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> wrote:

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(a)uva.nl> wrote:

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) 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 /+31 20 5256789 Skype: jaap.kaandorp email: J.A.Kaandorp(a)uva.nl fax: +31 20 5257490 URL: http://www.science.uva.nl/~jaapk/   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> 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         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 _______________________________________________ Biopredyn_af mailing list Biopredyn_af(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/biopredyn_af _______________________________________________ Biopredyn_af mailing list Biopredyn_af(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/biopredyn_af ___________________________________________ 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/

Hi Diego, Thanks for your comments, yes I agree with this We are considering to include new computational methods methods for analyzing omics data in the proposal, this would require global optimization methods, models, baysesian optimasation. For that reason we also would like to include scyfer (an SME specialized in Bayseian opt) in the consortium. We were also considering to include the group from James Sharpe (CRG) in the proposal, they do experimental work and collect gene expression data, Light Sheet Fluorescence Miicroscopy data. Bayesian opt and other opt methods are very suitable to find patterns in this I agree we should make an inventory of the available data in the consortium, other suitable data sources and also define a few suitable biotech cases i would appreciate it very much if you send us pieces of text about these topics which can try incorporate in first draft of the 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: Diego di Bernardo [dibernardo(a)tigem.it] Verzonden: donderdag 5 maart 2015 9:51 Aan: Julio R. Banga IIM-CSIC; Joke Blom; Kaandorp, Jaap CC: bioPreDyn_af(a)lists.crg.es; Veronica Raker Onderwerp: Re: [Biopredyn_af] BioPreDyn: H2020 proposal 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@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 /+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: 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@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 _______________________________________________ Biopredyn_af mailing list Biopredyn_af@lists.crg.es<mailto:Biopredyn_af@lists.crg.es> http://davinci.crg.es/mailman/listinfo/biopredyn_af _______________________________________________ Biopredyn_af mailing list Biopredyn_af(a)lists.crg.es http://davinci.crg.es/mailman/listinfo/biopredyn_af ___________________________________________ 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/