biopredyn_pi

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29 discussions

[Biopredyn_pi] BioPreDyn: first short interim report; CA

by Olaf Kostbahn

Dear BioPreDyn PIs, On 31 March 2012, the first 6-months period of BioPreDyn will end and we have to prepare the first short interim report as a Deliverable to the European Commission on this occasion. Please find attached a template (as well as our Description of Work for your reference) for this purpose. I would like to ask each Work Package Leader to collect the relevant information from his/her WP collaborators and to return the completed WP Report to me before 27 March 2012. Kindly note that - text which is highlighted in red indicates your requested input - each WP report should not to exceed 0.5-1 page - the format of the template shall not be changed. Thanks a lot. Finally, we also received the last countersigned Consortium Agreement. As agreed in October 2011, we will provide every partner institution with scanned copies of all other's partners CA signatures, while the CRG will keep the originals. Please do not hesitate to contact me in the case of any questions. Best regards, Olaf

12 years, 5 months

[Biopredyn_pi] GENTLE REMINDER - BioPreDyn: first short interim report

by Olaf Kostbahn

Dear BioPreDyn Work Package Leaders, (cc: PIs) This is to gently remind you to kindly submit your interim report contributions by tomorrow. Thanks a lot. Best regards, Olaf From: Olaf Kostbahn Sent: jueves, 15 de marzo de 2012 19:28 To: 'Julio R. Banga'; 'saezrodriguez(a)ebi.ac.uk'; 'J.A.Kaandorp(a)uva.nl'; 'Joke.Blom(a)cwi.nl'; 'dibernardo(a)tigem.it'; 'pedro.mendes(a)manchester.ac.uk'; 'N.Lawrence(a)sheffield.ac.uk'; 'eric.boix(a)thecosmocompany.com'; 'eric.boix(a)gmail.com'; 'klaus.mauch(a)insilico-biotechnology.com'; 'Jean-Marie Mouillon' Cc: biopredyn_pi(a)lists.crg.es; Yogi Jaeger; 'michela.bertero(a)crg.es' Subject: BioPreDyn: first short interim report; CA Dear BioPreDyn PIs, On 31 March 2012, the first 6-months period of BioPreDyn will end and we have to prepare the first short interim report as a Deliverable to the European Commission on this occasion. Please find attached a template (as well as our Description of Work for your reference) for this purpose. I would like to ask each Work Package Leader to collect the relevant information from his/her WP collaborators and to return the completed WP Report to me before 27 March 2012. Kindly note that - text which is highlighted in red indicates your requested input - each WP report should not to exceed 0.5-1 page - the format of the template shall not be changed. Thanks a lot. Finally, we also received the last countersigned Consortium Agreement. As agreed in October 2011, we will provide every partner institution with scanned copies of all other's partners CA signatures, while the CRG will keep the originals. Please do not hesitate to contact me in the case of any questions. Best regards, Olaf

12 years, 5 months

[Biopredyn_pi] BioPreDyn workshop - Jun 11-15, 2012 (additional information)

by Yogi Jaeger

Dear BioPreDyn PIs, Some more detailed information on the BioPreDyn workshop Jun 11-15. We would like to ask you to come to Barcelona for 2-3 days during that week. We will try to have people be here either the first or the second half of the week, so we could all have a meeting together on Wed to discuss the results of the work in the focus groups to define benchmark problems. It would be great if you could send your availability on either Mon-Wed, Jun 11-13 or Wed-Fri, Jun 13-15 to Eva Navarrete (eva.navarrete(a)crg.eu). The teaching format would be to have about 1-1.5 hours of theoretical lecture, followed by 1-2 hours of practical sessions (laptops can be provided by the CRG). We can accommodate a maximum of 16 participants. Lectures/practicals should be taught by PIs and/or senior postdocs. Academic partners would be expected to contribute. For commercial partners: it would be great if CoSMo could present their software framework in a bit more detail (theoretical lecture only?). Klaus (InSilico): it would be great if you would like to contribute to the session on high-performance, for example. But contributions by SMEs would be voluntary. Apart from letting us know about your availability, could you tell me what kind of topics you would like to cover. Julio Banga and I will co-ordinate your inputs into a (hopefully) coherent program for the workshop. Thanks a lot for your help with this! Best, Yogi

