biopredyn_pi

biopredyn_pi@lists.crg.es

29 discussions

by Pedro Mendes

Dear BioPreDyn colleagues, I have some news that I thought you should get in a separate email from me (instead of getting a mass mailing...). I will start by saying that these news do not change anything relating to BioPreDyn. As you may be aware, I've had a 20% position at Virginia Tech, being 80% at Manchester. From January I will no longer be at Virginia Tech. Instead I took up a 50% position at the University of Connecticut (in their medical school, in a new institute for "Quantitative Medicine"). As such my position in Manchester will also become 50% starting January. I will be roughly 1 month on either side of the Atlantic. As I said above, this will not affect our collaboration. The time I dedicate to BioPreDyn is included in my 50% in Manchester, but I will be engaged in the project even when I am in Connecticut. I already made sure that I will be on this side for our Course at the EBI. All that this requires is a bit more advance scheduling from my part (and hoping that any teleconference be in the afternoon!). That's it, I just thought it would be nicer if you heard about this on an email specific to BioPreDyn. all the best Pedro -- Pedro Mendes Professor of Computational Systems Biology School of Computer Science Manchester Centre for Integrative Systems Biology University of Manchester Manchester Institute of Biotechnology 131 Princess Street Manchester, M1 7DN, U.K.

10 years, 9 months

[Biopredyn_pi] Fwd: WP3 updates -- Fwd: [Biopredyn_af] BioPreDyn: interim report, titles for workshop teaching

by Julio R. Banga

Dear all, regarding *WP3*, please send me your updates (if any) following Veronica's request below. Please use Word track changes in the attached Word, save it putting your initials in the file name and send it back to me. Thanks and best regards, Julio R. Banga -------- Mensaje original -------- Asunto: [Biopredyn_af] BioPreDyn: interim report, titles for workshop teaching Fecha: Thu, 12 Sep 2013 15:54:13 +0200 De: Veronica Raker <Veronica.Raker(a)crg.eu> Para: bioPreDyn_af(a)lists.crg.es <bioPreDyn_af(a)lists.crg.es> Dear all, We have two upcoming deadlines: *1. (Another) project interim report: please send me your updates by 25 Sept* I need to submit a project interim report to the EC at the end of the month. If you can, please update your section(s) of the previous report. I will need your input by 25 Sept. FYI, I am attaching an excel file with internal communication, workshops attended, and publications (to be updated by all), and the Deliverable text (to be updated by the PIs) (these files are also in the Update folder of the intranet docs). To update, you have 3 options: 1. (preferred) update the files directly on the intranet that are in the "Updates" folder www.biopredyn.eu/share <http://www.biopredyn.eu/share> 2. update these files and send them back to me 3. send me the info to be added and I will update the common files *2.**Workshop teaching May 12-15: please send me titles by Monday 16 Sept* Before our annual meeting next year (May 15 afternoon-May 16) at the EBI (Hinxton, UK), we will give a workshop/course at the EBI, from May 12 (afternoon) to May 15 (morning). The workshop is deliverable D8.7 (Task 8.5); according to the DoW, this workshop "will aim at teaching outside researchers the theoretical and practical aspects of the methods and tools developed during this project" We now need to fix the talks/schedule. Please find below an outline, where you will find your acronym next to the topic(s) where you could participate. The titles for orientation and not carved in stone (some have been left as TBD). The idea is that these talks will be given by postdocs/PIs from each group. *Please give me (if possible, by next Monday, 16^th Sept) the title of the talk(s) and the names of the speakers from your group. *Again, this can be done either in the intranet (in the Update folder) or by sending me the info. best, Veronica

10 years, 11 months

[Biopredyn_pi] BioPreDyn - parameter estimation benchmark problems - *your reply needed*

by Julio R. Banga

Dear BioPreDyn partners, as you might remember, during the Naples meeting we discussed the possibility of setting up a collection of benchmark problems regarding parameter estimation in medium/large scale systems biology models. At that meeting we agreed to: 1- initially, CSIC and UNIMAN would prepare an initial set of problems and documentation, plus a draft manuscript describing their use 2- these documents could then be used, as templates, by other partners interested in participating with problems of their own. The manuscript would incorporate these new problems 3- the resulting final joint manuscript would be submitted to a journal, and the problem collection would be made available through a web site Alex (CSIC) and Kieran (UNIMAN) have worked on this and the resulting first draft and problem collection will be ready during the coming days. The problems considered so far are related with parameter estimation in large-scale kinetic models of microbial metabolism, and are available, as ready-to-run codes, in two formats, Copasi and Matlab. The dynamic models are also available as SBML. So, following the steps above, what we need now from you is: 1.-- please let us know *asap* if you are interested in contributing with parameter estimation problems from your group. Deadline: 30-June. (The only prerrequisites is that they are medium to large-scale problems, and that you have them implemented in ready-to-run code (ideally, Copasi or Matlab, but other implementations are fine if it is documented how to use different optimization solvers with the problem(s)) 2.- during the coming weeks, Alex will send to the interested groups the format template and the draft manuscript, so they can add their problems in a coherent format. 3.- after a few iterations, we set up the web site and submit the joint paper to a journal. Best regards, Julio R. Banga -- ------------------------------------------------------------- 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 -------------------------------------------------------------

