft.access.FileDataElement}} and {{Class|ru.biosoft.access.Entry}} are supported.<br />
;outputClass<br />
:Fully-qualified name of output class accepted by transformer. Must implement {{Class|ru.biosoft.access.DataElement}} interface.<br />
;transformerClass<br />
:Fully-qualified name of the transformer class. Must implement {{Class|ru.biosoft.access.Transformer}} interface. {{Method|ru.biosoft.access.Transformer.getInputType()}} must return '''inputClass''' and {{Method|ru.biosoft.access.Transformer.getOutputType()}} must return '''outputClass'''. In many cases it's easier to inherit {{Class|ru.biosoft.access.AbstractTransformer}} class.<br />
<br />
=== Example ===<br />
<extension id="image file transformer" point="ru.biosoft.access.transformer"> <br />
<transformer <br />
name="Image"<br />
inputClass="ru.biosoft.access.FileDataElement" <br />
outputClass="ru.biosoft.access.ImageDataElement" <br />
transformerClass="ru.biosoft.access.support.FileImageTransformer"/> <br />
</extension><br />
<br />
This extension allows {{Class|ru.biosoft.access.ImageDataElement}} objects to be converted to {{Class|ru.biosoft.access.FileDataElement}} and vice-versa via {{Class|ru.biosoft.access.support.FileImageTransformer}}. Thanks to this extension you can put {{Class|ru.biosoft.access.ImageDataElement}} objects to {{Class|ru.biosoft.access.generic.GenericDataCollection}} collections.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Lucene_indexes_creationLucene indexes creation2014-11-18T05:59:10Z<p>Lan@dote.ru: /* Indexes in BioUML server */</p>
<hr />
<div>'''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.<br />
<br />
__TOC__<br />
=== Indexes in BioUML workbench ===<br />
In [[BioUML workbench]] indexes are created automatically when you try to search the corresponding database:<br />
<br />
[[File:Lucene_indexes_creation_workbench.png|400px]]<br />
<br />
An indexes creation window will appear prompting you on which indexes you want to create. Upon pressing Ok button indexes recreation procedure will start. It may time a lot of time depending on the database:<br />
<br />
[[File:Lucene_indexes_creation_workbench_process.png|300px]]<br />
<br />
After it finishes you may use the search.<br />
<br />
=== Indexes in BioUML server ===<br />
To create indexes in [[BioUML server]] you have to use separate helper application which can be launched using <code>rebuild_indexes.sh</code> (on Unix) or <code>rebuild_indexes.bat</code> (on Windows) script. Place this script into <code>$SERVER_PATH</code> folder (see [[BioUML server installation]]).<br />
<br />
This application reads the configuration from <code>rebuild_indexes.properties</code> file, so you have to create one. It contains several rows in <code>key=value</code> manner. The following keys are defined:<br />
<br />
;user<br />
:user name (e-mail of the user to log in to BioUML server during indexes creation). This user must be a [[server administrator]] for the current server.<br />
;pass<br />
:password for the specified user<br />
;repositories<br />
:semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources<br />
;modules<br />
:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names started from 'databases/' will usually work)<br />
<br />
An example of <code>rebuild_indexes.properties</code> file is shown below.<br />
<br />
user=administrator@myserver.example.com<br />
pass=secretAdministratorPassword<br />
modules=databases/Ensembl;GO;Reactome<br />
repositories=repo<br />
<br />
After this file is created, launch rebuild_indexes script and it will try to create the missing indexes. It's desired to shutdown the BioUML server for the indexes creation procedure.<br />
<br />
=== Recreating indexes after the database update ===<br />
When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.<br />
<br />
=== See also ===<br />
* [[Databases installation]]<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Lucene_indexes_creationLucene indexes creation2014-11-18T05:58:22Z<p>Lan@dote.ru: /* Indexes in BioUML server */</p>
<hr />
<div>'''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.<br />
<br />
__TOC__<br />
=== Indexes in BioUML workbench ===<br />
In [[BioUML workbench]] indexes are created automatically when you try to search the corresponding database:<br />
<br />
[[File:Lucene_indexes_creation_workbench.png|400px]]<br />
<br />
An indexes creation window will appear prompting you on which indexes you want to create. Upon pressing Ok button indexes recreation procedure will start. It may time a lot of time depending on the database:<br />
<br />
[[File:Lucene_indexes_creation_workbench_process.png|300px]]<br />
<br />
After it finishes you may use the search.<br />
<br />
=== Indexes in BioUML server ===<br />
To create indexes in [[BioUML server]] you have to use separate helper application which can be launched using <code>rebuild_indexes.sh</code> (on Unix) or <code>rebuild_indexes.bat</code> (on Windows) script. Place this script into <code>$SERVER_PATH</code> folder (see [[BioUML server installation]]).<br />
<br />
This application reads the configuration from <code>rebuild_indexes.properties</code> file, so you have to create one. It contains several rows in <code>key=value</code> manner. The following keys are defined:<br />
<br />
;user<br />
:user name (e-mail of the user to log in to BioUML server during indexes creation). This user must be a [[server administrator]] for the current server.<br />
;pass<br />
:password for the specified user<br />
;repositories<br />
:semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources<br />
;modules<br />
:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names will usually work)<br />
<br />
An example of <code>rebuild_indexes.properties</code> file is shown below.<br />
<br />
user=administrator@myserver.example.com<br />
pass=secretAdministratorPassword<br />
modules=Ensembl;GO;Reactome<br />
repositories=repo<br />
<br />
After this file is created, launch rebuild_indexes script and it will try to create the missing indexes. It's desired to shutdown the BioUML server for the indexes creation procedure.<br />
<br />
=== Recreating indexes after the database update ===<br />
When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.<br />
<br />
=== See also ===<br />
* [[Databases installation]]<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Lucene_indexes_creationLucene indexes creation2014-11-18T05:58:00Z<p>Lan@dote.ru: /* Indexes in BioUML server */</p>
<hr />
<div>'''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.<br />
<br />
__TOC__<br />
=== Indexes in BioUML workbench ===<br />
In [[BioUML workbench]] indexes are created automatically when you try to search the corresponding database:<br />
<br />
[[File:Lucene_indexes_creation_workbench.png|400px]]<br />
<br />
An indexes creation window will appear prompting you on which indexes you want to create. Upon pressing Ok button indexes recreation procedure will start. It may time a lot of time depending on the database:<br />
<br />
[[File:Lucene_indexes_creation_workbench_process.png|300px]]<br />
<br />
After it finishes you may use the search.<br />
<br />
=== Indexes in BioUML server ===<br />
To create indexes in [[BioUML server]] you have to use separate helper application which can be launched using <code>rebuild_indexes.sh</code> (on Unix) or <code>rebuild_indexes.bat</code> (on Windows) script. Place this script into <code>$SERVER_PATH</code> folder (see [[BioUML server installation]]).<br />
<br />
This application reads the configuration from <code>rebuild_indexes.properties</code> file, so you have to create one. It contains several rows in <code>key=value</code> manner. The following keys are defined:<br />
<br />
;user<br />
:user name (e-mail of the user to log in to BioUML server during indexes creation). This user must be a [[server administrator]] for the current server.<br />
;pass<br />
:password for the specified user<br />
;repositories<br />
:semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources<br />
;modules<br />
:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list will work)<br />
<br />
An example of <code>rebuild_indexes.properties</code> file is shown below.<br />
<br />
user=administrator@myserver.example.com<br />
pass=secretAdministratorPassword<br />
modules=Ensembl;GO;Reactome<br />
repositories=repo<br />
<br />
After this file is created, launch rebuild_indexes script and it will try to create the missing indexes. It's desired to shutdown the BioUML server for the indexes creation procedure.<br />
<br />
=== Recreating indexes after the database update ===<br />
When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.<br />
<br />
=== See also ===<br />
* [[Databases installation]]<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Diagram_view_part_(extension_point)Diagram view part (extension point)2014-09-25T10:04:32Z<p>Lan@dote.ru: </p>
<hr />
<div>{{Extension point|diagramViewPart|biouml.workbench}}<br />
===Description===<br />
BioUML workbench provides special pane where viewers for some diagram data will be shown. Any plug-in can contribute specific viewers to show some diagram data. Typical example of viewer is Clipboard showing the copied element of diagram.<br />
<br />
===Configuration Markup===<br />
<code><br />
<!ELEMENT diagramViewPart><br />
<!ATTLIST diagramViewPart<br />
class CDATA #REQUIRED<br />
Name CDATA <br />
ShortDescription CDATA <br />
Priority CDATA<br />
><br />
</code><br />
<br />
;class<br />
:the fully-qualified name of a class which implements {{Class|ru.biosoft.gui.ViewPart}}.<br />
;Name<br />
:tab display name<br />
;ShortDescription<br />
:editor part short description, can be used as tooltip<br />
;Priority<br />
:tab priority, tabs will be sorted according they priority.<br />
<br />
<code>diagramViewPart</code> attributes are mapped to corresponding Action properties using the associated key, so other Action or user defined attributes can be used.<br />
See <code>Action.getValue(String key)</code> for details.<br />
<br />
===Examples===<br />
<br />
Following is an example of a Clipboard definition:<br />
<br />
<extension id="Clipboard" point="biouml.workbench.diagramViewPart"> <br />
<diagramViewPart <br />
class="biouml.workbench.diagram.ClipboardView" <br />
Name="Clipboard"<br />
ShortDescription="Diagram clipboard is used to copy and paste diagram elements from one diagram to another."<br />
Priority = "2.5"<br />
/> <br />
</extension><br />
<br />
===API Information===<br />
The value of the class attribute must represent an implementor of {{Class|ru.biosoft.gui.ViewPart}}.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2014-03-13T13:38:54Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
<center><br />
[http://www.biouml.org/vc2014 '''From virtual cell to virtual human and virtual patient''']<br />
<br />
''International workshop, Novosibirsk, Russia, June 20-22, 2014''<br />
<br />
<font color="red">Don't miss it! A lot of information about BioUML development and it's applications will be presented here.</font><br />
<br />
[http://forum.biouml.org/viewtopic.php?f=1&t=15 '''Programming in BioUML''']<br />
<br />
''Tutorial, Wolfenbüttel, Germany, March 11, 2014'' [http://biouml.org/presentations/20140311_BioUML_programming.pdf Slides]<br />
</center><br />
<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* http://ie.biouml.org/bioumlweb (free)<br />
* http://platform.genexplain.com (free, commercial)<br />
<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [[News]]<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
|}<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/PresentationsPresentations2014-03-13T13:37:16Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
<br />
==Selected presentations==<br />
<br />
* [http://www.biouml.org/presentations/2011-combine-biouml.ppt BioUML - open source integrated platform for collaborative and reproducible research in systems biology] {{New}}<br />(66 slides, 11 Mb). <br /><br />
* [http://www.biouml.org/presentations/2010-BGRS-BioUML.ppt BioUML - integrated platform for building virtual cell and virtual physiological human]<br />presented on [http://conf.nsc.ru/BGRSSB2010 BGRS\SB-2010] conference (77 slides, 8.4 Mb). <br /><br />
* [http://www.biouml.org/help/user/html/index.html?introduction.htm Introduction to BioUML workbench]<br />describes main features and concepts of BioUML workbench: visual modeling, meta-model, formal definition of graphic notations and plug-in based architecture.<br />
<br /><br />
<br />
==Presentations on conferences==<br />
<br />
===2014===<br />
* [http://forum.biouml.org/viewtopic.php?f=1&t=15 BioUML programming]<br/> March 11, Wolfenbüttel, Germany <br/><br />
** Tutorial: '''BioUML programming'''<br/> [http://biouml.org/presentations/20140311_BioUML_programming.pdf PDF presentation], 38 slides, 0.8 Mb, English.<br />
<br />
===2011-2013===<br />
{{Draft}}<br />
<br />
===2010===<br />
<br />
* [http://www.icsb2010.org.uk ICSB-2010]<br /> October 11-14, Edinburgh, Scotland <br /> <br />
** Tutorial: '''BioUML - integrated platform for building virtual cell and virtual physiological human'''<br /> [http://www.biouml.org/presentations/2010-icsb-biouml-tutorial.ppt MS Power Point presentation], 73 slides, 6.4 Mb, English. <br /> <br />
** Oral report: '''Modular Approach To Modeling Of The Apoptosis Machinery'''<br /> Kutumova E.O., Sharipov R.N., Lavrik I.N, Kolpakov F.A. <br /> <br />
** posters about BioUML and its usage for modelling of components of virtual cell and virtual physiological human: <br /> <br />
*** ''BioUML - Integrated Platform for Building Virtual Cell and Virtual Physiological Human''<br /> Kolpakov F.A., Tolstyh N.I., Kutumova E.O., Kiselev I.N., Shadrin A.A., Valeev T.F., Ryabova A. <br />[http://www.biouml.org/presentations/2010-icsb-biouml.ppt MS Power Point presentation], 1 slide, 1.3 Mb, English. <br /> <br />
*** ''Modular Approach To Modeling Of The Apoptosis Machinery''<br /> Kutumova E.O., Sharipov R.N., Kolpakov F.A. <br />[http://www.biouml.org/presentations/2010-icsb-apoptosis.ppt MS Power Point presentation], 1 slide, 1.5 Mb, English. <br /> <br />
*** ''The Optimization Plug-in For The BioUML Platform''<br /> Kutumova E.O., Ryabova A.S., Tolstyh N.I., Kolpakov F.A. <br />[http://www.biouml.org/presentations/2010-icsb-optimisation.ppt MS Power Point presentation], 1 slide, 0.8 Mb, English. <br /> <br />
*** ''Agent based modelling - plug-in for BioUML platform''<br /> Kiselev I.N., Semisalov B.V., Kolpakov F.A. <br />[http://www.biouml.org/presentations/2010-icsb-agent.ppt MS Power Point presentation], 1 slide, 0.8 Mb, English. <br /> <br />
*** ''Numerical analysis of complex model of human blood flow circulation using 1D hemodynamic model''<br /> Leonova T., Biberdorf E.A., Kolpakov F.A., Blokhin A.M., Markel A.L. <br />[http://www.biouml.org/presentations/2010-bgrs-blood-flow.ppt MS Power Point presentation], 1 slide, 0.5 Mb, English. <br /><br /><br />
<br />
* [http://sbml.org/Events/Forums/COMBINE_2010 COMBINE-2010]<br /> October 6-9, Edinburgh, Scotland <br /> <br />
** Report: Encoding and exchanging graphical representation: architecture and formats. <br />[http://www.biouml.org/_combine-2010/combine-2010.ppt MS Power Point presentation], 38 slides, 0.9 Mb, English. <br /> <br />
** Report: BioUML - integrated platform for building virtual cell and virtual physiological human <br />[http://www.biouml.org/_combine-2010/BioUML.ppt MS Power Point presentation], 49 slides, 3.5 Mb, English. <br /> <br />
** [http://www.biouml.org/combine-2010.shtml Presentations and supplementary materials]<br /><br /> <br />
<br />
* [http://conf.nsc.ru/BGRSSB2010 BGRS\SB-2010 conference]<br /> June 20-27, 1010, Novosibirsk, Russia<br />