12 years, 6 months

Re: [Biopredyn_pi] 1st BioPreDyn Workshop - Barcelona, Jun 11-15 - Draft Program

by Yogi Jaeger

Dear BioPreDyn PIs, Thanks a lot to all of those who have sent me feedback! Those of you who have not responded yet, please take a minute to check the schedule and let me know if it's ok. I would like to start advertising the workshop and open inscriptions by early next week. Based on your comments/suggestions, I've slightly adjusted the schedule of the workshop: Mon, Jun 11: morning: arrival 13:00-14:00 lunch 14:00-15:30 lecture: modeling/simulation, optimisation algorithms (Pedro) 15:30-16:00 coffee break 16:00-18:00 practical: COPASI (Pedro, with potential contribution from Fluxome) Tue, Jun 12 09:30-11:00 lecture: SB modelling cycle (part I), uncertainty quantification (Joke) 11:00-11:30 coffee break 11:30-13:00 practical/additional lecture (Joke) 13:00-14:30 lunch 14:30-16:00 lecture: introduction to Gaussian processes (Neil) 16:00-16:30 coffee break 16:30-18:00 practical/additional lecture (Neil) Wed, Jun 13 09:30-11:00 lecture: SB modelling cycle (part II), identifiability analysis (Julio B) 11:00-11:30 coffee break 11:30-13:00 lecture: optimal experimental design (Eva) 13:00-14:30 lunch 14:30-16:00 practical: identifiability analysis/optimal experimental design (Julio B/Eva) 16:00-16:30 coffee break 16:30-??:?? project steering committee meeting (PIs) Tue, Jun 14 09:30-11:00 lecture: logical models of signalling networks (Julio S/Martijn) 11:00-11:30 coffee break 11:30-13:00 practical: CellNOpt (Julio S/Martijn) 13:00-14:30 lunch 14:30-16:00 lecture: reverse-engineering developmental gene regulatory networks (Jaap/Yogi) 16:00-16:30 coffee break 16:30-18:00 practical/additional lecture (Jaap/Yogi) Fri, Jun 15 09:30-11:00 lecture and demo: CoSMo systems biology tools (Eric/Bertrand) 11:00-11:30 coffee break 11:30-13:00 discussion/evaluation 13:00-14:30 lunch afternoon: departure We will ask participants to bring their own laptop, and will also make them check a box in the application whether they have Matlab installed or not. This way, we should have enough laptops running Matlab to at least run it for participant groups of two. Let me know if you have any further questions. All the best, Yogi ---------- Previous message ---------- From: Johannes Jaeger <yogi.jaeger(a)crg.eu> Date: Mon, Mar 19, 2012 at 10:46 PM Subject: 1st BioPreDyn Workshop - Barcelona, Jun 11-15 - Draft Program To: biopredyn_pi(a)lists.crg.es Dear BioPreDyn PIs, Here is a draft program for our first workshop, to be held at the CRG in Barcelona on June 11-15, 2012. Please check it carefully, and complement/change the parts that concern your contribution. Please note that we have scheduled a steering committee meeting for all PIs on Wed afternoon. It would be great if all of you could be here for that. (PEDRO: please confirm if you could come the first, instead of the second part of the week. You had indicated that you would prefer the latter, but we had too many people who couldn't come the first half of the week at all. Besides, your topic would be a perfect opener for the course!) [HERE WAS THE OLD SCHEDULE] --- end of draft schedule --- It would be great if you could send me your feedback over the next few days. We will then go ahead and advertise the workshop among BioPreDyn participants. For the practical sessions, we would ask participants to bring their own laptops. Please let me know if you think this is a problem. In that case, we could rent a few additional laptops for the time of the course. Best, Yogi -- Dr. Johannes Jaeger EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona, Spain Phone: +34 93 316 02 85 Fax: +34 93 396 99 83 Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com URL: http://www.crg.es/johannes_jaeger ----- 3 FELLOWSHIPS AVAILABLE TO CARRY OUT INTERDISCIPLINARY POSTDOCTORAL STUDIES AT THE CENTER FOR GENOMIC REGULATION (INTERPOD), SUPPORTED BY CRG AND THE EUROPEAN COMMISSION FURTHER INFORMATION: www.crg.es/interpod

