BioUML development roadmap

From BioUML platform
Revision as of 01:33, 15 June 2013 by Fedor Kolpakov (Talk | contribs)

Jump to: navigation, search

This page describes the current plans for BioUML platform development in 2013 and includes a list of desired features that are not scheduled yet. Users, administrators and developers are welcome with their comments and suggestions about new features as well as feature implementation priorities. For this purpose, please, use the BioUML forum.

Plans for 2013

Release Description Date
v. 0.9.5
  • SBML level 3 packages:
    • hierarchic
    • FBC test suite
2013, Q2
v. 0.9.6
  • Modelling
    • Rule based modelling (implementation of BioNetGen approach)
    • Antimony support
    • Synchronisation between textual and graphical model representation (BioNetGen, Antimony)
  • New methods for analysis transcription factor binding sites
2013, June
v. 0.9.7
  • Server installation
    • repository - packages for Red Hat and Debian
    • Puppet cookbooks for server updates
  • Server
    • grid version - pilot task manager integration with SGE via DRMAA virtualisation
  • Web interface
    • mobile version (for web-browser)
    • web interface improvements diagrams - convenient for exchange and editing
  • NGS
    • ribo-seq
    • miRNA
    • rna-seq
  • Integration with genAbel - pilot
2013, Q3
v. 0.9.8
  • Server
    • grid version (alpha)
  • Further NGS analyses improvements
  • Integration with genAbel (beta)
  • SBGN-XML support
2013, Q3
v. 0.9.9
  • Server
    • grid version (beta)
  • Further NGS analyses improvements
2013, Q4


Other desired features

Component Features Priority
Core Major refactoring: complex, macromolecule state, reaction moderate
Parameters fitting

- optimization process as a workflow

- SED-ML as workflow

- save optimization results as the diagram state

moderate
Implementation of OQL subset for access to databases via BioUML object model moderate
Databases KEGG improvements:

- omics data visualisation

- graph search engine improvements (not include small molecules, search for related maps)

- organism - filter and highlighter

- visualization of chemical structure for substances

- diagram editing

- diagram export (KGML, BioPAX, SBML, +SVG, +PNG, +JPEG)

- set up wizard

low
Misc. SBRML support low
Further integration with Matlab low


See also

Personal tools
Namespaces

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