BioUML workbench v. 0.9.4 was released
Posted: 24 Mar 2013, 05:25We 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.
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.