Hi Julio,

Yes I agree it would be very good if we can have this uncertainty quantification in the proposal, I also agree about multi-objective optimization in metabolic engineering / GRN reconstruction that would be an important new thing in the H2020 proposal.

We are now working on a preliminary text (abstract) which we plan to send around soon, I would appreciate it very much if you can comment on it / add things!

all the best,

Jaap

Dr Jaap A. Kaandorp

Section Computational Science

Faculty of Science

University of Amsterdam

Science Park 904, room C3.147

1098 XH Amsterdam

The Netherlands

Phone: +31 20 5257539 /+31 20 5256789

Skype: jaap.kaandorp

email: J.A.Kaandorp@uva.nl

fax: +31 20 5257490

URL: http://www.science.uva.nl/~jaapk/

 

Van: biopredyn_af-bounces@lists.crg.es [biopredyn_af-bounces@lists.crg.es] namens Julio R. Banga IIM-CSIC [julio@iim.csic.es]
Verzonden: woensdag 4 maart 2015 18:53
Aan: Joke Blom
CC: bioPreDyn_af@lists.crg.es; Veronica Raker
Onderwerp: Re: [Biopredyn_af] BioPreDyn: H2020 proposal

Hi Jaap,
I think Joke's suggestion below is an interesting and important one.
Somewhat related, we could also do uncertainty quantification (Joke
has already done work on this) and modelling (e.g. ensemble modelling,
which worked well with INSIL CHO's model.
Another topic which deserves further exploration imho would be
multicriteria optimality of kinetic models, with applications in metabolic engineering
(fitting the call description) and other problems...
Best,

Julio

On Wed, Mar 4, 2015 at 12:43 PM, Joke Blom <Joke.Blom@cwi.nl> wrote:

That's good news! And Jaap: if you need an extra hand, just cross the road (real or virtual).

Idea: if we have individual cell data (e.g. gene expression over time), we could do this stochastic network reconstruction I talked about in one of my last slides; might even resolve non-identifiability.

Joke

----
Joke Blom, M245 / CWI / Science Park 123 / 1098 XG Amsterdam (NL)
email: gollum@cwi.nl         phone: +31 20 592 4263
URL: http://www.cwi.nl/~gollum/


On Mon, 2 Mar 2015, Veronica Raker wrote:

Dear all, 
We have volunteers! Jaap (as the official coordinator) and Kieran (as a
scientific co-coordinator) have stepped forward to offer to coordinate the
H2020 proposal (LEIT-BIO-2015) due 26 March (we discussed this at our
annual meeting last week, with a deadline of today to volunteer to
coordinate). We will discuss details a bit on Weds and let you know asap
after that how to proceed. If anyone has any brilliant, innovative ideas,
please let us know– otherwise, I will get in touch with you asap.

best,
Veronica






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