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Computational methods in systems biology

latest update: March 23, 2019, at 02:12 PM

News

06/2008, MedSys project granted:

The BMBF-funded project Modelling Pain Switches involves 9 teams (wet-lab’s as well as dry lab’s), one of them at the BTU Cottbus. The project aims at the mathematical modelling of signal switches responsible for pain sensitisation. Modelling and model analysis will apply qualitative, stochastic, and continuous Petri nets.

11/2007, iGEM:

For more details, see http://2007.igem.org/Glasgow/Modeling and [GXKF07].

08/2007, project funding granted:

ANR-BBSRC Systems Biology “Metabolomic systems biology analysis of differentiation in trypanosomes”, applicant: Barrett et al; University of Glasgow; Monika Heiner acts as external cooperation partner;

CMSB 2008

International Conference on Computational Methods in Systems Biology 2008

Rostock / Warnemünde, 12th–15th October 2008

Organising committee

Monika Heiner, University of Cottbus, Germany
Adelinde M. Uhrmacher, University of Rostock, Germany

http://wwwmosi.informatik.uni-rostock.de/cmsb08/static/cmsb08.html

Selected references

Tutorials / Workshops

• [BGHP09]
  R Breitling, DR Gilbert, M Heiner and C Priami (eds.):
  Formal Methods in Molecular Biology;
  volume 09091 of Dagstuhl Seminar Proceedings, May 2009. [ url ] [ BibTeX ]
• An introduction to biomodel engineering, illustrated for signalling pathways;
  The Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, 13–16 January 2009.
• [BGHO08]
  R Breitling, D Gilbert, M Heiner and R Orton:
  A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
  Briefings in Bioinformatics, 9(5):404–421, September 2008. [ doi ] [ BibTeX ]
• Schools on Formal Methods (SFM);
  Bertinoro/Italy, June 2008
• BioSysBio 2008;
  Imperial College London, April 2008
• [KH04.sld4]
  I Koch and M Heiner:
  Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets;
  Talk, Tutorial Notes, 5th Int. Conference on Systems Biology - ICSB 2004, Heidelberg/Germany, October 2004. [ pdf ] [ BibTeX ]

Posters

• BioModel Engineering – from Structure to Behaviour; CMSB 2008 [BGH08]
• Modelling and Analysing Biochemical Pathways Using Petri Nets; FORSYS Meeting 2008 [GHDB08b]
• A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets; ESF-UB Conference in Biomedicine, 2008 [GHDB08a]
• Modelling techniques and tools to support the design and construction process in Synthetic Biology – a practical comparative analysis; ECSB 2007 [GXKF07]
• Petri Net Based System Analysis, an overview; 2006 [HRT06b]
• Modelling signal transduction pathways of yeast with Petri nets; ECMTB 2005 [SHK05]

Some milestone papers, methodology oriented

• [HGD08]
  M Heiner, D Gilbert and R Donaldson:
  Petri Nets for Systems and Synthetic Biology;
  In SFM 2008, (M Bernardo, P Degano and G Zavattaro, Eds.), Springer, pages 215–264, 2008. [ pdf ] [ doi ] [ BibTeX ]
• [BGHO08]
  R Breitling, D Gilbert, M Heiner and R Orton:
  A structured approach for the engineering of biochemical network models, illustrated for signalling pathways;
  Briefings in Bioinformatics, 9(5):404–421, September 2008. [ doi ] [ BibTeX ]
• [GHL07b]
  D Gilbert, M Heiner and S Lehrack:
  A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets;
  In Proc. 5th International Conference on Computational Methods in Systems Biology (CMSB 2007), Edinburgh, Springer, LNCS/LNBI, volume 4695, pages 200-216, 2007. [ url ] [ pdf ] [ BibTeX ]
• [GH06]
  Gilbert, D. and Heiner, M.:
  From Petri nets to differential equations - an integrative approach for biochemical network analysis;
  In Proc. ICATPN 2006, LNCS 4024, Springer, pages 181–200, 2006. [ url ] [ pdf ] [ BibTeX ]
• [HK04]
  M Heiner and I Koch:
  Petri Net Based System Validation in Systems Biology;
  In Proc. ICATPN 2004, Bologna, June, Springer, LNCS, volume 3099, pages 216-237, 2004. [ pdf ] [ doi ] [ BibTeX ]
• [VHK03]
  K Voss, M Heiner and I Koch:
  Steady State Analysis of Metabolic Pathways Using Petri Nets;
  In Silico Biology, 3:367–387, 2003. [ url ] [ pdf ] [ BibTeX ]

Some papers, case studies oriented

• [GHR+08]
  D Gilbert, M Heiner, S Rosser, R Fulton, X Gu and M Trybio:
  A Case Study in Model-driven Synthetic Biology;
  In IFIP WCC 2008, 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC 2008), Milano, Springer, IFIP, volume 268, pages 163–175, September 2008. [ url ] [ pdf ] [ BibTeX ]
• [SHK06]
  A Sackmann, M Heiner and I Koch:
  Application of Petri net based analysis techniques to signal transduction pathways;
  BMC Bioinformatics 2006, 7:482, 2006. [ url ] [ doi ] [ BibTeX ]
• [GH06]
  Gilbert, D. and Heiner, M.:
  From Petri nets to differential equations - an integrative approach for biochemical network analysis;
  In Proc. ICATPN 2006, LNCS 4024, Springer, pages 181–200, 2006. [ url ] [ pdf ] [ BibTeX ]
• [KJH05]
  I Koch, BH Junker and M Heiner:
  Application of Petri Net Theory for Modelling and Validation of the Sucrose Breakdown Pathway in the Potato Tuber;
  Bioinformatics, April 2005, 21:1219 - 1226, 2005. [ doi ] [ BibTeX ]
• [Runge04b]
  T Runge:
  Application of Coloured Petri Nets in Systems Biology;
  In Proc. 5th Workshop CPN, Univ. of Aarhus, October 2004, pages 77-95, 2004. [ pdf ] [ BibTeX ]
• [VHK03]
  K Voss, M Heiner and I Koch:
  Steady State Analysis of Metabolic Pathways Using Petri Nets;
  In Silico Biology, 3:367–387, 2003. [ url ] [ pdf ] [ BibTeX ]

For more (including BTU reports, slides) see selected references.