11 years, 2 months

[Biopredyn_pi] Fwd: Survey: Tools, Methods, Standards, Collaborations in Computational and Systems Biology

by Julio R. Banga

Dear partners in BioPreDyn, (sorry if you already got this info) please find below a message from Edda Klipp with a link to an online questionnaire regarding data, tools and methods used in computational and systems biology. Since these are at the core of BioPreDyn, I thought you could be interested. Best, Julio R. Banga -------- Mensaje original -------- Asunto: Survey: Tools, Methods, Standards, Collaborations in Computational and Systems Biology Fecha: Thu, 16 May 2013 18:17:11 +0200 De: Edda Klipp <Edda.Klipp(a)biologie.hu-berlin.de> Para: Julio R. Banga <julio(a)iim.csic.es> Dear Julio, Currently, we witness intensive research in systems biology on all levels including traditional and emerging experimental technologies as well as proved and innovative modeling approaches. Sustained model development can only be successful, if both worlds can speak to each other in a educated way. In order to support these processes, we developed a new survey about data, tools and methods used in computational and systems biology. Because of its rising importance for scientific communication and exchange, we are also interested in the application and development of standardization principles. I would highly appreciate if you could take a moment to fill the online questionnaire: even partial answers would be helpful. We would also be grateful if you could send it to your colleagues and collaborators (especially if they are experimentalists working with you). Here is the link: http://jaguar.biologie.hu-berlin.de/~sdrulhe/sb_standards_survey_2013/index… <http://jaguar.biologie.hu-berlin.de/%7Esdrulhe/sb_standards_survey_2013/ind…> The preferential deadline is May the 31st. Thank you and best wishes, Edda Klipp -- Prof. Dr. Dr. h.c. Edda Klipp Humboldt-Universität zu Berlin Theoretical Biophysics Institute for Biology Invalidenstr. 42, 10115 Berlin, Germany Fon + 49 30 2093 9040 Fax + 49 30 2093 8813 email: edda.klipp(a)rz.hu-berlin.de <mailto:edda.klipp@rz.hu-berlin.de> https://www2.hu-berlin.de/biologie/theorybp/

11 years, 4 months

[Biopredyn_pi] BioPreDyn: COPASI workshop Jan 21-23

by Veronica Raker

Dear all, We are pleased to announce the BioPreDyn COPASI workshop, which will be lead by Pedro and Kieran on 21-23 Jan in Manchester. As mentioned in the attached announcement, this workshop is targeted not only to experienced COPASI users but also to complete beginners. I would highly encourage you to join if you are interested; the workshop will reserve several spots for BioPreDyn members. A detailed agenda will be included on the website shortly. Please register here: https://docs.google.com/spreadsheet/viewform?fromEmail=true&formkey=dEdyRlZ… Additionally, can you please tell everyone who might be interested about it? The workshop is announced on the biopredyn.eu<http://biopredyn.eu> website and will be announced on the COPASI website (www.copasi.org<http://www.copasi.org>). Best wishes, Veronica Veronica Raker, Ph.D. Scientific Project Manager International and Scientific Affairs Center for Genomic Regulation C/ Dr. Aiguader, 88 08003 Barcelona Tel. +34 933160374 www.4DCellFate.eu<http://www.4DCellFate.eu> www.biopredyn.eu<http://www.biopredyn.eu>

