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
-------------------------------------------------------------