biopredyn_pi June 2013

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[Biopredyn_pi] BioPreDyn - parameter estimation benchmark problems - *your reply needed*

by Julio R. Banga

Dear BioPreDyn partners, as you might remember, during the Naples meeting we discussed the possibility of setting up a collection of benchmark problems regarding parameter estimation in medium/large scale systems biology models. At that meeting we agreed to: 1- initially, CSIC and UNIMAN would prepare an initial set of problems and documentation, plus a draft manuscript describing their use 2- these documents could then be used, as templates, by other partners interested in participating with problems of their own. The manuscript would incorporate these new problems 3- the resulting final joint manuscript would be submitted to a journal, and the problem collection would be made available through a web site Alex (CSIC) and Kieran (UNIMAN) have worked on this and the resulting first draft and problem collection will be ready during the coming days. The problems considered so far are related with parameter estimation in large-scale kinetic models of microbial metabolism, and are available, as ready-to-run codes, in two formats, Copasi and Matlab. The dynamic models are also available as SBML. So, following the steps above, what we need now from you is: 1.-- please let us know *asap* if you are interested in contributing with parameter estimation problems from your group. Deadline: 30-June. (The only prerrequisites is that they are medium to large-scale problems, and that you have them implemented in ready-to-run code (ideally, Copasi or Matlab, but other implementations are fine if it is documented how to use different optimization solvers with the problem(s)) 2.- during the coming weeks, Alex will send to the interested groups the format template and the draft manuscript, so they can add their problems in a coherent format. 3.- after a few iterations, we set up the web site and submit the joint paper to a journal. Best regards, Julio R. Banga -- ------------------------------------------------------------- Prof. Julio R. Banga BioProcess Engineering Group Instituto de Investigaciones Marinas (C.S.I.C.) Spanish Council for Scientific Research C/Eduardo Cabello 6 36208 Vigo (SPAIN) E-mail: julio(a)iim.csic.es Web http://www.iim.csic.es/~julio/ http://www.iim.csic.es/~gingproc/ ph: +34 986 214 473 (direct) fax: +34 986 292 762 -------------------------------------------------------------

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biopredyn_pi June 2013