12 years, 6 months

[Biopredyn_pi] 1st BioPreDyn Workshop - Barcelona, Jun 11-15 - Draft Program

by Yogi Jaeger

Dear BioPreDyn PIs, Here is a draft program for our first workshop, to be held at the CRG in Barcelona on June 11-15, 2012. Please check it carefully, and complement/change the parts that concern your contribution. Please note that we have scheduled a steering committee meeting for all PIs on Wed afternoon. It would be great if all of you could be here for that. (PEDRO: please confirm if you could come the first, instead of the second part of the week. You had indicated that you would prefer the latter, but we had too many people who couldn't come the first half of the week at all. Besides, your topic would be a perfect opener for the course!) Mon, Jun 11: morning: arrival 13:00-14:00 lunch 14:00-15:30 lecture: modeling/simulation, optimisation algorithms (Pedro) 15:30-16:00 coffee break 16:00-18:00 practical: COPASI (Pedro) Tue, Jun 12 09:30-11:00 lecture: SB modelling cycle (part I), uncertainty quantification (Joke) 11:00-11:30 coffee break 11:30-13:00 practical/additional lecture (Joke) 13:00-14:30 lunch 14:30-16:00 lecture: introduction to Gaussian processes (Neil) 16:00-16:30 coffee break 16:30-18:00 practical/additional lecture (Neil) Wed, Jun 13 09:30-11:00 lecture: SB modelling cycle (part II), identifiability analysis (Eva) 11:00-11:30 coffee break 11:30-13:00 lecture: optimal experimental design (Julio B) 13:00-14:30 lunch 14:30-16:00 practical: identifiability analysis/optimal experimental design (Julio B/Eva) 16:00-16:30 coffee break 16:30-??:?? project steering committee meeting (PIs) Tue, Jun 14 09:30-11:00 lecture: logical models of signalling networks (Julio S/Martijn) 11:00-11:30 coffee break 11:30-13:00 practical: CellNOpt (Julio S/Martijn) 13:00-14:30 lunch 14:30-16:00 lecture: reverse-engineering developmental gene regulatory networks (Jaap/Yogi) 16:00-16:30 coffee break 16:30-18:00 practical/additional lecture (Jaap/Yogi) Fri, Jun 15 09:30-11:00 lecture: CoSMo systems biology tools (Eric/Bertrand) 11:00-11:30 coffee break 11:30-13:00 discussion/evaluation 13:00-14:30 lunch afternoon: departure --- end of draft schedule --- It would be great if you could send me your feedback over the next few days. We will then go ahead and advertise the workshop among BioPreDyn participants. For the practical sessions, we would ask participants to bring their own laptops. Please let me know if you think this is a problem. In that case, we could rent a few additional laptops for the time of the course. Best, Yogi -- Dr. Johannes Jaeger EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona, Spain Phone: +34 93 316 02 85 Fax: +34 93 396 99 83 Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com URL: http://www.crg.es/johannes_jaeger ----- 3 FELLOWSHIPS AVAILABLE TO CARRY OUT INTERDISCIPLINARY POSTDOCTORAL STUDIES AT THE CENTER FOR GENOMIC REGULATION (INTERPOD), SUPPORTED BY CRG AND THE EUROPEAN COMMISSION FURTHER INFORMATION: www.crg.es/interpod

