Presentations

Selected presentations

• BioUML - open source integrated platform for collaborative and reproducible research in systems biology
  (66 slides, 11 Mb).
  
• BioUML - integrated platform for building virtual cell and virtual physiological human
  presented on BGRS\SB-2010 conference (77 slides, 8.4 Mb).
  
• Introduction to BioUML workbench
  describes main features and concepts of BioUML workbench: visual modeling, meta-model, formal definition of graphic notations and plug-in based architecture.

Presentations on conferences

2016

• BioUML platform
  

Seminar at Novosibirsk State University October 18, Novosibirsk, Russia, 56 slides, 5.2 Mb, Russian.

2014

• BioUML programming
  March 11, Wolfenbüttel, Germany
  
  • Tutorial: BioUML programming
    PDF presentation, 38 slides, 0.8 Mb, English.

2011-2013

This page or section is under construction right now.

2010

• ICSB-2010
  October 11-14, 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.
      
      

• COMBINE-2010
  October 6-9, 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
    
    

• BGRS\SB-2010 conference
  June 20-27, 1010, Novosibirsk, Russia
  • oral presentation: Modular modeling of the apoptosis machinery
    Kutumova E.O., Sharipov R.N., Lavrik I.N, Kolpakov F.A.
    MS Power Point presentation, 52 slides, 7.8 Mb, English.
    
  • oral presentation: 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., Sharipov R.N., Kel A.E.
    MS Power Point presentation, 78 slides, 8.4 Mb, English.
    
  • 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.
      poster, pdf, 1 Mb, English.
      
    • Comparison of methods for reconstruction of models for gene expression regulation
      Shadrin A.A., Kiselev I.N., Kolpakov F.A.
      MS Power Point presentation, 1 slide, 0.8 Mb, English.
      
    • Web-based genome browser using AJAX and canvas technologies
      Valeev T.F., Tolstyh N.I., Kolpakov F.A.
      MS Power Point presentation, 1 slide, 0.5 Mb, English.
      
    • 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.
      MS Power Point presentation, 1 slide, 0.5 Mb, English.

2008

• The 9th International Conference on Systems Biology (ICSB-2008)
  August 22-28, 2008, Gothenburg, Sweden
  
  • Tutorial: New possibilities of BioUML workbench
    MS Power Point presentation, 151 slides, 7.3 Mb, English.
    
  • Poster: BioUML new concepts and possibilities
    Tolstykh N, Lapukhov S., Kiselev I., Shadrin A. and Kolpakov F.
    MS Power Point presentation, 1 slide A0, 1.1 Mb, English.
    

2004-2007

This page or section is under construction right now.

2003

• International conference of young scientists on mathematical modeling and informational technologies
  November 3-5, 2003, Krasnoyarsk, Russia.
  Report: BioUML software workbench for visual modeling biological and other complex systems.
  Abstract, Russian.
  
  
• German Conference on Bioinformatics
  October 12-14, 2003, Neuherberg/Garching, Germany.
  Poster: Comprehensive model for formalized description, visualization and simulation of biological systems.
  Extended abstract, PDF, 129 kb, English.
  MS Power Point presentation, 1 slide A0, 217 kb, English.
  
  
• VIII International Conference "Electronic publicating El-Pub2003"
  October 8-10, 2003, Novosibirsk, Russia.
  Report: BioUML - integrated framework for modeling of biological systems
  Abstract (English, Russian)
  MS Power Point presentation, 23 slides, 560 kb, Russian.
  
  
• European Respiratory Society 13th annual congress
  September 27 October 1, 2003, Vienna, Austria.
  Poster: New approaches to understanding of heavy metals role in pathogeneses of chronic respiratory diseases
  (about usage of BioUML workbench for formalized description of heavy metals role in pathogeneses of chronic respiratory diseases)
  Poster, PDF, 11 slides, 236 kb, English.
  
  
• Systems Biology Workshop and Tutorial
  September 18, 2003, Tokyo, Japan.
  Poster: BioUML - open source extensible Java workbench for systems biology.
  MS Power Point presentation, 1 slide, 182 kb, English.

2002

• 3rd Iinternational Conference on Systems Biology (ICSB-2002)
  Poster: Biouml - software framework for systems biology.
  Abstract,PDF, 50 kb, English.
  
  
• International conference of young scientists on mathematical modeling and informational technologies
  October 29-31, 2002, Novosibirsk, Russia.
  Report: Modeling biological systems using BioUML.
  MS Power Point presentation 30 slides, 571 kb, Russian.
  
  
• "Science in Siberia" section on SibFair-2002 exhibition
  October 28-31, 2002, Novosibirsk, Russia.
  Presentaion: BioUML - universal language for visual modeling of biological systems.
  MS Power Point presentation, 41 slides, 1.11 MB, Russian.
  
  
• First Regional Forum
  October, 21-24, 2002, Novosibirsk, Russia.
  Report: BioUML - integrated extensible framework for modeling of biological systems.
  
  
• VII International Conference "Electronic publicating El-Pub2002"
  September 23-27, 2002, Novosibirsk, Russia.
  Report: BioUML - integrated framework for modeling of biological systems
  MS Power Point presentation, 28 slides, 1.33 MB, Russian.
  
  
• BGRS'2002 - Third International Conference on Bioinformatics of Genome Regulation and Structure.
  July 14-20, 2002, Novosibirsk, Russia.
  Computer demonstration: "Using BioUML Framework for Systems Biology".
  Poster: "BioUML - framework for visual modeling and simulation of biological systems".
  
  
• New Technologies in Medicine.
  June 18-19, 2002, Novosibirsk, Russia.
  BioUML - Biological Unified Modeling Language.
  
  
• On-line conference "Computer applications in chemistry, biology, pharmaceutics and medicine."
  April 17 - June 13, 2002, Moscow, Russia.
  BioUML - Biological Unified Modeling Language.