5 Mar
2015
5 Mar
'15
10:03 a.m.
Hi Neil,
Yes I fully agree with this! We are currently talking with Scyfer (Max Welling is involved
in this SME, http://scyfer.nl), we could involve this SME in the project. This SME is
specialized in Bayseian optimisation, we could make a direct link between development
Bayesian optimization of differential equation models and biological experiments. I
already know that scyfer is very interested to participate in this proposal
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<mailto:J.A.Kaandorp@uva.nl>
fax: +31 20 5257490
URL: http://www.science.uva.nl/~jaapk/
________________________________
Van: Neil Lawrence [n.lawrence(a)sheffield.ac.uk]
Verzonden: donderdag 5 maart 2015 9:50
Aan: Kaandorp, Jaap
CC: Julio R. Banga IIM-CSIC; Joke Blom; bioPreDyn_af(a)lists.crg.es; Veronica Raker
Onderwerp: Re: [Biopredyn_af] BioPreDyn: H2020 proposal
I think Bayesian optimization of differential equation models or biological experiments
could be something very interesting to include.
On Thu, Mar 5, 2015 at 8:26 AM, Kaandorp, Jaap
<J.A.Kaandorp@uva.nl<mailto:J.A.Kaandorp@uva.nl>> wrote:
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<tel:%2B31%2020%205257539> /+31 20
5256789<tel:%2B31%2020%205256789>
Skype: jaap.kaandorp
email: J.A.Kaandorp@uva.nl<mailto:J.A.Kaandorp@uva.nl>
fax: +31 20 5257490<tel:%2B31%2020%205257490>
URL: http://www.science.uva.nl/~jaapk/
________________________________
Van: biopredyn_af-bounces@lists.crg.es<mailto:biopredyn_af-bounces@lists.crg.es>
[biopredyn_af-bounces@lists.crg.es<mailto:biopredyn_af-bounces@lists.crg.es>] namens
Julio R. Banga IIM-CSIC [julio@iim.csic.es<mailto:julio@iim.csic.es>]
Verzonden: woensdag 4 maart 2015 18:53
Aan: Joke Blom
CC: bioPreDyn_af@lists.crg.es<mailto: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<mailto: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<mailto:gollum@cwi.nl> phone: +31 20 592
4263<tel:%2B31%2020%20592%204263>
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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