12 years, 6 months

Re: [Biopredyn_pi] 1st BioPreDyn Workshop - Barcelona, Jun 11-15 - Draft Program

by Pedro Mendes

Dear Yogi, Yes, I can come in the beggining of the week. Best wishes Pedro Yogi Jaeger <Yogi.Jaeger(a)crg.eu> wrote: >Dear BioPreDyn PIs, > >Here is a draft program for our first workshop, to be held at the CRG >in Barcelona on June 11-15, 2012. Please check it carefully, and >complement/change the parts that concern your contribution. Please >note that we have scheduled a steering committee meeting for all PIs >on Wed afternoon. It would be great if all of you could be here for >that. > >(PEDRO: please confirm if you could come the first, instead of the >second part of the week. You had indicated that you would prefer the >latter, but we had too many people who couldn't come the first half of >the week at all. Besides, your topic would be a perfect opener for the >course!) > >Mon, Jun 11: > >morning: arrival >13:00-14:00 lunch >14:00-15:30 lecture: modeling/simulation, optimisation algorithms (Pedro) >15:30-16:00 coffee break >16:00-18:00 practical: COPASI (Pedro) > >Tue, Jun 12 > >09:30-11:00 lecture: SB modelling cycle (part I), uncertainty >quantification (Joke) >11:00-11:30 coffee break >11:30-13:00 practical/additional lecture (Joke) >13:00-14:30 lunch >14:30-16:00 lecture: introduction to Gaussian processes (Neil) >16:00-16:30 coffee break >16:30-18:00 practical/additional lecture (Neil) > >Wed, Jun 13 > >09:30-11:00 lecture: SB modelling cycle (part II), identifiability >analysis (Eva) >11:00-11:30 coffee break >11:30-13:00 lecture: optimal experimental design (Julio B) >13:00-14:30 lunch >14:30-16:00 practical: identifiability analysis/optimal experimental >design (Julio B/Eva) >16:00-16:30 coffee break >16:30-??:?? project steering committee meeting (PIs) > >Tue, Jun 14 > >09:30-11:00 lecture: logical models of signalling networks (Julio S/Martijn) >11:00-11:30 coffee break >11:30-13:00 practical: CellNOpt (Julio S/Martijn) >13:00-14:30 lunch >14:30-16:00 lecture: reverse-engineering developmental gene regulatory >networks (Jaap/Yogi) >16:00-16:30 coffee break >16:30-18:00 practical/additional lecture (Jaap/Yogi) > >Fri, Jun 15 > >09:30-11:00 lecture: CoSMo systems biology tools (Eric/Bertrand) >11:00-11:30 coffee break >11:30-13:00 discussion/evaluation >13:00-14:30 lunch >afternoon: departure > >--- end of draft schedule --- > >It would be great if you could send me your feedback over the next few >days. We will then go ahead and advertise the workshop among BioPreDyn >participants. > >For the practical sessions, we would ask participants to bring their >own laptops. Please let me know if you think this is a problem. In >that case, we could rent a few additional laptops for the time of the >course. > >Best, >Yogi > > >-- >Dr. Johannes Jaeger >EMBL/CRG Research Unit in Systems Biology >CRG - Centre de Regulació Genòmica >Dr. Aiguader 88 >08003 Barcelona, Spain >Phone: +34 93 316 02 85 >Fax: +34 93 396 99 83 >Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com >URL: http://www.crg.es/johannes_jaeger > >----- >3 FELLOWSHIPS AVAILABLE TO CARRY OUT INTERDISCIPLINARY POSTDOCTORAL >STUDIES AT THE CENTER FOR GENOMIC REGULATION (INTERPOD), SUPPORTED BY >CRG AND THE EUROPEAN COMMISSION >FURTHER INFORMATION: www.crg.es/interpod >_______________________________________________ >Biopredyn_pi mailing list >Biopredyn_pi(a)lists.crg.es >http://davinci.crg.es/mailman/listinfo/biopredyn_pi

12 years, 6 months

[Biopredyn_pi] code licenses

by Yogi Jaeger

Dear BioPreDyn Partners, I am writing to you in my function as the chair of the Innovation Board (IB) of our BioPreDyn consortium. As agreed during the kick-off meeting, one of the first tasks of the IB is collect information on what kind of code licenses are being used by all the BioPreDyn partners. It would be great if you could send us a brief description, ideally with web links to more detailed information, on the licensing schemes you are using or planning to use for software developed within the consortium. Please also provide us with information on why you use this particular licensing scheme, if possible. I would be grateful, if you could send me this information at your earliest convenience, but no later than mid January. We will compile a document with the different licensing strategies, which will then serve as a basis for the discussions of the IB. Thanks a lot for your collaboration! Best, Yogi -- Dr. Johannes Jaeger EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona, Spain Phone: +34 93 316 02 85 Fax: +34 93 396 99 83 Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com URL: http://www.crg.es/johannes_jaeger

