BioUML workbench v. 0.9.4 was released

[Fedor Kolpakov]

We are pleased to announce the a release of BioUML workbench 0.9.4 (beta).

New features and main changes in version 0.9.4:

Integration with Biostore (http://www.bio-store.org) for control of access rights and downloading

BioUML web:
Collaborative work on diagram (like Google documents)

UI improvements:
- automatic suggestions in search pane
- automatic opening of uploaded files
- select several elements to remove in repository tree

Genome browser improvements
- gene structure can be shown in a table cell

BioUML core:
History of diagram editing (like CVS or SVN)

Simulation engine
- stochastic modeling, following solvers were implemented:
- Gillespie (Gillespie, D.T. 1977)
- Gibson-Bruck (Gibson, J. Bruck 2000)
- Max Time step (Puchalka, J., Kierzek, A.M. 2004)
- Tau-leaping (Yang, C. et al. 2006)
- Discrete Stochastic Models Test Suite (DSMTS) was passed succesfully
- agent based modelling - new agent with ability to produce descendants. Is used to simulate cell population behaviour.

SBML support:
- bug fixing
- flux balance constraint models support (using org.apache.common.math3)
- all non composite tests from test-suite 2.3.2 (2013-02-04) passed.

Visual modelling
- composite diagrams improvements
- MathDiagramType - new diagram type for describing physial procsses. Automatically generates dependencies between equations.

Model analysis
- model reduction
- MCA (Metabolic Control Analysis, alpha version)

Analyses:
- convert table: ability to use column for ID
- filter table: ability to select top N or bottom N entries

User interface improvements
- perspectives - allows to group and filter UI components for specific user's tasks
- tree table component
- drag & drop for annotations

Genome browser improvements
- better navigation (chromosome switch, position input box, drag-and-scroll, zoom selection, mouse wheel support, etc.)
- improved sites information tab
- BAM tracks support
- gene structure can be shown in a table cell (only web)
- improved and new styles for genes structure visualization

Improved support of DAS protocol
- support for 1.53 and 1.6
- support for non positional features
- interactions
- ontologies

Integration with JMOL for visualization of 3D structures

BioUML server
Galaxy support
new section "Galaxy" in analyses tab allows to use all methods from Galaxy platform.