Difference between revisions of "Server ICT"

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(Available resources)
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==Available resources==
 
==Available resources==
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* 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.
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* 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].
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* Reactome - models imported (with preserving of the original layout) from the REACTOME pathway [https://reactome.org/ database]
  
 
==Examples==
 
==Examples==

Revision as of 19:47, 31 December 2018

This is will be main free BioUML server for systems biology.

It is located at Institute of Computational Technologies, Novosibirsk city, Russia.

Contents

How to start

Registration

Collaborative work

Project

Available resources

  • 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

Examples

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.

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.

Analysis

Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox