Computational Methods in Systems Biology

 N E W S 

06 / 2008, MedSys Project granted:

11 / 2007, iGEM :

"Glasgow team scoops the Environment prize and gold medal in the 2007 international Genetically Engineered Machines competition (Synthetic Biology);

The team comprised 11 highly talented undergraduate students and two instructors from 3 faculties (IBLS, FIMS, Engineering), plus a set of academics lead by Prof David Gilbert (Computing Science) and Dr Susan Rosser (BioMedical and Life Sciences). Prof Monika Heiner from Cottbus University, Germany, acted as an external advisor. Snoopy & Charlie, two Petri net tools developed in Cottbus, were used aiding in the process of formalising the original biologists’ models."

For more details see  www.brc.dcs.gla.ac.uk/iGEM/2007   and   poster

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;

 C M S B  2 0 0 8 

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/

 S E L E C T E D   R E F E R E N C E S

Tutorials / Workshops

• Formal Methods in Molecular Biology,
  Dagstuhl-Seminar 09091, 23.2.-27.2.2009
• An introduction to biomodel engineering, illustrated for signalling pathways;
  The Seventh Asia Pacific Bioinformatics Conference (APBC 2009), Beijing, China, 13-16 January 2009.
  
• A structured approach for the engineering of biochemical network models ;
  Sixteenth International Conference on Intelligent Systems for Molecular Biology (ISMB 2008), Toronto, July 2008.
• Schools on Formal Methods (SFM), Bertinoro/Italy, June 2008
• A structured approach for the engineering of biochemical network models, illustrated for signalling pathways (Workshop);
  BioSysBio 2008, , Imperial College London, April 2008.
• Qualitative Modelling and Analysis of Biochemical Pathways with Petri Nets, ICSB 2004

Posters

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

Some milestone papers, methodology oriented

• Petri Nets for Systems and Synthetic Biology; LNCS 5016, 2008
• A structured approach for the engineering of biochemical network models; Briefings in Bioinformatics 2008
• A unifying framework for qualitative, stochastic and continuous PN; CMSB 2007
• From Petri nets to differential equations (= continuous PN), ICATPN 2006
• How to bring time Petri nets into the play, J. FI 2005
• System validation using T-invariants, ICATPN 2004
• Coloured Petri nets for steady state analysis of metabolic networks, J. In Silicon Bio 2003
  

Some papers, case studies oriented

• self-powering biosensor (qualitative/stochastic/continuous PN), IFIP WCC 2008, BICC 2008
• ERK signal transduction pathway, 3-stage cascade of double phosphorylation by Levchenko (qualitative/stochastic/continuous PN), CMSB 2007
• mating pheromone response pathway in Saccharomyces cerevisiae, J. BMC Bioinformatics 2006
• influence of the Raf Kinase Inhibitor Protein (RKIP) on the Extracellular signal Regulated Kinase (ERK) signalling pathway (qualitative and continuous PN), ICATPN 2006
• the sucrose breakdown pathway in the potato tuber (metabolic network), J. Bioinformatics 2005
• apoptosis, the genetically programmed cell death, a basic model, J. Biosystems 2004
• the combined glycolysis and penthose phosphate pathway (metabolic network), CPN 2001/J. In Silicon Bio 2003, CPN 2004, book chapter 2008

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