2011

• June 17 - BioUML workbench version 0.9.2 was released. More...
  Development roadmap was updated.
   
• May 12 - BioUML supports CellDesigner 4.0/4.1 format
  more details
   

2010

• October 13 - BioUML workbench version 0.9.1 (alpha) was released. More...
   
• October 10-14 - ICSB-2010, Edinburgh, Scotland
  • Tutorial: BioUML - integrated platform for building virtual cell and virtual physiological human
    MS Power Point presentation, 73 slides, 6.4 Mb, English.
     
  • Oral report: Modular Approach To Modeling Of The Apoptosis Machinery
    Kutumova E.O., Sharipov R.N., Lavrik I.N, Kolpakov F.A.
     
  • posters about BioUML and its usage for modelling of components of virtual cell and virtual physiological human:
     
    • BioUML - Integrated Platform for Building Virtual Cell and Virtual Physiological Human
      Kolpakov F.A., Tolstyh N.I., Kutumova E.O., Kiselev I.N., Shadrin A.A., Valeev T.F., Ryabova A.
      MS Power Point presentation, 1 slide, 1.3 Mb, English.
       
    • Modular Approach To Modeling Of The Apoptosis Machinery
      Kutumova E.O., Sharipov R.N., Kolpakov F.A.
      MS Power Point presentation, 1 slide, 1.5 Mb, English.
       
    • The Optimization Plug-in For The BioUML Platform
      Kutumova E.O., Ryabova A.S., Tolstyh N.I., Kolpakov F.A.
      MS Power Point presentation, 1 slide, 0.8 Mb, English.
       
    • Agent based modelling - plug-in for BioUML platform
      Kiselev I.N., Semisalov B.V., Kolpakov F.A.
      MS Power Point presentation, 1 slide, 0.8 Mb, English.
       
    • Numerical analysis of complex model of human blood flow circulation using 1D hemodynamic model
      Leonova T., Biberdorf E.A., Kolpakov F.A., Blokhin A.M., Markel A.L. 
      MS Power Point presentation, 1 slide, 0.5 Mb, English.
       
• October 6-9 - COMBINE-2010, Edinburgh, Scotland
  • Report: Encoding and exchanging graphical representation: architecture and formats.
    MS Power Point presentation, 38 slides, 0.9 Mb, English.
  • Report: BioUML - integrated platform for building virtual cell and virtual physiological human
    MS Power Point presentation, 49 slides, 3.5 Mb, English.
  • Presentations and supplementary materials
     
• September 13
  • BioUML workbench version 0.9.0 (alpha) was released. More...
  • BioUML documentation was updated.
  • Development roadmap was updated.
     
• August 1 - new page was added: BioUML features.
   
• July 22 - BioUML web site was updated (home page, roadmap, presentations).
   
• July 2 - BioUML version 0.9.0 have passed all tests from SBML test suite version 2.0.0 beta 1 (SBML L1v2, L2v1-4, L3v1)
  Test details are available at: http://www.biouml.org/sbml_tests/overview.html
  You also can start any test via BioUML web edition:
  • server, Amazon, Ireland
  • server, Institute of Systems Biology, Russia
   
• June 20-27 - BGRS\SB-2010 conference
  • June 23 - oral presentation of Elena Kutumova: "Modular modeling of the apoptosis machinery"
  • June 24 - oral presentation of Fedor Kolpakov: "BioUML – integrated platform for building virtual cell and virtual physiological human";
  • June 24 - posters about BioUML and its usage for modelling of components of virtual cell and virtual physiological human:
    • Microarray data analysis plugin for BioUML
      Kiselev I.N., Shadrin A.A., Kolpakov F.A., Kondrakhin Y.V. 
    • Comparison of methods for reconstruction of models for gene expression regulation
      Shadrin A.A., Kiselev I.N., Kolpakov F.A. 
    • Web-based genome browser using AJAX and canvas technologies
      Valeev T.F., Tolstyh N.I., Kolpakov F.A. 
    • Simulating pulse wave in 1D hemodynamic model
      Leonova T., Kolpakov F.A., Biberdorf E.A. 
    • Numerical analysis of complex model of human blood flow circulation using 1D hemodynamic model
      Leonova T., Biberdorf E.A., Kolpakov F.A., Blokhin A.M., Markel A.L.
  presentations and posters
   
• January 8 - BioUML development roadmap was updated.
   