** oral presentation: '''Modular modeling of the apoptosis machinery'''<br /> Kutumova E.O., Sharipov R.N., Lavrik I.N, Kolpakov F.A. <br />[http://www.biouml.org/presentations/2010-BGRS-apoptos.ppt MS Power Point presentation], 52 slides, 7.8 Mb, English.<br /> <br />
** oral presentation: '''BioUML integrated platform for building virtual cell and virtual physiological human'''<br /> Kolpakov F.A., Tolstyh N.I., Kutumova E.O., Kiselev I.N., Shadrin A.A., Valeev T.F., Ryabova A., Sharipov R.N., Kel A.E. <br />[http://www.biouml.org/presentations/2010-BGRS-BioUML.ppt MS Power Point presentation], 78 slides, 8.4 Mb, English.<br /> <br />
** posters about BioUML and its usage for modelling of components of virtual cell and virtual physiological human:<br />
*** ''Microarray data analysis plugin for BioUML<br />''Kiselev I.N., Shadrin A.A., Kolpakov F.A., Kondrakhin Y.V.<br />[http://www.biouml.org/presentations/2010-bgrs-microarray.pdf poster], pdf, 1 Mb, English.<br /> <br />
*** ''Comparison of methods for reconstruction of models for gene expression regulation<br />''Shadrin A.A., Kiselev I.N., Kolpakov F.A.<br />[http://www.biouml.org/presentations/2010-bgrs-gene-expression.ppt MS Power Point presentation], 1 slide, 0.8 Mb, English.<br /> <br />
*** ''Web-based genome browser using AJAX and canvas technologies<br />''Valeev T.F., Tolstyh N.I., Kolpakov F.A. <br />[http://www.biouml.org/presentations/2010-bgrs-genome-browser.ppt MS Power Point presentation], 1 slide, 0.5 Mb, English.<br /> <br />
*** ''Simulating pulse wave in 1D hemodynamic model<br />''Leonova T., Kolpakov F.A., Biberdorf E.A.<br /><br />
*** ''Numerical analysis of complex model of human blood flow circulation using 1D hemodynamic model<br />''Leonova T., Biberdorf E.A., Kolpakov F.A., Blokhin A.M., Markel A.L. [http://www.biouml.org/presentations/2010-bgrs-blood-flow.ppt <br /> MS Power Point presentation], 1 slide, 0.5 Mb, English.<br />
<br />
===2008===<br />
<br />
* [http://www.icsb-2008.org The 9th International Conference on Systems Biology (ICSB-2008)]<br /> August 22-28, 2008, Gothenburg, Sweden<br /> <br />
** Tutorial: '''New possibilities of BioUML workbench'''<br />[http://www.biouml.org/presentations/2008-ICSB-BioUML%20tutorial.ppt MS Power Point presentation], 151 slides, 7.3 Mb, English.<br /><br />
** Poster: '''BioUML new concepts and possibilities'''<br />''Tolstykh N, Lapukhov S., Kiselev I., Shadrin A. and Kolpakov F.''<br />[http://www.biouml.org/presentations/2008-ICSB-BioUML.ppt MS Power Point presentation], 1 slide A0, 1.1 Mb, English.<br /> <br />
<br />
===2004-2007===<br />
<br />
{{Draft}}<br />
<br />
===2003===<br />
<br />
* [http://www.ict.nsc.ru/ws/YM2003 International conference of young scientists on mathematical modeling and informational technologies]<br /> November 3-5, 2003, Krasnoyarsk, Russia. <br /> Report: BioUML software workbench for visual modeling biological and other complex systems. <br />[http://www.ict.nsc.ru/ws/show_abstract.dhtml?ru+83+6325 Abstract], Russian.<br /><br /><br />
* [http://www14.in.tum.de/gcb03/ German Conference on Bioinformatics]<br /> October 12-14, 2003, Neuherberg/Garching, Germany.<br /> Poster: Comprehensive model for formalized description, visualization and simulation of biological systems.<br />[http://www.biouml.org/publications/pdf/gcb_2003.pdf Extended abstract], PDF, 129 kb, English.<br />[http://www.biouml.org/presentations/biouml_gcb_2003.ppt MS Power Point presentation], 1 slide A0, 217 kb, English.<br /><br /><br />
* [http://www.ict.nsc.ru/ws/elpub2002/index.en.html VIII International Conference "Electronic publicating El-Pub2003"]<br /> October 8-10, 2003, Novosibirsk, Russia. <br /> Report: BioUML - integrated framework for modeling of biological systems <br /> Abstract ([http://www.ict.nsc.ru/ws/show_abstract.dhtml?en+76+6037 English], [http://www.ict.nsc.ru/ws/show_abstract.dhtml?ru+76+6037+ Russian])[http://www.biouml.org/presentations/biouml_el_pub_2003.ppt <br /> MS Power Point presentation], 23 slides, 560 kb, Russian.<br /><br /><br />
* [http://ersnet.org/2/7/7_1.asp European Respiratory Society 13th annual congress]<br /> September 27 October 1, 2003, Vienna, Austria.<br /> Poster: [https://www.ersnetsecure.org/public/prg_congres.abstract?ww_i_presentation=9389 New approaches to understanding of heavy metals role in pathogeneses of chronic respiratory diseases]<br /> (about usage of BioUML workbench for formalized description of heavy metals role in pathogeneses of chronic respiratory diseases)<br />[http://www.biouml.org/publications/pdf/vienna_2003.pdf Poster], PDF, 11 slides, 236 kb, English.<br /><br /><br />
* [http://www.sbml.org/workshops/tokyotutorial/tutorial.htm Systems Biology Workshop and Tutorial]<br /> September 18, 2003, Tokyo, Japan.<br /> Poster: BioUML - open source extensible Java workbench for systems biology.<br />[http://www.biouml.org/presentations/biouml_tokyo_2003.ppt MS Power Point presentation], 1 slide, 182 kb, English.<br />
<br />
<br />
===2002===<br />
<br />
* [http://www.ki.se/icsb2002/ 3rd Iinternational Conference on Systems Biology (ICSB-2002)]<br /> Poster: Biouml - software framework for systems biology.<br />[http://www.biouml.org/publications/pdf/icsb_2002.pdf Abstract],PDF, 50 kb, English.<br /><br /><br />
* [http://www.ict.nsc.ru/ws/YM2002 International conference of young scientists on mathematical modeling and informational technologies]<br /> October 29-31, 2002, Novosibirsk, Russia. <br /> Report: Modeling biological systems using BioUML. <br />[http://www.biouml.org/presentations/biouml_modeling.ppt MS Power Point presentation] 30 slides, 571 kb, Russian.<br /><br /><br />
* "Science in Siberia" section on SibFair-2002 exhibition <br /> October 28-31, 2002, Novosibirsk, Russia. <br /> Presentaion: BioUML - universal language for visual modeling of biological systems. <br />[http://www.biouml.org/presentations/biouml_sibmarket.ppt MS Power Point presentation], 41 slides, 1.11 MB, Russian.<br /><br /><br />
* [http://www.sbras.ru/ws/SIIS2002/index.en.html First Regional Forum ]<br /> October, 21-24, 2002, Novosibirsk, Russia. <br /> Report: BioUML - integrated extensible framework for modeling of biological systems. <br /><br /><br />
* [http://www.ict.nsc.ru/ws/elpub2002/index.en.html VII International Conference "Electronic publicating El-Pub2002"]<br /> September 23-27, 2002, Novosibirsk, Russia. <br /> Report: BioUML - integrated framework for modeling of biological systems <br />[http://www.biouml.org/presentations/biouml_el_pub.ppt MS Power Point presentation], 28 slides, 1.33 MB, Russian.<br /><br /><br />
* [http://www.bionet.nsc.ru/meeting/bgrs2002 BGRS'2002] - Third International Conference on Bioinformatics of Genome Regulation and Structure. <br /> July 14-20, 2002, Novosibirsk, Russia. <br /> Computer demonstration: "Using BioUML Framework for Systems Biology". <br /> Poster: "BioUML - framework for visual modeling and simulation of biological systems". <br /><br /><br />
* [http://www.catalysis.nsk.su/chem/medicina/main_p.html New Technologies in Medicine]. <br /> June 18-19, 2002, Novosibirsk, Russia. <br />[http://www.catalysis.nsk.su/chem/medicina/_6/6_5.html BioUML - Biological Unified Modeling Language.]<br /><br /><br />
* [http://www.ncgroup.ru/conference On-line conference "Computer applications in chemistry, biology, pharmaceutics and medicine."]<br /> April 17 - June 13, 2002, Moscow, Russia. <br />[http://www.ncgroup.ru/conference/enter/paper.phtml?r=57 BioUML - Biological Unified Modeling Language.]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2014-03-07T11:34:41Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
<center><br />
[http://www.biouml.org/vc2014 '''From virtual cell to virtual human and virtual patient''']<br />
<br />
''International workshop, Novosibirsk, Russia, June 20-22, 2014''<br />
<br />
<font color="red">Don't miss it! A lot of information about BioUML development and it's applications will be presented here.</font><br />
<br />
[http://forum.biouml.org/viewtopic.php?f=1&t=15 '''Programming in BioUML''']<br />
<br />
''Tutorial, Wolfenbüttel, Germany, March 11, 2014''<br />
<br />
<font color="red">Technical tutorial will be conducted in geneXplain GmbH office (Am Exer 10, Wolfenbüttel, Germany). To participate please contact [mailto:info@genexplain.com info@genexplain.com].</font><br />
</center><br />
<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* http://ie.biouml.org/bioumlweb (free)<br />
* http://platform.genexplain.com (free, commercial)<br />
<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [[News]]<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
|}<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2014-03-07T11:34:30Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
<center><br />
[http://www.biouml.org/vc2014 '''From virtual cell to virtual human and virtual patient''']<br />
<br />
''International workshop, Novosibirsk, Russia, June 20-22, 2014''<br />
<br />
<font color="red">Don't miss it! A lot of information about BioUML development and it's applications will be presented here.</font><br />
<br />
[http://forum.biouml.org/viewtopic.php?f=1&t=15 Programming in BioUML]<br />
<br />
''Tutorial, Wolfenbüttel, Germany, March 11, 2014''<br />
<br />
<font color="red">Technical tutorial will be conducted in geneXplain GmbH office (Am Exer 10, Wolfenbüttel, Germany). To participate please contact [mailto:info@genexplain.com info@genexplain.com].</font><br />
</center><br />
<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* http://ie.biouml.org/bioumlweb (free)<br />
* http://platform.genexplain.com (free, commercial)<br />
<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [[News]]<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
|}<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2014-03-07T11:30:18Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
<center><br />
[http://www.biouml.org/vc2014 '''From virtual cell to virtual human and virtual patient''']<br />
<br />
''International workshop, Novosibirsk, Russia, June 20-22, 2014''<br />
<br />
<font color="red">Don't miss it! A lot of information about BioUML development and it's applications will be presented here.</font><br />
<br />
''Programming in BioUML, Wolfenbüttel, Germany, March 11, 2014''<br />
<br />
<font color="red">Technical tutorial will be conducted in geneXplain GmbH office (Am Exer 10, Wolfenbüttel, Germany). To participate please contact [mailto:info@genexplain.com info@genexplain.com].</font><br />
</center><br />
<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* http://ie.biouml.org/bioumlweb (free)<br />
* http://platform.genexplain.com (free, commercial)<br />
<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [[News]]<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
|}<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_wikiBioUML wiki2014-03-07T11:29:58Z<p>Lan@dote.ru: </p>
<hr />
<div>__NOTOC__<br />
Welcome to BioUML wiki! Now it is the main web site for BioUML platform.<br />
<br />
BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.<br />
<br />
Currently we have '''[[:Special:Statistics|{{NUMBEROFARTICLES}} articles]]'''.<br />
<br />
<center><br />
[http://www.biouml.org/vc2014 '''From virtual cell to virtual human and virtual patient''']<br />
<br />
''International workshop, Novosibirsk, Russia, June 20-22, 2014''<br />
<br />
<font color="red">Don't miss it! A lot of information about BioUML development and it's applications will be presented here.</font><br />
<br />
''Programming in BioUML, Wolfenbüttel, Germany, March 7, 2014''<br />
<br />
<font color="red">Technical tutorial will be conducted in geneXplain GmbH office (Am Exer 10, Wolfenbüttel, Germany). To participate please contact [mailto:info@genexplain.com info@genexplain.com].</font><br />
</center><br />
<br />
<br />
{|width="100%"<br />
|-<br />
|valign="top" width="33%"|<br />
<br />
== For BioUML users ==<br />
* [[BioUML|BioUML overview]]<br />
** [[BioUML workbench]]<br />
** [[BioUML web edition]]<br />
* [[Features|Main features]]<br />
* [[Download]]<br />
<br />
* [[BioUML user interface]]<br />
<br />
* [[Databases]]<br />
<br />
* Modelling <br />
** [[Simulation]]<br />
** [[Modular modeling]]<br />
<br />
* Analyses & workflows<br />
** [[Project]]s<br />
** [[:Category:Analyses|Analyses]]<br />
** [[Workflows]]<br />
** [[Using Galaxy in BioUML|Galaxy]]<br />
** [[Using R in BioUML|R]]<br />
** [[Using JavaScript in BioUML|JavaScript]]<br />
** [[:Category:File formats|File formats]]<br />
<br />
|valign="top" width="33%"|<br />
<br />
== For administrators/developers ==<br />
* [[BioUML installation]]<br />
* [[BioUML Development Kit]]<br />
* [[:Category:Plugins|Plugins]]<br />
* [[:Category:Extension points|Extension points]]<br />
* [[Creating Galaxy tool]]<br />
* [[BioUML_development_roadmap|Roadmap]]<br />
* [[BioUML_development_history|History]]<br />
<br />
<br />
=== Try BioUML web edition ===<br />
* http://ie.biouml.org/bioumlweb (free)<br />
* http://platform.genexplain.com (free, commercial)<br />
<br />
<br />
===Miscellaneous===<br />
* [[Tests]]<br />
* [[Presentations]]<br />
* [http://www.biouml.net/vc/agenda.shtml Presentations] (video, slides) <br />
from workshop "From virtual cell to virtual human and virtual patient"<br />
<br />
|valign="top" width="33%"|<br />
<br />
== Community ==<br />
* [[News]]<br />
* [http://forum.biouml.org/ Forum]<br />
* [[BioStore]]<br />
* [[Contributors]]<br />
** [[BioUML team]]<br />
** [[geneXplain]]<br />
<br />
<br />
=== Editing this wiki ===<br />
To edit this wiki you have to register in [https://bio-store.org/ BioStore].<br />
<br />
Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.<br />
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]<br />
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]<br />
* [https://toolserver.org/~diberri/cgi-bin/html2wiki/index.cgi HTML-to-wiki converter]<br />
|}<br />
<br />
<p align="center">[[Acknowledgements]]</p></div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_server_installationBioUML server installation2014-03-05T11:24:55Z<p>Lan@dote.ru: JDK 1.7</p>
<hr />
<div>This page describes how to install BioUML server provided that you have a CVS access to BioUML sources.<br />
<br />
== Paths ==<br />
The following paths will be referred within this document:<br />
* $SERVER_PATH - path to main BioUML installation folder. Usually it’s /opt/BioUML_Server.<br />
* $CATALINA_HOME - path to tomcat folder.<br />
* $SOURCES - path to BioUML sources<br />
<br />
== Prerequisites ==<br />
* Linux server. Ubuntu preferred.<br />
* Java. Oracle JDK 1.7 or OpenJDK 1.7.<br />
* Apache Tomcat (6+).<br />
aptitude install tomcat6<br />
* Apache Ant.<br />
aptitude install ant<br />
If you see compilation error about org.apache.tools.ant.util.regexp.Jdk14RegexpRegexp, you have to install one of the following:<br />
aptitude install ant-optional<br />
aptitude install ant-apache-regexp<br />
* MySQL (5+):<br />
aptitude install mysql-server<br />
* R (required for some functions such as microarray data normalization) — see [[R installation]] page.<br />
* Galaxy (required if you want to use Galaxy analyses or create your own analyses using Galaxy interface)<br />
* Eclipse Java IDE (preferred IDE for development, you may use others as well).<br />
<br />
== BioStore server registration ==<br />
In order to activate user account management server should be registered in BioStore system. For this perform the following steps:<br />
* Register in the BioStore: https://bio-store.org/biostore/ (leave “My first project” fields empty)<br />
* Write an e-mail to us specifying the following information:<br />
** The stable Internet address of your server (host:port). If it’s accessible via local network only, then it’s ok to specify your local address.<br />
** User-friendly server name.<br />
** List of logins (e-mails) registered via BioStore who should become server administrators.<br />
* We will create the server entry and change the permission settings, so you will be able to administer the server.<br />
Further there will be special form for automated server registration via Biostore<br />
<br />
== Getting sources ==<br />
CVS: use the following CVS-root:<br />
:pserver:<username>@cvs.developmentontheedge.com:/usr/cvsroot-biouml (please request an account via e-mail)<br />
<br />
== Deployment prepare ==<br />
Specify $SERVER_PATH in BioUML/src/build.xml:<br />
<property name="SERVER_PATH" value="C:/BioUML_Server_0.9.4" /><br />
Change it to the appropriate value.<br />
<br />
Depending on your Tomcat installation you may need to define DEPLOY_DIR inside “deploy.server” target. Add<br />
<property name="DEPLOY_DIR" value="$CATALINA_HOME/webapps/biouml" /><br />
<br />
=== Subdirectories in $SERVER_PATH ===<br />
The following should be located in $SERVER_PATH:<br />
* preferences.xml: copy $SOURCE/BioUML/preferences_server.xml, edit or remove “Proxy” section and “ServerLink” in “Global”.<br />
* analyses: copy $SOURCE/BioUML/analyses, edit “Galaxy/default.config” if necessary.<br />
* configuration, history, users: will be created automatically during build.<br />
* plugins: create a symlink from $SOURCE/BioUML/plugins to $SERVER_PATH/plugins:<br />
ln -s $SOURCE//BioUML/plugins $SERVER_PATH/plugins<br />
* repo: create the folder and copy contents of BioUML/data_network. New databases will be installed here (it will be discussed later). In security.properties file you should specify your stable server address (the same as registered via BioStore) in “securityProviderServer” field.<br />
* resources: create the folder and copy contents of BioUML/data_resources_network.<br />
<br />
All files in $SERVER_PATH (except plugins directory) must be owned by tomcat user (usually ‘tomcat6’). Use:<br />
chown -R tomcat6.tomcat6 $SERVER_PATH/*<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read $SERVER_PATH/plugins directory.<br />
<br />
=== bioumlsupport2 database ===<br />
* Create database bioumlsupport2. In MySQL console:<br />
create database bioumlsupport2;<br />
grant all on bioumlsupport2.* to `bioumlsupport2`@'localhost' identified by 'bioumlsupport2';<br />
* Import $SOURCE/BioUML/dumps/bioumlsupport2.dump.sql into the newly-created database.<br />
* Add administrative MySQL rights to bioumlsupport2 user (it’s used to create new projects)<br />
grant all privileges on *.* to `bioumlsupport2`@'localhost' with grant option;<br />
grant all privileges on *.* to `bioumlsupport2`@'%' with grant option;<br />
<br />
=== Web files ===<br />
Static web files should be available in $CATALINA_HOME/webapps/bioumlweb. Create a symlink from $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles:<br />
ln -s $SOURCE/BioUML/src/ru/biosoft/server/servlets/webservices/webfiles $CATALINA_HOME/webapps/bioumlweb<br />
<br />
Ensure that tomcat user (usually ‘tomcat6’) has enough access rights to read bioumlweb directory.<br />
<br />
Look into $CATALINA_HOME/webapps/bioumlweb/'''[[defines.js]]''' file. You may need to change some fields there.<br />
<br />
intro.html is the start page. You may edit it as you want.<br />
<br />
=== SimulationEngine workaround ===<br />
Comment following lines in build_bdk.xml:<br />
<nowiki><br />
<!-- copy file="${TOPDIR}/server.lcf" tofile="${TOMCAT_PROJECT_PATH}/../../server.lcf" /><br />
<copy todir="${TOMCAT_PROJECT_PATH}/../../bin/out"><br />
<fileset dir="${OUTDIR}"><br />
<include name="biouml/plugins/simulation/Model.class" /><br />
<include name="biouml/plugins/simulation/ae/AeModel.class" /><br />
<include name="biouml/plugins/simulation/ae/NewtonSolver.class" /><br />
<include name="biouml/plugins/simulation/java/JavaBaseModel.class" /><br />
<include name="biouml/plugins/simulation/ode/OdeModel.class" /><br />
<include name="ru/biosoft/math/MathRoutines.class" /><br />
</fileset><br />
</copy--></nowiki><br />
<br />
After compilation copy the following files from $SOURCE/BioUML/out to $CATALINA_HOME/out (usually /var/lib/tomcat6/out): <br />
* biouml/plugins/simulation/Model.class<br />
* biouml/plugins/simulation/ae/AeModel.class<br />
* biouml/plugins/simulation/ae/NewtonSolver.class<br />
* biouml/plugins/simulation/java/JavaBaseModel.class<br />
* biouml/plugins/simulation/ode/OdeModel.class<br />
* ru/biosoft/math/MathRoutines.class.<br />
<br />
=== Security properties ===<br />
* Enable everything in /usr/lib/jvm/java-6-sun/jre/lib/security/java.policy (or the corresponding file in your Java installation):<br />
grant {<br />
permission java.security.AllPermission;<br />
};<br />
* Enable everything in tomcat policy: $CATALINA_HOME/conf/catalina.policy (or policy.d): in the same way.<br />
<br />
=== Logging ===<br />
Logging configuration is in $SOURCE/BioUML/server.lcf file. Put it into $CATALINA_HOME, edit if necessary.<br />
<br />
== Compilation ==<br />
Compile in $SOURCE/BioUML/src directory. In general you should not edit build_bdk.xml: use clean CVS version. Some settings should be fixed in build.xml file (see above). To rebuild everything use: <code>ant deploy.server</code>. Make sure that after build biouml.war appears in $CATALINA_HOME/webapps. If not, probably there’s some misconfiguration in build.xml.<br />
<br />
To rebuild most of plugins only (faster): <code>ant plugin.all</code><br />
<br />
Rebuild specific plugin: ant plugin.<name> or ant server.servlets. See build.xml/build_bdk.xml for details.<br />
<br />
Clean: <code>ant clean.</code><br />
<br />
== Launch ==<br />
(Re)start tomcat server to get new changes.<br />
<br />
Open in the browser: http://localhost:8080/bioumlweb/ (address may differ if you changed the tomcat settings)<br />
<br />
== Troubleshooting ==<br />
Eclipse platform caches plugins configuration inside $SERVER_PATH/configuration/org.eclipse.* directories. If you feel that plugins configuration might change or experience strange errors after server restart, try to stop server, remove these directories and start it again. Actually you may remove them every time you restart the server (for example, by adding an appropriate command into server restart script).<br />
<br />
== Logs ==<br />
* Tomcat launch problems in $CATALINA_HOME/logs/catalina.out<br />
* BioUML launch problems in $SERVER_PATH/configuration/*.log (the most recent one)<br />
* BioUML running problems in $CATALINA_HOME/logs/biouml_server.log (though many junk messages are also appear there)<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_workbench_installationBioUML workbench installation2014-03-05T11:24:24Z<p>Lan@dote.ru: /* Prerequisites */</p>
<hr />
<div>{{stub}}<br />
<br />
This page describes how to install BioUML workbench<br />
<br />
== Prerequisites ==<br />
* Java 1.7 (either [http://www.oracle.com/technetwork/java/index.html Oracle] or [http://openjdk.java.net/ OpenJDK])<br />
<br />
== Download ==<br />
To download BioUML workbench you have to register on [[BioStore]] service. After registration and logging in you can find the BioUML workbench distribution in downloads area.<br />
<br />
For more details read[[Download| here]].<br />
<br />
==Installation==<br />
[[File:Workbench_installation.png|thumb|BioUML workbench installer at steps 1-4]]<br />
# Make sure you have got JDK installed on your computer. Please note that starting from v. 0.9.3 the BioUML workbench requires JDK 6 or later and will not work with earlier versions of Java. You can download JDK from [http://java.sun.com/javase/downloads/?intcmp=1281 the Sun Microsystems Inc website]. <br />
# Launch the BioUML workbench installer from the directory you saved it in during the download.<br />
# The BioUML installer will guide you through the installation process. The installation process is straightforward and consists of 5 steps:<br />
#* Target path - specify the directory where the BioUML workbench will be installed.<br />
#* Select installation packages - here you can see a list of BioUML plug-ins to be installed. We recommend selecting all of the items (by default).<br />
#* Installation - the installation process is displayed in the progress bar of the window as the components are being installed. When the installation progress has reached 100%, click '''Next'''.<br />
#* Set up shortcuts - allows you to create shortcuts in the '''Start''' menu and on the desktop to launch the BioUML workbench.<br />
#* Installation completed. Click '''Done'''.<br />
<br />
For some methods of data analyses you also need to install [[R installation|R]] and [http://www.bioconductor.org/ Bioconductor].<br />
<br />
When the installation has been completed successfully, you can start the BioUML workbench. The BioUML setup wizard will help you to configure the BioUML workbench and install remote databases from the [[BioUML server]].<br />
<br />
==Setup==<br />
<br />
The setup wizard will help you to configure BioUML workbench and configure connection with remote databases on BioUML server. The wizard is started automatically during first and further runs of BioUML workbench till you uncheck '''Show on startup''' check box.<br />
You can also start the setup wizard from the menu: File > Setup wizard.<br />
<br />
The wizard will guide you through seven steps:<br />
<br />
# '''Proxy settings''' - you are to specify the HTTP proxy server settings. This is essential if you would like to work with remote databases from the [[BioUML server]] and your network is protected by a firewall. <br />
# '''Single Sign On''' - this mechanism allows you to login into BioUML workbench only once. Then the BioUML workbench will store and use all your logins and passwords for access to protected databases on the BioUML server. This information is stored in an encrypted form. Check '''Use single sign on''' checkbox if you would like to use single sign on mechanism. After that you should specify your '''User name''' and '''Password'''. During next run BioUML workbench asks you this information for log in.<br />
# '''SQL settings''' - the dialog window allows the user to configure SQL connections. SQL connections can be used to save data into SQL database (for example, tables).<br />
# '''Connect databases''' - helps the user to configure connection of BioUML workbench with BioUML server for access to remote databases. This step of the wizard provides the same user interface as '''Load database''' dialog where you can find more details. <br />
# '''Connect DAS''' - helps the user configure connection of BioUML workbench with remote DAS servers.<br />
# '''Load project''' - helps the user load projects from BioUML server.<br />
# '''Create project''' - allows the user to create new research projects.<br />
<br />
==Updates==<br />
<br />
BioUML workbench provides automatic updates of installed plug-ins by newer versions from the specified update server.<br />
<br />
==See also==<br />
* [[BioStore]]<br />
* [[BioUML installation]]<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_workbenchBioUML workbench2014-03-05T11:24:08Z<p>Lan@dote.ru: +JDK 7</p>
<hr />
<div>{{Stub}}<br />
<br />
[[File:BioUML workbench screenshot.png|thumb|BioUML workbench]]<br />
<br />
BioUML workbench is a Java application which can work standalone or as "thick" client for [[BioUML server]].<br />
<br />
<br />
The minimum system requirements:<br />
<br />
'''Hardware'''<br />
* Pentium II 500 or higher.<br />
* 512 MB RAM.<br />
* 500 MB free hard disk drive space.<br />
<br />
'''Software'''<br />
* [[wikipedia:Java virtual machine|Java virtual machine]] - [[wikipedia:Java Development Kit|JDK]]<br />
* Starting from v. 0.9.3, BioUML workbench requires JDK 6 or later and will not work with earlier versions of Java. You can download JDK 6 from [http://www.oracle.com/technetwork/indexes/downloads/index.html Oracle web site].<br />
* Starting from v. 0.9.7, BioUML workbench will require JDK 7 and will not work with earlier versions of Java. You can download JDK 7 from [http://www.oracle.com/technetwork/indexes/downloads/index.html Oracle web site].<br />
<br />
The current version of BioUML workbench is {{BioUML current version}}.<br />
<br />
== See also ==<br />
* [[BioUML workbench installation]]<br />
<br />
[[Category:Software]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Defines.jsDefines.js2014-03-05T11:23:10Z<p>Lan@dote.ru: +loginMessage</p>
<hr />
<div>defines.js is the JavaScript file located on [[BioUML server]] in $CATALINA_HOME/webapps/bioumlweb/ directory (see [[BioUML server installation]]). It contains the configuration constants in the <code>appInfo</code> object, some of which should be modified by server administrator. All meaningful constants are listed here.<br />
<br />
;adminMail (String)<br />
:Server administrator e-mail address. It's displayed in user interface in various places like some error messages.<br />
;biostoreRegisterLink (String)<br />
:Relative URL to account registration page. In order to use standard BioStore registration, the value must be "../biouml/map?registration=1". If this parameter is absent, then no "Registration" button will appear in login box (of course this doesn't prevent the registration).<br />
;build (String)<br />
:number of web-scripts build. Used to work-around caching of scripts in some browsers. If you update the JavaScript code, you should change (increment) this value so users will get the new version of the code next time. There's default <code>ant</code> target in $CATALINA_HOME/webapps/bioumlweb/ directory which increments this value, so you can just launch <code>ant</code> in this directory after every update.<br />
;disableAnonymous (Boolean)<br />
:If true, then anonymous login will be disabled ("Demo" button will be removed from login box and empty login name will not be accepted). Please note that this option is not enough to secure your server from unwanted access: corresponding setup in [[BioStore]] must be performed as well.<br />
;edition (String)<br />
:Edition name (usually "web edition"). It's displayed in user interface in various places like page title.<br />
;help (String)<br />
:URL to manual pages. Used for "Help" button on the main toolbar.<br />
;jabberServer (String)<br />
:URL of Jabber server. If specified, custom Jabber server will be used for chat module. If absent or empty, default BioStore Jabber server will be used.<br />
;loginMessage (String)<br />
:(since 0.9.7) If specified, this message will be displayed in login dialog box. Use this to notify users for planned downtime, etc.<br />
;manual (String)<br />
:URL to manual PDF document. If specified, can be used to link manual from the start page. Currently used in [[geneXplain]] project only.<br />
;name (String)<br />
:Application name (usually "BioUML" or "geneXplain"). It's displayed in user interface in various places like page title.<br />
;serverAddress (String)<br />
:Absolute URL of this web-server. Currently this parameter is optional, though it's desired to specify it.<br />
;serverPath (String)<br />
:Relative URL to BioUML server location. Must be "../biouml/". Currently this value is still hardwritten in some code, thus don't try to install BioUML server to different location: even if you change this setting, you will experience some problems and malfunction.<br />
;userProjectsPath (String)<br />
:Path in BioUML repository to user projects folder. Usually "data/Collaboration" (for BioUML) or "data/Projects" (for [[geneXplain]]). Used for some functionality like list of projects in account manager, default location for open element dialog and so on. Please use correct value here.<br />
;version (String)<br />
:Current software version (for example, {{BioUML current version}}). It's displayed in user interface in various places like login box.<br />
<br />
=== Example ===<br />
Here's an example of defines.js file:<br />
<br />
var appInfo = <br />
{<br />
name: "BioUML",<br />
edition: "web edition",<br />
version: "{{BioUML current version}}",<br />
disableAnonymous: false,<br />
build: "11",<br />
adminMail: "contact_info@biosoft.ru",<br />
biostoreRegisterLink: "../biouml/map?registration=1",<br />
serverPath: "../biouml/",<br />
userProjectsPath: "data/Collaboration",<br />
help: "http://www.biouml.org/help/user/html/index.html",<br />
manual: "Manual geneXplain platform.pdf",<br />
serverAddress: "http://localhost",<br />
<br />
end: ""<br />
};<br />
<br />
[[Category:Installation]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Wizard_page_(extension_point)Wizard page (extension point)2013-11-21T08:21:31Z<p>Lan@dote.ru: ->ru.biosoft.workbench</p>
<hr />
<div>{{Extension point|wizardPage|ru.biosoft.workbench|since=0.8.5}}<br />
;Applicable for<br />
:[[BioUML workbench]]<br />
;Note<br />
:Moved from biouml.workbench.wizardPage to ru.biosoft.workbench.wizardPage in 0.9.6<br />
=== Description ===<br />
Define new step for BioUML setup wizard. Using this extension point plug-in can be configured from standard setup wizard.<br />
<br />
[[File:Workbench-wizard-page-screenshot.png]]<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT wizardPage><br />
<!ATTLIST wizardPage<br />
name CDATA #REQUIRED<br />
description CDATA #REQUIRED<br />
position CDATA #REQUIRED<br />
page CDATA #REQUIRED<br />
><br />
<br />
;name<br />
:the name of wizard sted.<br />
;description<br />
