5 Mar
2015
5 Mar
'15
10:28 a.m.
Dear all,
I think Diego's comments below are very relevant.
And the biotech application(s) is(are) certainly critical. The ones
mentioned
by Diego are great choices, but will need to be backed up by companies
in the
consortium (could we get such companies?).
I think we can also include metabolic engineering using kinetic models
as application,
assuming Evolva and INSIL will be onboard (?). They can probably add
more on this...
Best,
JulioB
El 05/03/2015 a las 9:51, Diego di Bernardo escribió:
Hi everyone,
just a quick comment, I guess we need to keep in mind that the call
states that the main objective is to exploit available databases (or
assemble new meta-databases and visualisation tools) to derive
predictive models among other things. Here is an excerpt from the call:
One of the greatest challenge facing the biotechnology community today
is to be able to make use of the vast and dynamic influx of "omics" data.
Therefore I think we need to have as a starting point the
currently available data and explicitly mention this in the proposal.
If we want to propose metabolic models are there public metabolomic
databases? if we propose to use single-cell gene expression, are there
available data? moreover we need to keep in mind the focus of the
call, i.e. which is the biotech application we want to
tackle? remember that this is an Industrial Leadership program and we
need to focus on an application, in my opinion. It could geared
towards novel antibiotics or cancer but we need to decide and build
the proposal around that.
That’s my two pennies :)
best,
Diego
On 5 March 2015 at 09:29:04, Kaandorp, Jaap (j.a.kaandorp(a)uva.nl
<mailto:j.a.kaandorp@uva.nl>) wrote:
--
-------------------------------------------------------------
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
-------------------------------------------------------------
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(a)uva.nl <mailto:J.A.Kaandorp@uva.nl>
fax: +31 20 5257490
URL: http://www.science.uva.nl/~jaapk/
<http://www.science.uva.nl/%7Ejaapk/>
------------------------------------------------------------------------
*Van:* biopredyn_af-bounces(a)lists.crg.es
[biopredyn_af-bounces(a)lists.crg.es] namens Julio R. Banga IIM-CSIC
[julio(a)iim.csic.es]
*Verzonden:* woensdag 4 maart 2015 18:53
*Aan:* Joke Blom
*CC:* bioPreDyn_af(a)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(a)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(a)cwi.nl <mailto:gollum@cwi.nl> phone: +31 20 592
4263 <tel:%2B31%2020%20592%204263>
URL: http://www.cwi.nl/~gollum/ <http://www.cwi.nl/%7Egollum/>
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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___________________________________________
Diego di Bernardo, Ph.D.
___________________________________________
Principal Investigator
Telethon Institute of Genetics and Medicine
(TIGEM)
Via Campi Flegrei 34, 80078 Pozzuoli (Naples), Italy
Research Assistant Professor (Ricercatore)
Faculty of Engineering
Dept of Computer and Systems Engineering
University of Naples "Federico II"
___________________________________________
Tel: +39 081 6132 319/Fax: +39 081 6132 351
Web: http://dibernardo.tigem.it/