Difference between revisions of "Server ICT"
From BioUML platform
Ilya Kiselev (Talk | contribs) (→Examples) |
Ilya Kiselev (Talk | contribs) (→Available resources) |
||
| Line 14: | Line 14: | ||
==Available resources== | ==Available resources== | ||
| + | * 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] | ||
==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
- Start without login - https://ict.biouml.org/bioumlweb
- Start - https://ict.biouml.org/bioumlweb
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
- 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.