:short description of wizard step<br />
;position<br />
:step number (beginning from 0).<br />
;page<br />
:the fully-qualified name of wizard page class<br />
<br />
=== Examples ===<br />
This is example of adding databases configuration page to setup wizard.<br />
<br />
<extension id="Databases wizard page" point="biouml.workbench.wizardPage"> <br />
<wizardPage <br />
name="Connect databases" <br />
description="Connect databases from server" <br />
position="2" <br />
page="biouml.workbench.module.DatabasesWizardPage"<br />
/> <br />
</extension><br />
<br />
=== API Information ===<br />
<br />
The value of the page attribute must represent an implementor of {{Class|ru.biosoft.gui.setupwizard.WizardPage}}.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Perspective_(extension_point)Perspective (extension point)2013-11-21T08:19:59Z<p>Lan@dote.ru: -helpId (BioUML 0.9.6) /* Configuration markup */</p>
<hr />
<div>{{Extension point|perspective|biouml.workbench|since=0.9.3|registry=biouml.workbench.perspective.PerspectiveRegistry}}<br />
=== Description ===<br />
This extension point allows you to add your own [[perspective]].<br />
<br />
=== Configuration markup ===<br />
<!ELEMENT perspective (repository,viewparts)><br />
<!ATTLIST perspective<br />
name CDATA #REQUIRED<br />
priority CDATA #REQUIRED<br />
intro CDATA #IMPLIED<br />
/><br />
<br />
;name<br />
:name of the perspective (how it will be displayed to the user).<br />
;priority<br />
:number which controls the position of the perspective in the perspectives selection box. Perspectives with higher priorities are displayed on top. The highest priority perspective is the default one. Currently the default perspective has the priority 100, thus please use lower numbers if you don't want to override it.<br />
;intro<br />
:if specified, points to the name of alternative start page html file for [[BioUML web edition]]. For example, if you specify <code>intro="intro-my-perspective"</code>, you should put file named <code>intro-my-perspective.html</code> to the webfiles directory. This option is ignored in [[BioUML workbench]].<br />
<br />
<!ELEMENT repository (tab)*><br />
<!ELEMENT tab><br />
<!ATTLIST tab<br />
title CDATA #REQUIRED<br />
path CDATA #REQUIRED<br />
databases CDATA #IMPLIED<br />
/><br />
<br />
;title<br />
:title of the [[repository pane]] tab.<br />
;path<br />
:path to the root collection displayed in this tab.<br />
;databases<br />
:if defined and set to <code>"true"</code>, instructs the BioUML workbench that current tab is "Databases" tab, which may be treated specially (e.g. search bar is displayed). Ignored in BioUML web edition.<br />
<br />
<!ELEMENT viewparts (allow|deny)*><br />
<!ELEMENT allow><br />
<!ATTLIST allow<br />
id CDATA #REQUIRED<br />
/><br />
<!ELEMENT deny><br />
<!ATTLIST deny<br />
id CDATA #REQUIRED<br />
/><br />
<br />
These options define which [[viewpart]]s will be allowed in given perspective. Each viewpart has an internal ID. You may allow or deny specific viewparts or sets of viewparts using wildcards in id attribute.<br />
<br />
=== Example ===<br />
<extension id="Proteome perspective" point="biouml.workbench.perspective"><br />
<perspective name="Proteome" priority="20" intro="intro-proteome"><br />
<repository><br />
<tab title="Proteome" path="Proteome"/><br />
</repository><br />
<viewparts><br />
<deny id="*"/><br />
<allow id="table.*"/><br />
<allow id="common.log"/><br />
<allow id="common.description"/><br />
</viewparts><br />
</perspective><br />
</extension><br />
<br />
This extension defines the perspective called "Proteome" with priority "20" and custom intro page "intro-proteome.html". Repository pane will consist of only one tab with the name "Proteome" displayed root collection named "Proteome". All viewparts are disabled except "common.log", "common.description" and all table-related viewparts.<br />
<br />
=== Notes ===<br />
* No Java code is necessary for this extension.<br />
* You may consider also defining [[Virtual collection (extension point)|virtual collections]] to alter the content of [[repository pane]].</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioNetGenBioNetGen2013-11-18T07:11:31Z<p>Lan@dote.ru: Links</p>
<hr />
<div>==BioNetGen plugin==<br />
[[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for [[BioUML]] 0.9.6 aims to combine two representations of the rule based model in BioUML:<br />
* visual representation as BioUML {{Type link|diagram}} using special BNG-notation;<br />
* text-based representation using BioNetGen Language (BNGL)<ref> [http://bionetgen.org http://bionetgen.org] </ref><ref>[[BioNetGen diagram (file format)]]</ref>.<br />
<br />
Plugin allows user to edit model both as BioUML {{Type link|diagram}} and BNG-text. Visual representation being changed BNG-text is updated on the fly.<br><br />
Text changes are applied to the diagram on demand (after <i>"Apply BioNetGen"</i> button have been pressed).<br><br />
Besides model representations synchronisation, also care is taken of preserving user diagram layout as well as BNG-text formatting (spaces, comments, etc.)<br><br />
<b>Please note:</b> text changes would be applied only after <i>"Apply BioNetGen"</i> button have been pressed. If diagram is changed before this button have been pressed, all changes in text will be lost!<br><br />
It is allowed to remove connection with current version of BNG-text. To do it <i>"Remove connection"</i> button should be pressed. If this button is pressed text is recreated using diagram.<br><br />
<b>Note:</b> all text formatting and some of comments will be removed. Also BNG-attribute will be removed.<br><br />
<i>"Deploy"</i> button being pressed deployed model is generated. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br><br />
<b>Note:</b> source diagram won't be changed and won't be replaced.<br><br />
<br />
==Features overview==<br />
<br />
Currently plugin is in alpha version, so some features of the BioNetGen aren't supported. Also we want to achieve full synchronisation between BioNetGen and plugin.<br />
<br />
{| border="1" cellpadding="4" cellspacing="0" align="center"<br />
|-<br />
! style="background:#efefef;" | Features which are supported within plugin<br />
! style="background:#efefef;" | Features of the BioNetgen which are not supported in the alpha-version<br />
|-<br />
|<br />
* Creating, removal and properties editing of species, molecules, molecule components, observables;<br />
* Creating, removal and properties editing of reactions with reactants and products;<br />
* Creating, removal and editing of variables' initial assignment (scalar rate equation);<br />
* Deploying diagram.<br />
|<br />
* Molecule types (can be read from file, but there is no any check);<br />
* Functions;<br />
* Nf and stochastic simulations;<br />
|}<br />
<br><br />
<b>Note:</b> plugin also does not support changing of the species' initial value in the actions block.<br />
<br />
==References==<br />
<References/><br />
<br />
== See also ==<br />
<br />
* [[Visual modeling]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioNetGenBioNetGen2013-11-18T07:10:07Z<p>Lan@dote.ru: Plugi-in -> plugin; link to plugin</p>
<hr />
<div>==BioNetGen plugin==<br />
[[Biouml.plugins.bionetgen (plugin)|BioNetGen (BNG) plugin]] for BioUML 0.9.6 aims to combine two representations of the rule based model in BioUML:<br />
* visual representation as BioUML-diagram using special BNG-notation;<br />
* text-based representation using BioNetGen Language (BNGL)<ref> [http://bionetgen.org http://bionetgen.org] </ref><ref>[[BioNetGen diagram (file format)]]</ref>.<br />
<br />
Plugin allows user to edit model both as BioUML-diagram and BNG-text. Visual representation being changed BNG-text is updated on the fly.<br><br />
Text changes are applied to the diagram on demand (after <i>"Apply BioNetGen"</i> button have been pressed).<br><br />
Besides model representations synchronisation, also care is taken of preserving user diagram layout as well as BNG-text formatting (spaces, comments, etc.)<br><br />
<b>Please note:</b> text changes would be applied only after <i>"Apply BioNetGen"</i> button have been pressed. If diagram is changed before this button have been pressed, all changes in text will be lost!<br><br />
It is allowed to remove connection with current version of BNG-text. To do it <i>"Remove connection"</i> button should be pressed. If this button is pressed text is recreated using diagram.<br><br />
<b>Note:</b> all text formatting and some of comments will be removed. Also BNG-attribute will be removed.<br><br />
<i>"Deploy"</i> button being pressed deployed model is generated. Source diagram will be substituted by deployed diagram (it will not be saved without pressing of the save button, and will have "_deployed" suffix in its name).<br><br />
<b>Note:</b> source diagram won't be changed and won't be replaced.<br><br />
<br />
==Features overview==<br />
<br />
Currently plugin is in alpha version, so some features of the BioNetGen aren't supported. Also we want to achieve full synchronisation between BioNetGen and plugin.<br />
<br />
{| border="1" cellpadding="4" cellspacing="0" align="center"<br />
|-<br />
! style="background:#efefef;" | Features which are supported within plugin<br />
! style="background:#efefef;" | Features of the BioNetgen which are not supported in the alpha-version<br />
|-<br />
|<br />
* Creating, removal and properties editing of species, molecules, molecule components, observables;<br />
* Creating, removal and properties editing of reactions with reactants and products;<br />
* Creating, removal and editing of variables' initial assignment (scalar rate equation);<br />
* Deploying diagram.<br />
|<br />
* Molecule types (can be read from file, but there is no any check);<br />
* Functions;<br />
* Nf and stochastic simulations;<br />
|}<br />
<br><br />
<b>Note:</b> plugin also does not support changing of the species' initial value in the actions block.<br />
<br />
==References==<br />
<References/><br />
<br />
== See also ==<br />
<br />
* [[Visual modeling]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/User:Manikitos@yandex.ruUser:Manikitos@yandex.ru2013-11-18T07:06:46Z<p>Lan@dote.ru: Created page with "Nikita Mandrik. Developer at Institute of Systems Biology. BioUML developer."</p>
<hr />
<div>Nikita Mandrik.<br />
<br />
Developer at [[Institute of Systems Biology]].<br />
<br />
[[BioUML]] developer.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/User:Buharov@developmentontheedge.comUser:Buharov@developmentontheedge.com2013-11-18T07:06:31Z<p>Lan@dote.ru: Created page with "Alexander Buharov. Developer at Institute of Systems Biology. BioUML developer."</p>
<hr />
<div>Alexander Buharov.<br />
<br />
Developer at [[Institute of Systems Biology]].<br />
<br />
[[BioUML]] developer.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_workbenchBioUML workbench2013-11-18T07:05:50Z<p>Lan@dote.ru: Sun -> Oracle</p>
<hr />
<div>{{Stub}}<br />
<br />
[[File:BioUML workbench screenshot.png|thumb|BioUML workbench]]<br />
<br />
BioUML workbench is a Java application which can work standalone or as "thick" client for [[BioUML server]].<br />
<br />
<br />
The minimum system requirements:<br />
<br />
'''Hardware'''<br />
* Pentium II 500 or higher.<br />
* 512 MB RAM.<br />
* 500 MB free hard disk drive space.<br />
<br />
'''Software'''<br />
* [[wikipedia:Java virtual machine|Java virtual machine]] - [[wikipedia:Java Development Kit|JDK]]<br />
* Starting from v. 0.9.3, BioUML workbench requires JDK 6 or later and will not work with earlier versions of Java. You can download JDK 6 from [http://www.oracle.com/technetwork/indexes/downloads/index.html Oracle web site].<br />
<br />
<br />
The current version of BioUML workbench is {{BioUML current version}}.<br />
<br />
== See also ==<br />
* [[BioUML workbench installation]]<br />
<br />
[[Category:Software]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Template:BioUML_current_versionTemplate:BioUML current version2013-11-18T07:05:05Z<p>Lan@dote.ru: </p>
<hr />
<div>0.9.6</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_development_roadmapBioUML development roadmap2013-11-18T07:01:03Z<p>Lan@dote.ru: /* Plans for 2013-2014 */</p>
<hr />
<div><br />
This page describes the current plans for BioUML platform development in 2013 and includes a list of desired features that are not scheduled yet.<br />
Users, administrators and developers are welcome with their comments and suggestions about new features as well as feature implementation priorities. <br />
For this purpose, please, use the [http://forum.biouml.org/ BioUML forum].<br />
<br />
===Plans for 2013-2014===<br />
<br />
<center><br />
{| class="wikitable"<br />
!Release!!Description!!Date<br />
|-<br />
|v. 0.9.7<br />
|<br />
*Server <br />
**grid version - pilot task manager integration with SGE via DRMAA virtualisation <br />
**repository - packages for Red Hat and Debian<br />
**Puppet cookbooks for server updates <br />
*NGS<br />
**miRNA <br />
**ribo-seq<br />
|2013, December<br />
|-<br />
|v. 0.9.8<br />
|<br />
*Web interface<br />
**mobile version (for web-browser) <br />
**web interface improvements diagrams - convenient for exchange and editing <br />
|2014, Q1<br />
|}<br />
</center><br />
<br />
===Other desired features===<br />
<br />
<center><br />
{| class="wikitable"<br />
!Component!!Features!!Priority<br />
|-<br />
|Core<br />
|*Major refactoring: complex, macromolecule state, reaction<br />
*Parameters fitting - optimization process as a workflow<br />
*SED-ML as workflow<br />
*Save optimization results as the diagram state<br />
*SBGN-XML support <br />
*Implementation of OQL subset for access to databases via BioUML object model<br />
|style="background-color:LightSalmon;"|moderate<br />
|-<br />
|Databases<br />
|<br />
*KEGG support improvements:<br />
*Diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)<br />
*Set up wizard<br />
|style="background-color:CornflowerBlue;"|low<br />
|-<br />
|Misc.<br />
|<br />
*SBRML support<br />
*Further integration with MATLAB<br />
|style="background-color:CornflowerBlue;"|low<br />
|}<br />
</center><br />
<br />
==See also==<br />
* [[BioUML]]<br />
* [[Features]]<br />
* [[BioUML development history]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_development_historyBioUML development history2013-11-18T07:00:46Z<p>Lan@dote.ru: +0.9.6 /* 2012 - 2013 */</p>
<hr />
<div>[[BioUML]] has been continuously developed by scientists from the Institute of Systems Biology in Novosibirsk, Russia, since 2002.<br />
<br />
The BioUML project was started by [[User:Fkolpakov@gmail.com|Fedor Kolpakov]] in February 2002, during his work with [http://www.developmentontheedge.com/ Development On The Edge.com, LLC] in Novosibirsk, Russia. In 2005 the [[Institute of Systems Biology]], LLC was formed as a specialized subsidiary of Development On The Edge.com, LLC. <br />
<br />
The current version of the platform is {{BioUML current version}}. <br />
<br />
Further below one can find the history of its development, where each record includes the version number, date of release and a concise description of the updates in the release. The records are listed in chronological order and grouped by year.<br />
<br />
== Predecessors ==<br />
<br />
Prior to the first BioUML release a number of attempts had been undertaken to create versatile and convenient tools for retrieval, analysis, modelling and visualization of biological (particularly, genetic) data:<br />
* [[MGL]]<br />
* [[TRRD viewer]] <br />
* Computer system "[[GeneNet]]"<br />
* [[Transplorer]]<br />
<br />
<br />
==2003 - 2007==<br />
<br />
<br />
<br />
{| class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|June 13, 2003<br />
|style="background-color:Gainsboro"| v. 0.7.0<br />
|Plug-in based architecture using Eclipse runtime, SBML format support, ontology diagram type, Html editor for diagram description, etc.<br />
|-<br />
|September 1, 2003 <br />
|style="background-color:Gainsboro "| v. 0.7.1<br />
|Shell mode, JavaScript custom functions and host objects, JavaScript help, SBW integration using JavaScript.<br />
|- style="background-color: Lavender"<br />
| <br />
|style="background-color:Gainsboro"| v. 0.7.2<br />
|GeneNet module, database search, diagram editor enhancements, graph layouts and graph search support.<br />