12 years, 6 months

[Biopredyn_pi] BioPreDyn Workshop June 2012

by Eva Navarrete Espuna

Dear all, Please fill in the doodle to find a date to celebrate a BioPreDyn Workshop at the CRG in June 2012. http://www.doodle.com/zwf89q2rvgsa8fs6 Thanks in advance for your collaboration and happy 2012 Eva Eva Navarrete Systems Biology CRG -Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona Ph: +34933160375 Fax: +34933969983 eva.navarrete(a)crg.eu<mailto:eva.navarrete@crg.eu> www.crg.es/systems_biology<http://www.crg.es/systems_biology> www.crg.es<http://www.crg.es/> 10 FELLOWSHIPS AVAILABLE TO CARRY OUT PhD STUDIES AT THE CENTER FOR GENOMIC REGULATION, FUNDED BY "LA CAIXA". MORE INFORMATION AT: www.crg.eu/lacaixa_fellowships<http://www.crg.eu/lacaixa_fellowships> Aquest correu electrònic conté informació confidencial emparada pel secret professional. Qualsevol reproducció, distribució o divulgació del seu contingut estan estrictament prohibides. Si vostè no és el destinatari, li preguem no faci difusió ni copiï el seu contingut i ens ho notifiqui al més aviat possible per telèfon (+34 93 3160100) o a la adreça email suport(a)crg.es<mailto:suport@crg.es> <mailto:suport@crg.es> Este correo electrónico contiene información confidencial amparada por el secreto profesional. Cualquier reproducción, distribución o divulgación de su contenido están estrictamente prohibidas. Si usted no es el destinatario, le rogamos no difunda ni copie su contenido y nos lo notifique de inmediato por teléfono (+34 93 3160100) o a la dirección suport(a)crg.es<mailto:suport@crg.es> <mailto:suport@crg.es>. This electronic transmission contains confidential information guaranteed by professional privacy. Any reproduction, distribution or spreading of the content is strictly forbidden. If you are not the intended addressee, you are kindly requested not to disclose nor to copy this transmission and to notify us as soon as possible by phone (+34 93 3160100) or by email to the suport(a)crg.es<mailto:suport@crg.es> <mailto:suport@crg.es> address.

12 years, 8 months

[Biopredyn_pi] BioPreDyn - focus groups

by Yogi Jaeger

Dear BioPreDyn Partners, As agreed during the BioPreDyn meeting, one of our first actions should be to define benchmark models for our algorithms. For this purpose, we have defined the following focus groups: - E. coli: metabolic & regulatory network (Pedro) - Yeast: metabolic & regulatory network (Pedro, Fluxome) - Chinese Hamster Ovary (CHO) Cells: metabolic, regulatory & signaling network model (Diego, Insilico, Julio S, Pedro) - Developmental Gene Regulatory Networks in animal systems (Yogi, Jaap) We need to establish for each of these benchmark problems what kind of data are available for modeling. This should be done as soon as possible. I would suggest that each focus group compiles the available data sets and writes a brief report on the nature and quality (completeness, technical accuracy etc.) of the data. I think we should aim at collecting such reports for each problem in February. To facilitate information exchange, we have set up folders on our Alfresco sharing platform (see Olaf's last email for information on how to access it) for each Focus Group. This allows you to store and share your contributions centrally. The idea is that each partner in a focus group contributes descriptions of those data sets they know about. The different WP leaders can then collect this information for the specific modeling tasks in each work package. Let me know if you have any problems/questions. I will try to provide an example report for the animal development focus group as soon as possible, and will be bugging you some more about this in the near future. Happy holidays! Best, Yogi -- Dr. Johannes Jaeger EMBL/CRG Research Unit in Systems Biology CRG - Centre de Regulació Genòmica Dr. Aiguader 88 08003 Barcelona, Spain Phone: +34 93 316 02 85 Fax: +34 93 396 99 83 Email: yogi.jaeger(a)crg.es or yoginho(a)gmail.com URL: http://www.crg.es/johannes_jaeger

12 years, 9 months

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