Server ICT
This is main free BioUML server for systems biology.
It is located at Institute of Computational Technologies, Novosibirsk city, Russia.
Its main features.
Contents |
How to start
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.
Registration
BioStore is the central authentication and authorization server for all BioUML-related products.
See BioStore page for more details how to register.
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.
Modeling
Available resources
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
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
- 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.