|-<br />
| <br />
|style="background-color:Gainsboro"| v. 0.7.3<br />
|Database modules: KEGG, TRANSPATH. Using relational database for data storage, client/server mode.<br />
|- style="background-color: Lavender"<br />
|October 10, 2004<br />
|style="background-color:Gainsboro"| v. 0.7.4<br />
|MathML support, SBML level 2 support, CellML support, <br />
Java simulation engine, rule and event concepts, <br />
<br />
update for Eclipse 3.0, JavaHelp support (only few help topics were written).<br />
<br />
State and transition concept support.<br />
|-<br />
|January 14, 2005<br />
|style="background-color:Gainsboro"| v. 0.7.5<br />
|Matlab and Java simulation engines passed 100% SBML semantic test suite 100%.<br />
Support of algebraic equations, delay, piece wise functions, all MathML functions (factorial, sh, tgh, ctgh, ash, atgh, etc.)<br />
<br />
SBML semantic suite now is part of BDK ([[BioUML Development Kit]])<br />
<br />
Support of diagram import (SBML, CellML, GinSim) and export (PNG, JPEG, SVG, GXL, SBML) <br />
SBW 2.0.0<br />
|- style="background-color: Lavender"<br />
|May 10, 2005<br />
|style="background-color:Gainsboro"| v. 0.7.6<br />
|User interface improvements: preferences, possibility to load and change look & feel, user interface for editing rules and events. <br />
Performance improvements.<br />
ODE solver for stiff problems.<br />
|-<br />
|October 24, 2007<br />
|style="background-color:Gainsboro"| v. 0.7.7<br />
|Full text search engine (uses Lucene), graph search, graph layout improvements<br />
<br />
BioPAX format - import/export, OBO format - import/export<br />
<br />
Ensembl support (spike solution)<br />
<br />
Clipboard pane<br />
<br />
CDK library is used to visualize chemical structures on diagrams<br />
arbitrary images (GIF, PNG, etc.) for graph nodes<br />
<br />
Client-server architecture, BioUML can be started as standalone server or as a servlet<br />
<br />
BioUML network edition<br />
<br />
New installer based on IzPack<br />
<br />
Initial draft of user manual<br />
|}<br />
<br />
==2008==<br />
<br />
{| class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|January 28, 2008 (alpha)<br />
<br />
March 20, 2008 (beta)<br />
|style="background-color:Gainsboro"| v. 0.7.8<br />
|Graphic notation editor, SBGN (alpha version)<br />
<br />
Library of predefined kinetic law functions (SBO)<br />
<br />
BioModels - comparison with other simulators (Copasi, CVODE, RoadRunner, Jarnac, JSim, Oscill8 Core, SBWOdeSolver, MathSBML)<br />
<br />
Database references editor<br />
<br />
Equations editor<br />
<br />
Microarray plug-in (alpha version)<br />
|-<br />
|July 2, 2008<br />
|style="background-color:White"| v. 0.8.0<br />
|Composite database module<br />
<br />
Database module editor<br />
<br />
SBML extensions for BioModels database (experiment, simulation, parameters, result, plot)<br />
<br />
XML diagram type<br />
<br />
Experiments<br />
<br />
Loading of modules from BioUML server:<br />
<br />
EBI data pack (Ensembl, UniProt, ChEBI, IntAct, BioModels) - free databases from EBI as BioUML modules<br />
|- style="background-color: Lavender"<br />
|July 22, 2008<br />
|style="background-color:White"| v. 0.8.1<br />
|Workbench update from the site<br />
<br />
Third party libraries update: JFreeChart, Lucene, Rhino, JHelp<br />
<br />
UI improvements: graphics (for simulation results) - now node titles instead of node IDs are used<br />
<br />
Several HTML tags can be used in titles for graph nodes: <nowiki><br>, <sub>, <sup>, <b>, <i>, <font color, size></nowiki><br />
|-<br />
|August 9, 2008<br />
|style="background-color:White"| v. 0.8.2<br />
|Graphic notation skins: KEGG notation for metabolic pathway diagrams, Regensburg notation for metabolic pathway diagrams<br />
<br />
Simple line path editor<br />
<br />
Microarray data and analysis results as documents (they are opened in tabs similar with diagrams)<br />
<br />
Microarray analysis - identification up/down regulated genes using t-statistics and hyperheometric distribution<br />
|- style="background-color: Lavender"<br />
|August 28, 2008<br />
|style="background-color:White"| v. 0.8.3<br />
|Authorization subsystem (login)<br />
<br />
hierarchical models, block component (proof of concept)<br />
<br />
JavaScript functions for: <br />
* data access, <br />
* operations on data sets (union, overlap, etc.), <br />
* microarray statistical analyses<br />
|-<br />
|December 12, 2008<br />
|style="background-color:White"| v. 0.8.4<br />
|New database modules on BioUML server (pilot version):<br />
<br />
* SABIO-RK ([http://sabio.villa-bosch.de/ System for the Analysis of Biochemical Pathways Reaction Kinetics]) <br />
* EHMN ([http://wwwtest.bioinformatics.ed.ac.uk/wiki/PublicCSB/EHMN Edinburgh Human Metabolic Network])<br />
* LipidMAPS ([http://www.lipidmaps.org/data/structure/ LIPID Metabolites And Pathways Strategy])<br />
* KEGG LIGAND<br />
* KEGG Pathways<br />
* TRANSPATH<br />
<br />
General refactoring - now tabs in repository are called: <br />
* Databases (instead of Modules)<br />
* Data<br />
* Analyses<br />
<br />
New architecture for methods of analyses:<br />
* extension point, registry for methods of analyses<br />
* methods are shown in analyses tab<br />
* new version of dialog for microarray analyses <br />
<br />
Parameters fitting (initial version)<br />
<br />
Refinements, bug fixing:<br />
* authorization subsystem<br />
* repository tree<br />
<br />
Setup wizard - wizard to configure BioUML on first start.<br />
|}<br />
<br />
<br />
==2009==<br />
<br />
{|class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|January 28, 2009 (alpha)<br />
<br />
February 17, 2009 (beta)<br />
|style="background-color:White"| v. 0.8.5<br />
|SBGN 1.0 implementation - alpha version<br />
<br />
KEGG improvements:<br />
* graph layout improvements, orthogonal path finder<br />
* labels location<br />
* graph search engine improvements<br />
<br />
UI improvements:<br />
* grid<br />
* snap to grid<br />
* arrows and lines selection<br />
* keyboard navigation for diagram editing<br />
* repository tree shows database status using icons (public, free, log-in, preloaded, etc.)<br />
* possibility to edit diagrams on display without saving for read only databases<br />
<br />
Parameters fitting (alpha version)<br />
<br />
Bug fixing:<br />
* MATLAB simulation engine - pass SBML semantic test suite again<br />
<br />
JavaHelp refactoring: new tool for help writing - Help&Manual 5<br />
* introduction<br />
* installation and configuration<br />
* databases<br />
|-<br />
|July 31, 2009 (alpha)<br />
<br />
August 7, 2009 (beta)<br />
|style="background-color:White"| v. 0.8.6<br />
|JavaScript:<br />
<br />
* editor - JavaScript files can be opened and edited in BioUML workbench<br />
* debugger<br />
* new functions: plot, view<br />
<br />
Integration with {{R}} - special R object in JavaScript allows to evaluate R expressions as well as to show R graphic output<br />
<br />
Genome viewer (alpha version):<br />
* Ensembl tracks initial support (genes, repeats)<br />
* map document - displays sequences and sites grouped by tracks <br />
* project pane - the project HTML description<br />
* regions pane - allows to specify sequence regions to be visualized as well as sequence visualization options<br />
* tracks pane - allows to specify tracks to be visualized as well as site visualization options<br />
* sites pane - shows the list of site displayed on the map document<br />
<br />
Sequence analysis (alpha version):<br />
* special section in repository: Data/Sequence analyses<br />
* sequences import <br />
<br />
SBML level 2 version 2-4 support<br />
<br />
Parameters fitting (beta version)<br />
<br />
JavaHelp: <br />
* new chapter: JavaScript (pane, editor, shell, functions)<br />
* new chapter: R<br />
* new chapter: parameters fitting<br />
|- style="background-color: Lavender"<br />
|November 30, 2009<br />
<br />
(Web edition)<br />
|style="background-color:Gainsboro"|v. 0.9.0<br />
|'''BioUML web edition:'''<br />
<br />
first public version<br />
<br />
'''BioUML core:'''<br />
<br />
SBGN:<br />
* SBGN - graphic notation update<br />
* <sbgn> extension for SBML <br />
* support for BioModels <br />
* support for TRANSPATH<br />
<br />
Databases:<br />
* BioModels are installed on BioUML server (public)<br />
* EndoNet database support (pilot version, protected)<br />
<br />
Graph layout improvements:<br />
* PathwayLayouter is used as decorator for other graphs to take into account compartments and peculiarities of diagrams <br />
<br />
(for example all math elements are located on the top of diagram) <br />
* layout preview<br />
* possibility to reuse layout for similar diagrams<br />
<br />
New graph layout algorithms:<br />
* cross grid layout - Kato,M. et al. (2005) Automatic drawing of biological networks using cross cost.<br />
* fast grid layout - Kaname, K., Masao, N. and Satoru, M. (2008) Fast grid layout algorithm for biological networks with sweep calculation.<br />
<br />
UI improvements:<br />
* quick search field in repository pane<br />
* quick search for diagrams that contain specified component<br />
* templates for HTML generation for list of species, reactions, variables, parameters and equations<br />
* database loading dialog - possibility to specify login/password to see the list of protected databases.<br />
<br />
Simulation engine:<br />
* JVODE solvers (ported to Java version of CVODE)<br />
* bug fixing (correct reading of piecewise from SBML)<br />
<br />
'''BioUML server:'''<br />
* network repository for group working<br />
|}<br />
<br />
==2010==<br />
<br />
{|class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|July 2, 2010<br />
<br />
(Web edition)<br />
<br />
September 13, 2010 <br />
<br />
(Workbench; alpha)<br />
|style="background-color:Gainsboro"| v. 0.9.0<br />
|'''BioUML core (common for workbench and web edition):'''<br />
<br />
Simulation engine<br />
* fast reactions support<br />
* new ODE/DAE solver - RADAU IIA<br />
* refactoring and bug fixing<br />
<br />
Optimisation engine<br />
* refactoring<br />
* support for steady state<br />
* optimisation document (to handle all data related with optimisation)<br />
* JavaScript API<br />
* performance optimisation (now it much faster then COPASI)<br />
<br />
SBML<br />
* support L2v4, L3V1<br />
* simulation engine passed all SBML tests<br />
<br />
Data analysis - a lot of new methods for analyses microarray data and gene regulatory regions<br />
* microarray analyses<br />
** data normalisation<br />
** identification of [[Up and Down Identification (analysis)|up/down regulated genes]] using different statistical criteria<br />
** [[Enrichment analysis|gene set enrichment analysis]] (using GO and MSigDB databases)<br />
** building gene regulation models on the base of microarray time series<br />
** [[Cluster analysis by K-means (analysis)|cluster analysis]]<br />
* [[Site search on track (analysis)|search for transcription factors binding sites]]<br />
* ChiP-seq analyses ([[Run MACS 1.3.7 on ChiP-Seq (analysis)|MACS algorithm]])<br />
* [[Venn diagrams (analysis)|Venn diagrams]]<br />
<br />
Reproducible research<br />
* research journal (collects all user actions related with data analyses)<br />
* research diagram (graphical representation of research journal)<br />
* [[workflows]] support<br />
<br />
User interface<br />
* filtering table rows according to some JavaScript condition<br />
<br />
'''BioUML workbench:'''<br />
* new tabs in setup wizard (SQL settings, connect DAS, Load project, Create project)<br />
* literature editor (refactoring and bugfixing)<br />
<br />
'''BioUML web edition:'''<br />
* data analyses<br />
* [[genome browser]]<br />
* diagrams export (png, gif, jpeg, svg, sbml, sbgn, dml)<br />
* diagrams import ([[SBML (file format)|sbml]])<br />
* tables import ([[Tabular (file format)|csv]]) and export (csv)<br />
<br />
'''BioUML server:'''<br />
* sandbox for JavaScript<br />
<br />
JavaHelp: <br />
* new chapters: Genome browser, Optimisation<br />
* updated chapters: Simulation<br />
|-<br />
|October 13, 2010<br />
|style="background-color:Gainsboro"| v. 0.9.1<br />
|'''BioUML core (common for workbench and web edition):'''<br />
<br />
Simulation engine:<br />
* composite models (beta version, apoptosis model as an example)<br />
* agent based modeling (beta version, cardiovascular system as an example)<br />
<br />
Chemoinformatics support (on the base of CDK and JChemPaint):<br />
* import 2D structures (SDF, MOL and other format)<br />
* special document type for 2D structures <br />
* 2D structures rendering and editing<br />
* JavaScript API for CDK<br />
* PASS (Prediction of Activity Spectra for Substances) integration<br />
<br />
Tasks manager:<br />
* tasks list as a special viewpart<br />
* tasks management (interrupt, see status and results)<br />
<br />
'''BioUML web edition:'''<br />
* diagrams export (sbml, sbgn)<br />
* diagrams import into custom folders (sbml)<br />
|}<br />
<br />
==2011==<br />
<br />
{|class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|May 6, 2011<br />
|colspan="2"| '''''Version 1.0 of the [[geneXplain]] platform (based on [[BioUML]])'''''<br />
|-<br />
|May 7, 2011<br />
<br />
(Web edition)<br />
<br />
June 14, 2011 <br />
<br />
(Workbench; beta)<br />
|style="background-color:Gainsboro"| v. 0.9.2<br />
|'''BioUML core (common for workbench and web edition):'''<br />
<br />
Import for Process Diagrams in CellDesigner 4.0/4.1 format<br />
<br />
Data analysis<br />
* a lot of new methods for analyses of microarray data, import data in different formats and other<br />
* JavaScript API to work with models and simulation engine (JavaScript host objects model and simulationEngine)<br />
<br />
[[Workflows]] support (beta version)<br />
* improved graphic editor<br />
* cycles<br />
* patterns for input/output parameters<br />
* automatic orthogonal layout for edges<br />
<br />
Simulation engine<br />
* composite models (beta version)<br />
** graphic notation improvements<br />
** special preprocessor to generate flat model<br />
* agent based models - improved, new elements<br />
<br />
User interface improvements:<br />
* a lot of new icons<br />
* drag & drop support<br />
* improved filter for tables (user can filter rows using some expression) <br />
* improved graph layout<br />
** hierarchical layout<br />
** orthogonal layout<br />
* mathematical expressions<br />
** special editor for all mathematical expressions<br />
** user can use node title (instead of its name/identifier) in math expressions<br />
** different modes to show variable names (using id or title)<br />
<br />
Coloring diagram using omics data (redesigned)<br />
<br />
'''BioUML server:'''<br />
* PantherDB pathways in CellDesigner 4.1 format (ftp://ftp.pantherdb.org/pathway/current_release/CD4.1.zip)<br />
* Reactome database<br />
** direct access using SQL<br />
** display diagrams in SBGN graphic notation <br />
* security improvements<br />
|- style="background-color: Lavender"<br />
|May 12, 2011<br />
|colspan="2"| '''''the first [http://www.biodatomics.com/home BioDatomics] release (built around the [[BioUML]] platform)'''''<br />
|-<br />
|October 31, 2011 <br />
<br />
(Workbench; beta)<br />
|style="background-color:Gainsboro"| v. 0.9.3<br />
|'''BioUML core:'''<br />
<br />
Core update<br />
* Eclipse runtime is updated to Equinox version 3.6.0<br />
* Java 7<br />
* fixed problems for Windows 7<br />
<br />
[http://www.sed-ml.org/ SED-ML] (Simulation Experiment Description Markup Language) support (alpha version)<br />
* import and handling of SED-ML files<br />
* run and edited as workflows<br />
* used to generate simulation plots<br />
<br />
Improved BioPAX support<br />
* BioPAX import/export, level 2, 3 (alpha version)<br />
* display BioPAX pathways in SBGN notation<br />
* graph search, full text search<br />
<br />
Graph search enhancements <br />
* flexible merging of previous search results<br />
* improved graph layout: hierarchical layout, orthogonal layout<br />
<br />
Diagram state refactoring<br />
* using transactions for compound edits<br />
* possibility to remove transaction from changes<br />
<br />
Data import/export improvements:<br />
