https://wiki.biouml.org/index.php?action=history&feed=atom&title=BioUML_server 2026-04-13T07:17:28Z Revision history for this page on the wiki MediaWiki 1.20.3 https://wiki.biouml.org/index.php?title=BioUML_server&diff=5124&oldid=prev 2013-08-19T04:02:36Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 04:02, 19 August 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>&#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">'''</ins>BioUML server<ins class="diffchange diffchange-inline">''' </ins>is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [[wikipedia:Eclipse (software)|Eclipse]] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [[wikipedia:Eclipse (software)|Eclipse]] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 14:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*XML databases (for example, databases in BioPAX or SBML formats)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*XML databases (for example, databases in BioPAX or SBML formats)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*databases available via web services (for example, SABIO-RK database)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*databases available via web services (for example, SABIO-RK database)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">== See also ==</ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">* [[:Category:Administration|Server administration related topics]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Software]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Category:Software]]</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server&diff=4633&oldid=prev 2013-06-19T09:40:46Z

<p>+<a href="/index.php/Category:Software" title="Category:Software">Category:Software</a></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 09:40, 19 June 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*XML databases (for example, databases in BioPAX or SBML formats)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*XML databases (for example, databases in BioPAX or SBML formats)</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*databases available via web services (for example, SABIO-RK database)</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*databases available via web services (for example, SABIO-RK database)</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Category:Software]]</ins></div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server&diff=3786&oldid=prev 2013-05-17T10:40:55Z

<p>wikipedia: namespace used</p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 10:40, 17 May 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [<del class="diffchange diffchange-inline">http://en.</del>wikipedia<del class="diffchange diffchange-inline">.org/wiki/Eclipse_</del>(software) Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [<ins class="diffchange diffchange-inline">[</ins>wikipedia<ins class="diffchange diffchange-inline">:Eclipse </ins>(software)<ins class="diffchange diffchange-inline">|</ins>Eclipse<ins class="diffchange diffchange-inline">]</ins>] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*access service - provides access to databases (read/write),</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*access service - provides access to databases (read/write),</div></td></tr> </table>

Lan@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server&diff=953&oldid=prev 2013-04-15T10:41:30Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 10:41, 15 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 2:</td> <td colspan="2" class="diff-lineno">Line 2:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Server architecture.png|thumb|Architecture of BioUML server]]</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [http://en.wikipedia.org/wiki/Eclipse_(software)Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [http://en.wikipedia.org/wiki/Eclipse_(software) Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*access service - provides access to databases (read/write),</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*access service - provides access to databases (read/write),</div></td></tr> </table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server&diff=952&oldid=prev 2013-04-15T10:38:49Z

<p></p> <table class='diff diff-contentalign-left'> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr style='vertical-align: top;'> <td colspan='2' style="background-color: white; color:black;">← Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 10:38, 15 April 2013</td> </tr><tr><td colspan="2" class="diff-lineno">Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). &#160;</div></td></tr> <tr><td colspan="2">&#160;</td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[File:Server architecture.png|thumb|Architecture of BioUML server]]</ins></div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [http://en.wikipedia.org/wiki/Eclipse_(software)Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>Like [[BioUML workbench]] it also uses [http://en.wikipedia.org/wiki/Eclipse_(software)Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*database service - provides information about database and secure access to it,</div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 7:</td> <td colspan="2" class="diff-lineno">Line 8:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Lucene service - provides full text search and its configuration,</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*Lucene service - provides full text search and its configuration,</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*query service - provides indexed search for a database,</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>*query service - provides indexed search for a database,</div></td></tr> <tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">[[File:Server architecture.png|thumb|Architecture of BioUML server]]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>&#160;</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server supports access to different types of databases, such as:</div></td><td class='diff-marker'>&#160;</td><td style="background: #eee; color:black; font-size: smaller;"><div>BioUML server supports access to different types of databases, such as:</div></td></tr> </table>

Stan.lo@dote.ru https://wiki.biouml.org/index.php?title=BioUML_server&diff=950&oldid=prev 2013-04-15T10:35:00Z

<p>info on BioUML server architecture added</p> <p><b>New page</b></p><div><br /> BioUML server is a Java application that is started as servlet on J2EE compatible server (Tomcat server is being used). <br /> Like [[BioUML workbench]] it also uses [http://en.wikipedia.org/wiki/Eclipse_(software)Eclipse] runtime to manage plug-ins that provide different services. The main services provided by BioUML server are:<br /> *database service - provides information about database and secure access to it,<br /> *access service - provides access to databases (read/write),<br /> *diagram service - provides protocol to read/write diagram and all diagram elements during one HTTP request,<br /> *Lucene service - provides full text search and its configuration,<br /> *query service - provides indexed search for a database,<br /> [[File:Server architecture.png|thumb|Architecture of BioUML server]]<br /> <br /> BioUML server supports access to different types of databases, such as:<br /> *relational databases (for example, Ensembl database that is available as MySQL dump)<br /> *text databases (for exampe, KEGG/Ligand database)<br /> *XML databases (for example, databases in BioPAX or SBML formats)<br /> *databases available via web services (for example, SABIO-RK database)</div>

Stan.lo@dote.ru