2009

• December 19 - templates for SBML models to display (combobox in left bottom pane):
  reactions, variables, parameters, math (functions, equations, events), ODE.
   
• November 30 - BioUML web edition - first public release!
  It was tested for IE Explorer 6, 7; FireFox; Google Chrome.
  http://server.biouml.org/bioumlweb
   
• August 8 - web site content is updated: site menu, home page. Added: on-line help for BioUML workbench and BDK, BioUML tutorial from ICSB-2008, several posters and publications.
   
• August 7 - BioUML workbench version 0.8.6 (beta) was released.
  More...
   
• February 17 - BioUML workbench version 0.8.5 (beta) was released.
  More...
   
• February 17 - BioUML development roadmap was updated.
   
• January 28 - BioUML workbench version 0.8.5 (alpha) was released.
  More...
   

2008

• December 13 - BioUML development kit version 0.8.4 (beta) was released.
  More...
   
• December 12 - BioUML workbench version 0.8.4 (beta) was released.
  More...
   
• August 28 - BioUML workbench version 0.8.3 (alpha) was released.
  More...
   
• August 23, 9-11 a.m - tutorial "New possibilities of BioUML workbench" on ICSB conference.
   
• August 9 - BioUML workbench version 0.8.2 (alpha) was released.
  More...
   
• July 22 - BioUML workbench version 0.8.1 (alpha) was released.
  More...
   
• July 2 - BioUML workbench version 0.8.0 (beta) and BDK 0.8.0 were released.
  More...
   
• May 29 - flash movies
  We have created 7 flash movies that demonstrate main BioUML features.
  Movies
   
• March 29 - Simulation results from ByoDyn were included into simulator comparisons. 
  Our congratulations to ByoDyn team with the excellent results!
  It is interesting that it changed BioUML results. Previously only BioUMl have generated values for some parameters in several tests and we believed these tests to be passed successfully. Now results from ByoDyn are available for these parameters and they are differ from values produced by BioUML - so such tests now are considered for BioUML as failed (significant difference). Previously BioUML passed 142 tests without difference, now only 136.
  More..
   
• March 20 - Simulation results from Virtual Cell were included into simulator comparisons.
  More...
   
• March 20 - BioUML workbench version 0.7.8 (beta) was released.
  More...
   
• March 18 - BioUML workbench version 0.7.8 (beta) was able to simulate all 150 SBML models from BioModlels database (release 9).
  According to our metrics now BioUML is the best simulator for SBML models.
  More...
   
• January 30 - updated version of BioUML workbench and BDK 0.7.8 were released
  More...
   
• January 30 - a set of materials for virtual participation in SBGN were updated
  More...
   
• January 28 - a set of materials for virtual participation in SBGN super-hackathon was published on the web site.
  More...
   
• January 28 - BioUML workbench version 0.7.8 (alpha) was released.
  This is alpha version for SBGN super-hackathon
  More...
   
• January  27 - BioUML development roadmap was updated.
  

2007

• October 29 - minor BioUML Development Kit (BDK) update (version 0.7.7 download page)
  Hopefully now BDK can be compiled by 3-rd party developers without problems.
   
• October 29 - minor web site update
  added: news, user manual
  updated: menu, comments, team
   
• October 28 - draft versionf of user manual for BioUML workbench is available.
  More...
   
• October 24 - BioUML workbench version 0.7.7 was released.
  More...
   
• October 6 - Embedding formal graphic notations into SBML models (560 kb)
  The Twelfth Workshop on Software Platforms for Systems Biology,
  Hyatt Regency Hotel, Long Beach, California, USA
   
• October 5 - Formal description and visual modeling of complex biological systems using BioUML workbench and BioUML Network Edition" (1.4 Mb)
  The Twelfth Workshop on Software Platforms for Systems Biology,
  Hyatt Regency Hotel, Long Beach, California, USA
   
• October 1 - tutorial on ICSB 2007:
  Formal description and visual modeling of complex biological systems using BioUML workbench and BioUML Network Edition.