* [[Upload from FTP (analysis)|FTP upload]] - possibility to upload huge data from user’s ftp site<br />
* [[Text file|text]] and [[HTML file|html]] files can be imported <br />
* several [[Image file|image formats]] can be imported and viewed (jpg, png, etc.)<br />
* results can be exported as generic, text, html, or image files.<br />
* special document types for user data: {{Type link|text}}, {{Type link|image}}s, {{Type link|html}}<br />
<br />
Data handling improvements:<br />
* multiple tables can be [[Join several tables (analysis)|joined]];<br />
* columns with identical names may be merged automatically.<br />
<br />
[[Workflows]] improvements:<br />
* possibility to include JavaScripts into workflows<br />
* more comfortable handling of folders and result files<br />
* handling of circular processes<br />
<br />
Algorithms for NGS and sequence analysis:<br />
* [http://bowtie-bio.sourceforge.net/index.shtml Bowtie] wrapper<br />
* peak detection [http://liulab.dfci.harvard.edu/MACS/ MACS] (update)<br />
* motif discovery wrapper for [http://line.imb.ac.ru/smbsm/librettos/libretto_chipmunk/chipmunk_home.rhtml ChIPMunk]<br />
* motif discovery IPS-align<br />
* motif logo (on the base of PWM)<br />
* errors estimation: false positive, FDR, ROC curves<br />
<br />
Embedded chat for collaborative work and on-line consultations (pilot version)<br />
<br />
''(you need to register before at https://biostore.biouml.org)'' <br />
<br />
'''BioUML server'''<br />
* new system for authorization and access rights: [[BioStore]] (https://bio-store.org)<br />
* ChIP-SEQ pipeline (available only on test server yes)<br />
<br />
|}<br />
<br />
==2012 - 2013==<br />
<br />
{|class="wikitable"<br />
!width="15%"|Date!!width="5%"|Release!!width="75%"|Description<br />
|- style="background-color: Lavender"<br />
|2012<br />
<br />
(Web edition)<br />
|style="background-color:Gainsboro"| v. 0.9.4<br />
|Integration with [[BioStore]] (www.bio-store.org) for control of access rights and downloading<br />
|-<br />
|2013, March 20<br />
<br />
(Workbench)<br />
|style="background-color:Gainsboro"| v. 0.9.4<br />
|'''BioUML web:''' <br />
<br />
Collaborative work on diagram (like Google documents)<br />
<br />
UI improvements:<br />
* automatic suggestions in search pane<br />
* automatic opening of uploaded files<br />
* select several elements to remove in repository tree<br />
<br />
'''BioUML core (both workbench and web version):''' <br />
<br />
History of diagram editing (like CVS or SVN)<br />
<br />
Simulation engine<br />
* stochastic modeling, following solvers were implemented:<br />
** Gillespie (Gillespie, D.T. 1977)<br />
** Gibson-Bruck (Gibson, J. Bruck 2000)<br />
** Max Time step (Puchalka, J., Kierzek, A.M. 2004)<br />
** Tau-leaping (Yang, C. et al. 2006)<br />
* Discrete Stochastic Models Test Suite (DSMTS) was passed succesfully<br />
* agent based modelling - new agent with ability to produce descendants. Is used to simulate cell population behaviour.<br />
<br />
SBML support:<br />
* bug fixing<br />
* flux balance constraint models support (using org.apache.common.math3)<br />
* all non composite tests from test-suite 2.3.2 (2013-02-04) passed.<br />
<br />
Visual modelling<br />
* composite diagrams improvements<br />
* MathDiagramType - new diagram type for describing physial procsses. Automatically generates dependencies between equations.<br />
<br />
Model analysis <br />
* model reduction <br />
* [[Metabolic Control Analysis|MCA]] (Metabolic Control Analysis, alpha version)<br />
<br />
Analyses:<br />
* [[Convert table (analysis)|convert table]]: ability to use column for ID<br />
* [[Filter table (analysis)|filter table]]: ability to select top N or bottom N entries<br />
<br />
User interface improvements<br />
* [[perspective]]s - allows to group and filter UI components for specific user's tasks<br />
* tree table component<br />
* drag & drop for annotations<br />
<br />
[[Genome browser]] improvements<br />
* better navigation (chromosome switch, position input box, drag-and-scroll, zoom selection, mouse wheel support, etc.)<br />
* improved sites information tab<br />
* BAM tracks support<br />
* gene structure can be shown in a table cell (only web)<br />
* improved and new styles for genes structure visualization<br />
<br />
Improved support of DAS protocol<br />
* support for 1.53 and 1.6 <br />
* support for non positional features<br />
* interactions<br />
* ontologies<br />
<br />
Integration with JMOL for visualization of 3D structures<br />
<br />
'''BioUML server''' <br />
<br />
{{Galaxy}} support<br />
<br />
new section "Galaxy" in analysis tab allows to use all methods from [[Using Galaxy in BioUML|Galaxy platform]]<br />
<br />
|- style="background-color: Lavender"<br />
|2013, June 15<br />
|style="background-color:Gainsboro"|v. 0.9.5<br />
|<br />
* Simulation engine<br />
**SBML level 3 packages:<br />
***Hierarchical Model Composition<br />
***Flux Balance Constraints<br />
|-<br />
|2013, November 18<br />
|style="background-color:Gainsboro"|v. 0.9.6<br />
|<br />
*BioUML workbench (desktop version)<br />
**integration of Galaxy<br />
**rule based modelling (implementation of BioNetGen approach, [[BioNetGen|details]])<br />
**Antimony support ([[Antimony|details]])<br />
**Synchronisation between textual and graphical model representation (BioNetGen, Antimony)<br />
<br />
*Interface improvements<br />
**display name and actions for table cell values<br />
<br />
*R integration<br />
**improved interface and bug fixes<br />
**possibility to call BioUML from R using rbiouml package (http://cran.r-project.org/web/packages/rbiouml)<br />
<br />
*JavaScript support (web version)<br />
** new JavaScript editor, CodeMirror (http://codemirror.net/).<br />
<br />
*GTRD database<br />
**perspective<br />
**special start page<br />
**improved web interface<br />
<br />
*New methods for analysis of transcription factor binding sites<br />
|}<br />
<br />
==See also==<br />
<br />
* [[BioUML]]<br />
* [[Features]]<br />
* [[BioUML development roadmap]]<br />
<br />
[[Category:BioUML history]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Script_viewpartScript viewpart2013-09-13T07:52:22Z<p>Lan@dote.ru: +{{Outdated}}</p>
<hr />
<div>{{Outdated|Script selection}}<br />
<br />
;Viewpart title in [[BioUML workbench]]<br />
:JavaScript<br />
;Viewpart title on [[BioUML web edition]]<br />
:Script<br />
<br />
Script [[viewpart]] allows you to type expressions in [[Using JavaScript in BioUML|JavaScript]] language and execute them immediately. In BioUML workbench result is displayed directly in viewpart. In BioUML web edition a special page will be opened in document area to display the results. To get starting type <code>help</code> command there.<br />
<br />
== Screenshots ==<br />
<gallery><br />
File:BioUML workbench JavaScript viewpart.png|BioUML workbench JavaScript viewpart<br />
File:BioUML web edition script viewpart.png|BioUML web edition script viewpart<br />
</gallery><br />
<br />
[[Category:Viewparts]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Application_log_(viewpart)Application log (viewpart)2013-09-13T07:51:48Z<p>Lan@dote.ru: </p>
<hr />
<div>{{Outdated}}<br />
<br />
[[File:BioUML workbench application log viewpart.png|thumb|300px|Application log viewpart displaying the information messages of [[File:Data-Annotate-table-icon.png]] [[Annotate table (analysis)|Annotate table]] analysis]]<br />
'''Application log''' viewpart is available in [[BioUML workbench]] only. It displays any informational or error messages produced by application including the following:<br />
* [[analysis (element type)|Analysis]] execution;<br />
* [[Workflow]] execution;<br />
* File import;<br />
* Optimization tasks;<br />
* Other processes.<br />
<br />
In [[BioUML web edition]] this viewpart is absent. Common logs of [[BioUML server]] are stored in <code>$CATALINA_HOME/logs/biouml_server.log</code> or other file depending on your logging configuration. Logs for [[analysis (element type)|analysis]] and [[workflow]] execution are displayed directly in [[analysis document]].<br />
<br />
[[Category:Viewparts]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Template:OutdatedTemplate:Outdated2013-09-13T07:51:08Z<p>Lan@dote.ru: Created page with "{| style="color:#000000; width: 70%; border:solid 1px #A8A8A8; padding:0.5em; margin:0.5em 0; background-color:#FEFEB0;font-size:95%; vertical-align:middle; text-align: center..."</p>
<hr />
<div>{| style="color:#000000; width: 70%; border:solid 1px #A8A8A8; padding:0.5em; margin:0.5em 0; background-color:#FEFEB0;font-size:95%; vertical-align:middle; text-align: center;"<br />
| This page or section need to be updated to reflect new changes in BioUML.<br />
|}</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Diff_manager_(extension_point)Diff manager (extension point)2013-09-13T07:47:51Z<p>Lan@dote.ru: Created page with "{{Extension point|diffManager|ru.biosoft.access|registry=ru.biosoft.access.history.HistoryFacade}} === Description === This extension point allows to register difference manag..."</p>
<hr />
<div>{{Extension point|diffManager|ru.biosoft.access|registry=ru.biosoft.access.history.HistoryFacade}}<br />
=== Description ===<br />
This extension point allows to register difference managers for history data collections. Difference manages are used to build difference between two versions of the element.<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT diffManager><br />
<!ATTLIST diffManager<br />
class CDATA #REQUIRED<br />
><br />
<br />
;class<br />
:Fully-qualified name of the difference manager class (must implement {{Class|ru.biosoft.access.history.DiffManager}} interface).<br />
<br />
=== Example ===<br />
<extension point="ru.biosoft.access.diffManager"><br />
<diffManager class="biouml.standard.state.DiagramDiffManager"/><br />
</extension><br />
<br />
This extension registers {{Class|biouml.standard.state.DiagramDiffManager}} as difference manager.<br />
<br />
=== Implementation details ===<br />
Only one instance of difference manager class will be created.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Data_collection_listener_(extension_point)Data collection listener (extension point)2013-09-13T07:42:56Z<p>Lan@dote.ru: Created page with "{{Extension point|dataCollectionListener|ru.biosoft.access}} === Description === This extension point allows to register classes which can be used as listeners for data collec..."</p>
<hr />
<div>{{Extension point|dataCollectionListener|ru.biosoft.access}}<br />
=== Description ===<br />
This extension point allows to register classes which can be used as listeners for data collections. Only registered listeners will be added automatically if specified in initial data collection properties (see the constructor of {{Class|ru.biosoft.access.AbstractDataCollection}}).<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT dataCollectionListener><br />
<!ATTLIST dataCollectionListener<br />
class CDATA #REQUIRED<br />
><br />
<br />
;class<br />
:Fully-qualified name of the data collection listener class (must implement {{Class|ru.biosoft.access.DataCollectionListener}} interface).<br />
<br />
=== Example ===<br />
<extension id="lucene DataCollection listener" point="ru.biosoft.access.dataCollectionListener"> <br />
<dataCollectionListener class="biouml.plugins.lucene.LuceneInitListener"/> <br />
</extension><br />
<br />
This extension registers {{Class|biouml.plugins.lucene.LuceneInitListener}} as possible data collection listener class.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Query_system_(extension_point)Query system (extension point)2013-09-13T07:38:03Z<p>Lan@dote.ru: Created page with "{{Extension point|querySystem|ru.biosoft.access}} === Description === This extension point allows to register classes which can be used as DataCollection query system. === Co..."</p>
<hr />
<div>{{Extension point|querySystem|ru.biosoft.access}}<br />
=== Description ===<br />
This extension point allows to register classes which can be used as DataCollection query system.<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT querySystem><br />
<!ATTLIST querySystem<br />
class CDATA #REQUIRED<br />
><br />
<br />
;class<br />
:Fully-qualified name of the query system class (must implement {{Class|ru.biosoft.access.QuerySystem}} interface).<br />
<br />
=== Example ===<br />
<extension id="lucene query system" point="ru.biosoft.access.querySystem"> <br />
<querySystem class="biouml.plugins.lucene.LuceneQuerySystemImpl"/> <br />
</extension><br />
<br />
This extension registers {{Class|biouml.plugins.lucene.LuceneQuerySystemImpl}} as possible query system class.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Script_type_(extension_point)Script type (extension point)2013-09-13T07:32:12Z<p>Lan@dote.ru: Created page with "{{Extension point|scriptType|ru.biosoft.access|since=0.9.6|registry=ru.biosoft.access.javascript.ScriptTypeRegistry}} === Description === This extension point allows to regist..."</p>
<hr />
<div>{{Extension point|scriptType|ru.biosoft.access|since=0.9.6|registry=ru.biosoft.access.javascript.ScriptTypeRegistry}}<br />
=== Description ===<br />
This extension point allows to register new script languages supported by [[BioUML]].<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT scriptType><br />
<!ATTLIST scriptType<br />
type CDATA #REQUIRED<br />
title CDATA #REQUIRED<br />
class CDATA #REQUIRED<br />
lexer CDATA #REQUIRED<br />
product CDATA #IMPLIED<br />
><br />
<br />
;type<br />
:short name of script type. It's used mostly as internal script type identifier, but can be exposed to user, for example, as default extension for new script elements<br />
;title<br />
:user-friendly name of script language.<br />
;class<br />
:fully-qualified name of data element class representing the script written on this language (must extend {{Class|ru.biosoft.access.javascript.ScriptDataElement}} abstract class).<br />
;lexer<br />
:fully-qualified name of class representing the language lexer used for syntax highlighting in [[BioUML workbench]] (must extend {{Class|com.Ostermiller.Syntax.Lexer.Lexer}}).<br />
;product<br />
:if specified, then [[BioUML server]] user must be subscribed to given product in order to use this type of scripts.<br />
<br />
=== Example ===<br />
<extension point="ru.biosoft.access.scriptType"><br />
<scriptType <br />
type="R" <br />
title="R script" <br />
product="R" <br />
class="ru.biosoft.plugins.jri.RElement" <br />
lexer="ru.biosoft.plugins.jri.lex.RLexer"<br />
/><br />
</extension><br />
<br />
This extension registers R scripts with title "R script" which are available for subscribers of "R" product only.</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Analysis_method_developmentAnalysis method development2013-09-13T07:06:09Z<p>Lan@dote.ru: /* Implementing parameters */</p>
<hr />
<div>BioUML analysis method is a function which takes some user-defined parameters, processes them somehow (probably using [[repository]] elements and databases) and produces some results, storing them in the repository. This page describes implementation details on how to create your own analysis method.<br />
<br />
If you want to create your analysis method in new plugin, please read [[plugin development]] page first.<br />
<br />
== Classes ==<br />
To create analysis method, you should create at least three classes:<br />
# '''Analysis class''': class implementing {{Class|ru.biosoft.analysis.AnalysisMethod}} interface. It's strongly recommended to extend {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} class parameterizing it via parameters class.<br />
# '''Parameters class''': bean class for analysis parameters, which must implement {{Class|ru.biosoft.analysis.AnalysisParameters}} interface. It's strongly recommended to extend {{Class|ru.biosoft.analysis.AbstractAnalysisParameters}} class.<br />
# '''Bean info for parameters class''': class implementing {{Class|java.beans.BeanInfo}} interface which describes parameters class. Must have the same name as parameters class with <code>BeanInfo</code> suffix. It's strongly recommended to extend {{Class|ru.biosoft.util.bean.BeanInfoEx2}} class.<br />
<br />
