Difference between revisions of "Server ICT"
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| − | + | Welcome to [http://ict.biouml.org/biouml-landing BioUML at ICT]: main free [[BioUML]] server for systems biology. | |
| − | It is located at | + | It is located at [http://www.ict.nsc.ru/en Institute of Computational Technologies], Novosibirsk city, Russia. |
| − | + | Its main [[features]]. | |
| − | * | + | |
| + | =How to start= | ||
| + | * [https://ict.biouml.org/bioumlweb/#anonymous=true Start without login] | ||
* Start - https://ict.biouml.org/bioumlweb | * Start - https://ict.biouml.org/bioumlweb | ||
| + | * [http://ict.biouml.org/biouml-landing Landing page] | ||
| + | |||
| + | =Collaborative work= | ||
| + | Collaborative research is any research project, especially a large one involving various areas of expertise, that is carried out by at least two people. | ||
| + | |||
| + | To enable collaborative research BioUML sustains the following functionality: | ||
| + | * [[BioStore#InvitingOthers|sharing projects with other users]], | ||
| + | * [[collaborative diagram editing]], | ||
| + | * access to [[diagram editing history]] (both session and version). | ||
| + | |||
| + | Diagram editors provide possibility to edit the same diagram by several users simultaneously like in Google documents. | ||
==Registration== | ==Registration== | ||
| + | [[BioStore]] is the central authentication and authorization server for all BioUML-related products. | ||
| − | + | See [[BioStore]] page for more details how to register. | |
==Project== | ==Project== | ||
| + | A project in BioUML is a group of folders which contains data and history for the current research. | ||
| − | ==Available resources== | + | You can get access to your project to other users. |
| + | |||
| + | See [[BioStore]] page for more details. | ||
| + | |||
| + | =Modeling= | ||
| + | * [[Features]] | ||
| + | * [[Visual modeling]] | ||
| + | * [[Diagram document]] | ||
| + | * [[Simulation]] | ||
| + | * [[Modular modeling]] | ||
| + | * [[Antimony]] | ||
| + | * [[BioNetGen]] | ||
| + | |||
| + | =Available resources= | ||
| + | ==Databases== | ||
| + | * Biomodels - latest version of computational models of biological processes developed by [https://www.ebi.ac.uk/biomodels/ EMBL-EBI European Bioinformatics Institute] | ||
| + | * Tests SBML - test suite version 3.3.0 (latest) developed by creators of Systems Biology Markup Language (SBML). | ||
| + | Results for different tools are presented [http://sbml.org/Facilities/Database/Simulator SBML site]. BioUML currently is the only tool on the site which passes every test. | ||
| + | * Tests Stochastic - discrete stochastic models test suite developed for for stochastic simulators (Gillespie-type) | ||
| + | * PantherDB - models imported (with preserving of the original layout) from the latest version of PANTHER (Protein ANalysis THrough Evolutionary Relationships) [http://www.pantherdb.org/ database]. | ||
| + | * Reactome - models imported (with preserving of the original layout) from the REACTOME pathway [https://reactome.org/ database] | ||
| + | |||
| + | ==Analysis and workflows== | ||
| + | There are also a number of methods to work with models. | ||
| + | |||
| + | See [[:Category:Analyses]] for more details. | ||
| + | |||
| + | Analysis can be arranged into [[workflows]]. | ||
==Examples== | ==Examples== | ||
[[File:Lorenz_result.png|thumb|SImulation result of the Lorenz model diagram in BioUML]] | [[File:Lorenz_result.png|thumb|SImulation result of the Lorenz model diagram in BioUML]] | ||
* DAE models - examples of dynamic models including ordinary differential and algebraic equations. Including simulation of ball jumping off walls and classic Lorenz model. | * DAE models - examples of dynamic models including ordinary differential and algebraic equations. Including simulation of ball jumping off walls and classic Lorenz model. | ||
| − | To perform numerical calculation should open <b>Simulation</b> tab and push <b>Simulate</b> button | + | To perform numerical calculation should open <b>Simulation</b> tab and push <b>Simulate</b> button (see fig to the right). |
* SBGN - examples of Systems Biology Graphic Notation diagrams created in BioUML. | * SBGN - examples of Systems Biology Graphic Notation diagrams created in BioUML. | ||
* Optimization - examples of parameter fitting of dynamic models. | * Optimization - examples of parameter fitting of dynamic models. | ||
* SedML - workflows automatically generated from SedML documents into BioUML. | * SedML - workflows automatically generated from SedML documents into BioUML. | ||
| − | == | + | |
| + | = See also = | ||
| + | |||
| + | * [[BioUML user interface]] | ||
| + | * [http://ict.biouml.org/biouml-landing BioUML at ICT landing page] | ||
Latest revision as of 16:32, 7 May 2019
Welcome to BioUML at ICT: main free BioUML server for systems biology.
It is located at Institute of Computational Technologies, Novosibirsk city, Russia.
Its main features.
Contents |
[edit] How to start
[edit] Collaborative work
Collaborative research is any research project, especially a large one involving various areas of expertise, that is carried out by at least two people.
To enable collaborative research BioUML sustains the following functionality:
- sharing projects with other users,
- collaborative diagram editing,
- access to diagram editing history (both session and version).
Diagram editors provide possibility to edit the same diagram by several users simultaneously like in Google documents.
[edit] Registration
BioStore is the central authentication and authorization server for all BioUML-related products.
See BioStore page for more details how to register.
[edit] Project
A project in BioUML is a group of folders which contains data and history for the current research.
You can get access to your project to other users.
See BioStore page for more details.
[edit] Modeling
[edit] Available resources
[edit] Databases
- Biomodels - latest version of computational models of biological processes developed by EMBL-EBI European Bioinformatics Institute
- Tests SBML - test suite version 3.3.0 (latest) developed by creators of Systems Biology Markup Language (SBML).
Results for different tools are presented SBML site. BioUML currently is the only tool on the site which passes every test.
- Tests Stochastic - discrete stochastic models test suite developed for for stochastic simulators (Gillespie-type)
- PantherDB - models imported (with preserving of the original layout) from the latest version of PANTHER (Protein ANalysis THrough Evolutionary Relationships) database.
- Reactome - models imported (with preserving of the original layout) from the REACTOME pathway database
[edit] Analysis and workflows
There are also a number of methods to work with models.
See Category:Analyses for more details.
Analysis can be arranged into workflows.
[edit] Examples
- DAE models - examples of dynamic models including ordinary differential and algebraic equations. Including simulation of ball jumping off walls and classic Lorenz model.
To perform numerical calculation should open Simulation tab and push Simulate button (see fig to the right).
- SBGN - examples of Systems Biology Graphic Notation diagrams created in BioUML.
- Optimization - examples of parameter fitting of dynamic models.
- SedML - workflows automatically generated from SedML documents into BioUML.