The following naming conventions are used. Consider, you want to create some analysis to "process data". Then analysis class should be named as <code>ProcessData</code> or <code>ProcessDataAnalysis</code>, parameters class should be named as <code>ProcessDataParameters</code> and bean info for parameters class should be named as <code>ProcessDataParametersBeanInfo</code>.<br />
<br />
If your analysis has not very much code, you may consider putting parameters class and its bean info as nested static classes into analysis class in the following manner:<br />
<br />
public class ProcessDataAnalysis extends {{Class|ru.biosoft.analysis.AnalysisMethodSupport}}<ProcessDataAnalysis.ProcessDataParameters><br />
{<br />
...<br />
public static class ProcessDataParameters extends {{Class|ru.biosoft.analysis.AbstractAnalysisParameters}}<br />
{<br />
...<br />
}<br />
<br />
public static class ProcessDataParametersBeanInfo extends {{Class|ru.biosoft.util.bean.BeanInfoEx2}}<br />
{<br />
...<br />
}<br />
}<br />
<br />
== Extension ==<br />
To make your analysis available in the tree, you must register it as extension for [[Method (extension point)|ru.biosoft.analysis.method]] extension point. Consider also creating [[method description HTML file]] and JavaScript host object (or use existing one).<br />
<br />
== Implementing parameters ==<br />
Parameters class must have default constructor and getter and setter methods for all parameters used in analysis method. Setters must call {{Method|com.beanexplorer.beans.Option.firePropertyChange}} superclass method. Getters can be annotated using {{Annotation|ru.biosoft.util.bean.PropertyName}} and {{Annotation|ru.biosoft.util.bean.PropertyDescription}} annotations. Usual implementation look like this:<br />
<br />
public class ProcessDataParameters extends {{Class|ru.biosoft.analysis.AbstractAnalysisParameters}}<br />
{<br />
private DataElementPath inputPath, outputPath;<br />
private String myStringParameter;<br />
private boolean myBooleanParameter;<br />
<br />
@PropertyName("Input table")<br />
@PropertyDescription("Table to process")<br />
public DataElementPath getInputPath()<br />
{<br />
return inputPath;<br />
}<br />
<br />
public void setInputPath(DataElementPath inputPath)<br />
{<br />
Object oldValue = this.inputPath;<br />
this.inputPath = inputPath;<br />
firePropertyChange("inputPath", oldValue, this.inputPath);<br />
}<br />
<br />
@PropertyName("String parameter")<br />
@PropertyDescription("String which will be used during processing")<br />
public String getMyStringParameter()<br />
{<br />
return myStringParameter;<br />
}<br />
<br />
public void setMyStringParameter(String myStringParameter)<br />
{<br />
Object oldValue = this.myStringParameter;<br />
this.myStringParameter = myStringParameter;<br />
firePropertyChange("myStringParameter", oldValue, myStringParameter);<br />
}<br />
<br />
@PropertyName("Verbose output")<br />
@PropertyDescription("Whether to print additional messages during processing")<br />
public boolean isMyBooleanParameter()<br />
{<br />
return myBooleanParameter;<br />
}<br />
<br />
public void setMyBooleanParameter(boolean myBooleanParameter)<br />
{<br />
Object oldValue = this.myBooleanParameter;<br />
this.myBooleanParameter = myBooleanParameter;<br />
firePropertyChange("myBooleanParameter", oldValue, myBooleanParameter);<br />
}<br />
}<br />
<br />
=== Parameter types ===<br />
Many parameter types are supported, including (but not limited to) the following:<br />
* Primitive types (boolean, short, int, long, float, double);<br />
* {{Class|java.lang.String}} for textual parameters;<br />
* {{Class|ru.biosoft.access.DataElementPath}} for paths to the [[repository]] elements (both for inputs and outputs);<br />
* {{Class|ru.biosoft.access.DataElementPathSet}} for sets of input [[repository]] elements;<br />
* {{Class|biouml.standard.type.Species}} for selection of species from preinstalled list;<br />
* {{Class|ru.biosoft.bsa.BasicGenomeSelector}} and {{Class|ru.biosoft.bsa.GenomeSelector}} for convenient selection of the genome (either in preinstalled database or user-uploaded);<br />
* {{Class|java.awt.Color}} for color selection;<br />
* Java arrays of any supported types (array elements can be added or deleted by user).<br />
<br />
You may use your own bean as complex parameter type, but the following requirements should be met:<br />
* Your bean should extend {{Class|com.beanexplorer.beans.Option}} class.<br />
* Your bean should be serializable via {{Method|ru.biosoft.util.TextUtil.fromString}}/{{Method|ru.biosoft.util.TextUtil.toString}} methods. See [[text serialization]] for details.<br />
<br />
=== Writing bean info class for parameters ===<br />
Bean info class must have the same name as parameters class with <code>BeanInfo</code> suffix. It must have default constructor which calls superclass constructor passing parameters class name:<br />
<br />
public class ProcessDataParametersBeanInfo extends {{Class|ru.biosoft.util.bean.BeanInfoEx2}}<br />
{<br />
public ProcessDataParametersBeanInfo()<br />
{<br />
super(ProcessDataParameters.class);<br />
}<br />
}<br />
<br />
To register parameters override {{Method|com.beanexplorer.beans.BeanInfoEx.initProperties()}} superclass method. For each parameter you should create {{Class|java.beans.PropertyDescriptor}} and add it via {{Method|ru.biosoft.util.bean.BeanInfoEx2.add(PropertyDescriptor)}} superclass method. There are also some helper methods defined in {{Class|ru.biosoft.util.bean.BeanInfoEx2}} which make things easier:<br />
* <code>add(String name)</code> - create {{Class|java.beans.PropertyDescriptor}} with default getter/setter names and add it.<br />
* <code>add(String name, Class<?> editor)</code> - the same as above, but also sets custom property editor class.<br />
* <code>addHidden(String name, String hiddenMethodName)</code> - create conditionally hidden option. The hiddenMethodName is name of parameters class method which takes no parameters and returns boolean value (true if parameter must be hidden)<br />
* <code>addHidden(String name, Class<?> editor, String hiddenMethodName)</code> - the same as above, but also sets custom property editor class.<br />
and so on.<br />
<br />
Parameters will appear in the form in the registration order. By convention first should be input repository elements, then other parameters and finally output repository elements. If parameter X depends on parameter Y, then X must be registered after Y.<br />
<br />
=== Registering complex parameters ===<br />
For simple data types like primitives or {{Class|java.lang.String}} calling <code>add(parameterName)</code> is enough to register the parameter. In case of more complex parameters special editor must be set as well as some additional {{Class|java.beans.PropertyDescriptor}} parameters. Usually this can be done using special convenience methods.<br />
<br />
* Repository elements should be registered via static methods defined in {{Class|ru.biosoft.access.repository.DataElementPathEditor}}:<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerInput}} methods to register input element (user will be forced to select existing element of given type).<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerInputMulti}} methods to register set of input elements (user will be able to select several elemens using Ctrl or Shift buttons).<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerOutput}} methods to register output element (user will be asked for confirmation to overwrite an existing item).<br />
* {{Type link|table|Table}} column name selector should be registered via static methods defined in {{Class|ru.biosoft.table.columnbeans.ColumnNameSelector}}:<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerSelector}} methods to allow selection of any column.<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerNumericSelector}} methods to allow selection of numerical column only.<br />
*: <b>Note</b>: column name must be defined as {{Class|java.lang.String}} in parameters class and its default value must be either {{Constant|ru.biosoft.table.columnbeans.ColumnNameSelector.NONE_COLUMN}} or any existing column (not null).<br />
* Set of {{Type link|table}} column names should be registered via static methods defined in {{Class|ru.biosoft.table.columnbeans.ColumnNamesSelector}}:<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerSelector}} methods to allow selection of any columns.<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerNumericSelector}} methods to allow selection of numerical columns only.<br />
*: <b>Note</b>: column names must be defined as {{Class|java.lang.String[]}} in parameters class.<br />
* Selector for predefined species can be registered using {{Method|ru.biosoft.workbench.editors.DataElementComboBoxSelector.registerSelector}} method with {{Constant|biouml.standard.type.Species.SPECIES_PATH}} as collectionPath parameter.<br />
* Selector for [[reference type]] should be registered via {{Method|ru.biosoft.workbench.editors.ReferenceTypeSelector.registerSelector}} methods.<br />
* For {{Class|java.awt.Color}} parameter type set {{Class|com.beanexplorer.editors.ColorEditor}} property editor class.<br />
<br />
=== Creating custom parameter editor ===<br />
{{Stub}}<br />
<br />
== Implementing analysis ==<br />
If your analysis extends {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} abstract class, then it's necessary to create constructor and override {{Method|ru.biosoft.analysis.AnalysisMethodSupport.justAnalyzeAndPut}} method where actual analysis must be performed. Normally constructor looks like this:<br />
public ProcessData(DataCollection<?> origin, String name)<br />
{<br />
super(origin, name, new ProcessDataParameters());<br />
}<br />
Adding any other initialization code is not recommended. It's better to initialize analysis inside {{Method|ru.biosoft.analysis.AnalysisMethodSupport.justAnalyzeAndPut}} method.<br />
<br />
Analysis parameters are accessible in {{Field|ru.biosoft.analysis.AnalysisMethodSupport.parameters}} field.<br />
<br />
=== justAnalyzeAndPut implementation ===<br />
The <code>justAnalyzeAndPut</code> method is called at most once per analysis class object. If user launches the same analysis several times, new objects will be created.<br />
<br />
The return value of this method can be either resulting element or Java array of resulting elements. System will try to store analysis parameters in these elements info and open them automatically. Return null if your analysis don't create any result (but throw an exception if your analysis should be considered as failed).<br />
<br />
=== Parameters validation ===<br />
Analysis parameters are validated before <code>justAnalyzeAndPut</code> is called.<br />
<br />
By default only repository paths are validated. The following validations are performed:<br />
* Input elements must exist, must have the requested element type and [[reference type]] (if it was constrained).<br />
* Parent collection for output element must exist. If it doesn't exist, validator will try to create this collection.<br />
* Parent collection for output element must be writable.<br />
* It must be possible to save the requested output element type to the parent collection.<br />
* Output path cannot be the same as any of input paths.<br />
<br />
To add your own validation code, override {{Method|ru.biosoft.analysis.AnalysisMethodSupport.validateParameters()}} method. There are some handy check* methods in {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} class which will make basic validations easy.<br />
<br />
Please remember that even if user interface doesn't allow to enter invalid value (for example, restricting choise with drop-down list), parameters can be filled in the various ways:<br />
* Using [[workflow]] mechanism;<br />
* Executing analysis from JavaScript console;<br />
* Executing analysis via BioUML API (using [[BioUML web client]] or [[rbiouml]] R package).<br />
Thus you may still encounter values which might be impossible to enter using UI controls.<br />
<br />
=== Logging ===<br />
To log messages during analysis execution, use {{Field|ru.biosoft.analysis.AnalysisMethodSupport.log}} logger instance. This instance is connected with analysis or [[workflow]] log. In case of unrecoverable error, it's better to throw [[BioUML exceptions|BioUML exception]] out of <code>justAnalyzeAndPut</code> method than to log it by yourself.<br />
<br />
=== Progress bar ===<br />
{{Stub}}<br />
<br />
=== Parallelization ===<br />
{{Stub}}<br />
<br />
[[Category:Development]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Analysis_method_developmentAnalysis method development2013-09-13T07:05:36Z<p>Lan@dote.ru: /* Classes */</p>
<hr />
<div>BioUML analysis method is a function which takes some user-defined parameters, processes them somehow (probably using [[repository]] elements and databases) and produces some results, storing them in the repository. This page describes implementation details on how to create your own analysis method.<br />
<br />
If you want to create your analysis method in new plugin, please read [[plugin development]] page first.<br />
<br />
== Classes ==<br />
To create analysis method, you should create at least three classes:<br />
# '''Analysis class''': class implementing {{Class|ru.biosoft.analysis.AnalysisMethod}} interface. It's strongly recommended to extend {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} class parameterizing it via parameters class.<br />
# '''Parameters class''': bean class for analysis parameters, which must implement {{Class|ru.biosoft.analysis.AnalysisParameters}} interface. It's strongly recommended to extend {{Class|ru.biosoft.analysis.AbstractAnalysisParameters}} class.<br />
# '''Bean info for parameters class''': class implementing {{Class|java.beans.BeanInfo}} interface which describes parameters class. Must have the same name as parameters class with <code>BeanInfo</code> suffix. It's strongly recommended to extend {{Class|ru.biosoft.util.bean.BeanInfoEx2}} class.<br />
<br />
The following naming conventions are used. Consider, you want to create some analysis to "process data". Then analysis class should be named as <code>ProcessData</code> or <code>ProcessDataAnalysis</code>, parameters class should be named as <code>ProcessDataParameters</code> and bean info for parameters class should be named as <code>ProcessDataParametersBeanInfo</code>.<br />
<br />
If your analysis has not very much code, you may consider putting parameters class and its bean info as nested static classes into analysis class in the following manner:<br />
<br />
public class ProcessDataAnalysis extends {{Class|ru.biosoft.analysis.AnalysisMethodSupport}}<ProcessDataAnalysis.ProcessDataParameters><br />
{<br />
...<br />
public static class ProcessDataParameters extends {{Class|ru.biosoft.analysis.AbstractAnalysisParameters}}<br />
{<br />
...<br />
}<br />
<br />
public static class ProcessDataParametersBeanInfo extends {{Class|ru.biosoft.util.bean.BeanInfoEx2}}<br />
{<br />
...<br />
}<br />
}<br />
<br />
== Extension ==<br />
To make your analysis available in the tree, you must register it as extension for [[Method (extension point)|ru.biosoft.analysis.method]] extension point. Consider also creating [[method description HTML file]] and JavaScript host object (or use existing one).<br />
<br />
== Implementing parameters ==<br />
Parameters class must have default constructor and getter and setter methods for all parameters used in analysis method. Setters must call {{Method|com.beanexplorer.beans.Option.firePropertyChange}} superclass method. Getters can be annotated using {{Annotation|ru.biosoft.util.bean.PropertyName}} and {{Annotation|ru.biosoft.util.bean.PropertyDescription}} annotations. Usual implementation look like this:<br />
<br />
public class ProcessDataParameters extends AbstractAnalysisParameters<br />
{<br />
private DataElementPath inputPath, outputPath;<br />
private String myStringParameter;<br />
private boolean myBooleanParameter;<br />
<br />
@PropertyName("Input table")<br />
@PropertyDescription("Table to process")<br />
public DataElementPath getInputPath()<br />
{<br />
return inputPath;<br />
}<br />
<br />
public void setInputPath(DataElementPath inputPath)<br />
{<br />
Object oldValue = this.inputPath;<br />
this.inputPath = inputPath;<br />
firePropertyChange("inputPath", oldValue, this.inputPath);<br />
}<br />
<br />
@PropertyName("String parameter")<br />
@PropertyDescription("String which will be used during processing")<br />
public String getMyStringParameter()<br />
{<br />
return myStringParameter;<br />
}<br />
<br />
public void setMyStringParameter(String myStringParameter)<br />
{<br />
Object oldValue = this.myStringParameter;<br />
this.myStringParameter = myStringParameter;<br />
firePropertyChange("myStringParameter", oldValue, myStringParameter);<br />
}<br />
<br />
@PropertyName("Verbose output")<br />
@PropertyDescription("Whether to print additional messages during processing")<br />
public boolean isMyBooleanParameter()<br />
{<br />
return myBooleanParameter;<br />
}<br />
<br />
public void setMyBooleanParameter(boolean myBooleanParameter)<br />
{<br />
Object oldValue = this.myBooleanParameter;<br />
this.myBooleanParameter = myBooleanParameter;<br />
firePropertyChange("myBooleanParameter", oldValue, myBooleanParameter);<br />
}<br />
}<br />
<br />
=== Parameter types ===<br />
Many parameter types are supported, including (but not limited to) the following:<br />
* Primitive types (boolean, short, int, long, float, double);<br />
* {{Class|java.lang.String}} for textual parameters;<br />
* {{Class|ru.biosoft.access.DataElementPath}} for paths to the [[repository]] elements (both for inputs and outputs);<br />
* {{Class|ru.biosoft.access.DataElementPathSet}} for sets of input [[repository]] elements;<br />
* {{Class|biouml.standard.type.Species}} for selection of species from preinstalled list;<br />
* {{Class|ru.biosoft.bsa.BasicGenomeSelector}} and {{Class|ru.biosoft.bsa.GenomeSelector}} for convenient selection of the genome (either in preinstalled database or user-uploaded);<br />
* {{Class|java.awt.Color}} for color selection;<br />
* Java arrays of any supported types (array elements can be added or deleted by user).<br />
<br />
You may use your own bean as complex parameter type, but the following requirements should be met:<br />
* Your bean should extend {{Class|com.beanexplorer.beans.Option}} class.<br />
* Your bean should be serializable via {{Method|ru.biosoft.util.TextUtil.fromString}}/{{Method|ru.biosoft.util.TextUtil.toString}} methods. See [[text serialization]] for details.<br />
<br />
=== Writing bean info class for parameters ===<br />
Bean info class must have the same name as parameters class with <code>BeanInfo</code> suffix. It must have default constructor which calls superclass constructor passing parameters class name:<br />
<br />
public class ProcessDataParametersBeanInfo extends BeanInfoEx2<br />
{<br />
public ProcessDataParametersBeanInfo()<br />
{<br />
super(ProcessDataParameters.class);<br />
}<br />
}<br />
<br />
To register parameters override {{Method|com.beanexplorer.beans.BeanInfoEx.initProperties()}} superclass method. For each parameter you should create {{Class|java.beans.PropertyDescriptor}} and add it via {{Method|ru.biosoft.util.bean.BeanInfoEx2.add(PropertyDescriptor)}} superclass method. There are also some helper methods defined in {{Class|ru.biosoft.util.bean.BeanInfoEx2}} which make things easier:<br />
* <code>add(String name)</code> - create {{Class|java.beans.PropertyDescriptor}} with default getter/setter names and add it.<br />
* <code>add(String name, Class<?> editor)</code> - the same as above, but also sets custom property editor class.<br />
* <code>addHidden(String name, String hiddenMethodName)</code> - create conditionally hidden option. The hiddenMethodName is name of parameters class method which takes no parameters and returns boolean value (true if parameter must be hidden)<br />
* <code>addHidden(String name, Class<?> editor, String hiddenMethodName)</code> - the same as above, but also sets custom property editor class.<br />
and so on.<br />
<br />
Parameters will appear in the form in the registration order. By convention first should be input repository elements, then other parameters and finally output repository elements. If parameter X depends on parameter Y, then X must be registered after Y.<br />
<br />
=== Registering complex parameters ===<br />
For simple data types like primitives or {{Class|java.lang.String}} calling <code>add(parameterName)</code> is enough to register the parameter. In case of more complex parameters special editor must be set as well as some additional {{Class|java.beans.PropertyDescriptor}} parameters. Usually this can be done using special convenience methods.<br />
<br />
* Repository elements should be registered via static methods defined in {{Class|ru.biosoft.access.repository.DataElementPathEditor}}:<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerInput}} methods to register input element (user will be forced to select existing element of given type).<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerInputMulti}} methods to register set of input elements (user will be able to select several elemens using Ctrl or Shift buttons).<br />
** Use {{Method|ru.biosoft.access.repository.DataElementPathEditor.registerOutput}} methods to register output element (user will be asked for confirmation to overwrite an existing item).<br />
* {{Type link|table|Table}} column name selector should be registered via static methods defined in {{Class|ru.biosoft.table.columnbeans.ColumnNameSelector}}:<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerSelector}} methods to allow selection of any column.<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerNumericSelector}} methods to allow selection of numerical column only.<br />
*: <b>Note</b>: column name must be defined as {{Class|java.lang.String}} in parameters class and its default value must be either {{Constant|ru.biosoft.table.columnbeans.ColumnNameSelector.NONE_COLUMN}} or any existing column (not null).<br />
* Set of {{Type link|table}} column names should be registered via static methods defined in {{Class|ru.biosoft.table.columnbeans.ColumnNamesSelector}}:<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerSelector}} methods to allow selection of any columns.<br />
** Use {{Method|ru.biosoft.table.columnbeans.ColumnNameSelector.registerNumericSelector}} methods to allow selection of numerical columns only.<br />
*: <b>Note</b>: column names must be defined as {{Class|java.lang.String[]}} in parameters class.<br />
* Selector for predefined species can be registered using {{Method|ru.biosoft.workbench.editors.DataElementComboBoxSelector.registerSelector}} method with {{Constant|biouml.standard.type.Species.SPECIES_PATH}} as collectionPath parameter.<br />
* Selector for [[reference type]] should be registered via {{Method|ru.biosoft.workbench.editors.ReferenceTypeSelector.registerSelector}} methods.<br />
* For {{Class|java.awt.Color}} parameter type set {{Class|com.beanexplorer.editors.ColorEditor}} property editor class.<br />
<br />
=== Creating custom parameter editor ===<br />
{{Stub}}<br />
<br />
== Implementing analysis ==<br />
If your analysis extends {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} abstract class, then it's necessary to create constructor and override {{Method|ru.biosoft.analysis.AnalysisMethodSupport.justAnalyzeAndPut}} method where actual analysis must be performed. Normally constructor looks like this:<br />
public ProcessData(DataCollection<?> origin, String name)<br />
{<br />
super(origin, name, new ProcessDataParameters());<br />
}<br />
Adding any other initialization code is not recommended. It's better to initialize analysis inside {{Method|ru.biosoft.analysis.AnalysisMethodSupport.justAnalyzeAndPut}} method.<br />
<br />
Analysis parameters are accessible in {{Field|ru.biosoft.analysis.AnalysisMethodSupport.parameters}} field.<br />
<br />
=== justAnalyzeAndPut implementation ===<br />
The <code>justAnalyzeAndPut</code> method is called at most once per analysis class object. If user launches the same analysis several times, new objects will be created.<br />
<br />
The return value of this method can be either resulting element or Java array of resulting elements. System will try to store analysis parameters in these elements info and open them automatically. Return null if your analysis don't create any result (but throw an exception if your analysis should be considered as failed).<br />
<br />
=== Parameters validation ===<br />
Analysis parameters are validated before <code>justAnalyzeAndPut</code> is called.<br />
<br />
By default only repository paths are validated. The following validations are performed:<br />
* Input elements must exist, must have the requested element type and [[reference type]] (if it was constrained).<br />
* Parent collection for output element must exist. If it doesn't exist, validator will try to create this collection.<br />
* Parent collection for output element must be writable.<br />
* It must be possible to save the requested output element type to the parent collection.<br />
* Output path cannot be the same as any of input paths.<br />
<br />
To add your own validation code, override {{Method|ru.biosoft.analysis.AnalysisMethodSupport.validateParameters()}} method. There are some handy check* methods in {{Class|ru.biosoft.analysis.AnalysisMethodSupport}} class which will make basic validations easy.<br />
<br />
Please remember that even if user interface doesn't allow to enter invalid value (for example, restricting choise with drop-down list), parameters can be filled in the various ways:<br />
* Using [[workflow]] mechanism;<br />
* Executing analysis from JavaScript console;<br />
* Executing analysis via BioUML API (using [[BioUML web client]] or [[rbiouml]] R package).<br />
Thus you may still encounter values which might be impossible to enter using UI controls.<br />
<br />
=== Logging ===<br />
To log messages during analysis execution, use {{Field|ru.biosoft.analysis.AnalysisMethodSupport.log}} logger instance. This instance is connected with analysis or [[workflow]] log. In case of unrecoverable error, it's better to throw [[BioUML exceptions|BioUML exception]] out of <code>justAnalyzeAndPut</code> method than to log it by yourself.<br />
<br />
=== Progress bar ===<br />
{{Stub}}<br />
<br />
=== Parallelization ===<br />
{{Stub}}<br />
<br />
[[Category:Development]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/BioUML_web_clientBioUML web client2013-09-13T07:01:24Z<p>Lan@dote.ru: Created page with "{{Stub}} '''BioUML web client''' or '''bwc''' is a command line utility which allows user to run analyses and workflows on remote BioUML server..."</p>
<hr />
<div>{{Stub}}<br />
<br />
'''BioUML web client''' or '''bwc''' is a command line utility which allows user to run [[:Category:Analyses|analyses]] and [[workflows]] on remote [[BioUML server]]. Currently it's not freely available. Contact BioUML team if you need it.<br />
<br />
If you're using {{R}}, consider [[rbiouml]] package which has the same and even more functionality than BioUML web client.<br />
<br />
[[Category:Software]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/RbioumlRbiouml2013-09-13T06:54:38Z<p>Lan@dote.ru: </p>
<hr />
<div>'''rbiouml''' is an {{R}} package which allows accessing [[BioUML server]] from R script. It's available on CRAN repository. <br />
<br />
== Main capabilities ==<br />
* Retrieving {{Type link|table}}s from BioUML (including any items which can be represented as tables: {{Type link|profile}}s, some kinds of {{Type link|track}}s, etc.);<br />
* Storing {{Type link|table}}s in BioUML;<br />
* Listing items in BioUML repository;<br />
* Launching BioUML analyses;<br />
* Launching BioUML workflows.<br />
<br />
== Installation ==<br />
Use the following R command to install rbiouml:<br />
install.packages("rbiouml")<br />
To update from older version use:<br />
update.packages("rbiouml")<br />
<br />
== External links ==<br />
* [http://cran.r-project.org/web/packages/rbiouml/ CRAN rbiouml page]<br />
* [http://cran.r-project.org/web/packages/rbiouml/vignettes/rbiouml.pdf Getting started with rbiouml]<br />
<br />
[[Category:R]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/RbioumlRbiouml2013-09-13T06:54:20Z<p>Lan@dote.ru: </p>
<hr />
<div>'''rbiouml''' is an {{R}} package which allows accessing [[BioUML server]] from R script. It's available on CRAN repository. <br />
<br />
== Main capabilities ==<br />
* Retrieving {{Type link|table}}s from BioUML (including any items which can be represented as tables: {{Type link|profile}}s, some kinds of {{Type link|track}}s, etc.)<br />
* Storing {{Type link|table}}s in BioUML.<br />
* Listing items in BioUML repository.<br />
* Launching BioUML analyses.<br />
* Launching BioUML workflows.<br />
<br />
== Installation ==<br />
Use the following R command to install rbiouml:<br />
install.packages("rbiouml")<br />
To update from older version use:<br />
update.packages("rbiouml")<br />
<br />
== External links ==<br />
* [http://cran.r-project.org/web/packages/rbiouml/ CRAN rbiouml page]<br />
* [http://cran.r-project.org/web/packages/rbiouml/vignettes/rbiouml.pdf Getting started with rbiouml]<br />
<br />
[[Category:R]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/RbioumlRbiouml2013-09-13T06:53:52Z<p>Lan@dote.ru: </p>
<hr />
<div>'''rbiouml''' is an {{R}} package which allows accessing [[BioUML server]] from R script. It's available on CRAN repository. <br />
<br />
== Main capabilities ==<br />
* Retrieving {{Type link|table}}s from BioUML (including any items which can be represented as tables: {{Type link|profile}}s, some kinds of {{Type link|track}}s, etc.)<br />
* Storing {{Type link|table}}s in BioUML.<br />
* Listing items in BioUML repository.<br />
* Launching BioUML analyses.<br />
* Launching BioUML workflows.<br />
<br />
== Installation ==<br />
Use the following R command to install rbiouml:<br />
install.packages("rbiouml")<br />
To update from older version use:<br />
update.packages("rbiouml")<br />
<br />
== See also ==<br />
* [http://cran.r-project.org/web/packages/rbiouml/ CRAN page]<br />
* [http://cran.r-project.org/web/packages/rbiouml/vignettes/rbiouml.pdf Getting started with rbiouml]<br />
<br />
[[Category:R]]</div>Lan@dote.ruhttp://wiki.biouml.org/index.php/Method_(extension_point)Method (extension point)2013-09-13T05:19:46Z<p>Lan@dote.ru: +Analysis method development</p>
<hr />
<div>{{Extension point|method|ru.biosoft.analysis|registry=ru.biosoft.analysis.AnalysisMethodRegistry}}<br />
=== Description ===<br />
This extension point allows you to define new analyses method. Analysis methods appear under <code>analyses/Methods</code> path in the repository.<br />
<br />
=== Configuration Markup ===<br />
<!ELEMENT analysisClass><br />
<!ATTLIST analysisClass<br />
class CDATA #REQUIRED<br />
group CDATA #REQUIRED<br />
name CDATA #REQUIRED<br />
description CDATA #REQUIRED<br />
js CDATA #IMPLIED<br />
><br />
<br />
;class<br />
:fully-qualified name of method class. This class must implement {{Class|ru.biosoft.analysis.AnalysisMethod}} interface. <br />
;group<br />
:analysis group (subfolder under <code>analyses/Methods</code>) to place the analysis to.<br />
;name<br />
:analysis name<br />
;description<br />
:either textual description or path to [[method description HTML file]].<br />
;js<br />
:name of autogenerated JavaScript function which represents this analysis in the hostObject.function format.<br />
<br />
=== Examples ===<br />
<br />
The following example defines "Track statistics" analysis method:<br />
<br />
<extension id="Track statistics" point="ru.biosoft.analysis.method"> <br />
<analysisClass<br />
class="ru.biosoft.bsa.analysis.stats.SequenceStatistics"<br />
group="BSA"<br />
name="Track statistics"<br />
description="Gather various statistics about track or FASTQ file"<br />
js="siteAnalysis.trackStats"/> <br />
</extension><br />
<br />
=== JavaScript implementation ===<br />
<br />
JavaScript analysis implementation will be automatically generated if you perform the following steps:<br />
<br />
* Create JavaScript host object class which extends {{Class|ru.biosoft.analysis.javascript.JavaScriptAnalysisHost}}.<br />
* Register it via [[Host object (extension point)#Host_objects_for_analyses|hostObject]] extension point.<br />
* Add "js" attribute with registered host object name and desired method name separated by point as <code>"siteAnalysis.trackStats"</code> in the example above.<br />
<br />
=== See also ===<br />
* [[Analysis method development]]</div>Lan@dote.ru