11 years, 9 months

[Biopredyn_pi] on-line petition against EU science budget cuts

by Veronica Raker

Dear all, I would like to draw your attention to the petition started by Maria Leptin, against EU science budget cuts. If you agree with it, maybe you can forward it also to your colleagues. http://www.no-cuts-on-research.eu<http://www.no-cuts-on-research.eu/> Thanks! Best regards, Veronica Veronica Raker, Ph.D. Scientific Project Manager International and Scientific Affairs Center for Genomic Regulation C/ Dr. Aiguader, 88 08003 Barcelona Tel. +34 933160374 www.4DCellFate.eu<http://www.4DCellFate.eu> www.biopredyn.eu<http://www.biopredyn.eu> -----Original Message----- From: Maria Leptin [mailto:maria.leptin@embo.org] Sent: martes, 23 de octubre de 2012 02:13 p.m. Subject: Please forward - Petition to protect EU science budget Dear colleagues, The discussions at the next summit of the European Union heads of state or government, which is scheduled for 22 and 23 November, will be decisive in determining the EU research budget for the next seven years. Several Member States are demanding severe cuts on the total EU budget and research will have to compete with other policy priorities. This is a time when we, the scientific community, should act together and make our case to protect research funding, including that of the European Research Council (ERC), from cuts. Decisions will be prepared in discussions among politicians at the national level. All of us must look for opportunities to affect these decisions and send a strong signal to the heads of state or government. An open letter signed by European Nobel laureates has been published in top European newspapers this week. The impact of this letter will be increased if it is followed by a mobilization of the national scientific communities. To keep the momentum going, an online petition has been launched: http://www.no-cuts-on-research.eu<http://www.no-cuts-on-research.eu/> I would like to ask you to sign it and to encourage all your colleagues to do likewise. Note that in the past, less than 30 000 scientists signed the largest petition for a European scientific cause compared to the hundreds of thousands of signatures on petitions from other groups of society. We must do better than that. This action is coordinated by the Initiative for Science in Europe (ise(a)i-se.org<mailto:ise@i-se.org>; www.initiative-science-europe.org<http://www.initiative-science-europe.org/>), of which EMBO is a member. Please contact Wolfgang Eppenschwandtner, Executive Coordinator of the ISE if you have any questions or suggestions. Best regards, Maria Leptin Director EMBO - excellence in life sciences Meyerhofstr. 1 69117 Heidelberg, Germany tel +49-6221-8891-102 fax +49-6221-8891-202 maria.leptin(a)embo.org<mailto:maria.leptin@embo.org>

11 years, 11 months

[Biopredyn_pi] BioPreDyn: 29 Oct meeting Bcn

by Veronica Raker

Dear all, Sorry for the late notice, but here's the general agenda for the meeting on the 29th. Everyone should prepare a brief overview of their progress (of about 12 min, with a few minutes for discussion). We will dedicate more time for Cosmo, to get updated about software integration and what's working (and what's not). After lunch, we will discuss the direction of the project without Fluxome, as well as managerial issues (deliverables, etc). A couple of people have mentioned that they won't make the dinner on Sunday evening; I will reserve for the remaining people (let me know if you are vegetarian etc). The final 2nd interim report is posted on the intranet; please let me know if you want me to mail it to you. Thanks a lot for your cooperation with that! Best wishes, Veronica Veronica Raker, Ph.D. Scientific Project Manager International and Scientific Affairs Center for Genomic Regulation C/ Dr. Aiguader, 88 08003 Barcelona Tel. +34 933160374 www.4DCellFate.eu<http://www.4DCellFate.eu> www.biopredyn.eu<http://www.biopredyn.eu>

11 years, 11 months

[Biopredyn_pi] BioPreDyn: issues to be addressed for 29 Oct meeting

by Veronica Raker

Dear all, We are preparing the agenda for the meeting on Oct. 29th. The general format will likely be: short scientific talks in the morning (from 9-13), and a general assembly discussion in the afternoon (14-16). I have a couple of questions: 1. Which issues need to be addressed? The most pressing one, of course, is how to proceed without Fluxome, and we will spend time discussing this. Are there other additional issues which you think we should address? (problems with hiring personnel, for example…). I would appreciate it if you could let me know before Monday, so I can introduce them into the agenda. 2. Will you NOT be able to attend the dinner 28 Oct (20:30-22:00)? We unfortunately don't have the budget to cover this, so I would ask each to pay from their own budget. I would make a reservation in a restaurant with a fixed price menu, to make it easier to get individual receipts for this. Could you let me know if you will NOT be able to attend? Also, please let me know if you do not eat fish. (3. And please don't forget to let me know by Monday if I should change anything in the interim report!) Thanks. best wishes, Veronica Veronica Raker, Ph.D. Scientific Project Manager International and Scientific Affairs Center for Genomic Regulation C/ Dr. Aiguader, 88 08003 Barcelona Tel. +34 933160374 www.4DCellFate.eu<http://www.4DCellFate.eu> www.biopredyn.eu<http://www.biopredyn.eu>

11 years, 11 months

[Biopredyn_pi] BioPreDyn: 2nd interim report

by Veronica Raker

Dear all, The interim report was delayed on my side, as I was waiting to clarify the situation of the consortium without Fluxome with the EU officers (which is still underway). Here is the draft I would like to submit. Could you please look through it to see if it is accurate? If you find anything that should be changed, I would appreciate it if you could get it back to me before Monday Oct. 15th (when I will submit it). Sorry for the short time I'm giving you for this review. Best wishes, Veronica

11 years, 11 months

[Biopredyn_pi] Project manager position at CRG

by Veronica Raker

Dear all, I would just like to inform you that we have a scientific project manager position open in our institute (please see attached file) that should be filled ASAP (depending however on having an excellent person available). If you know anyone who might be interested, and who would like to join a fantastic team in a great city, could you please pass it on? Thanks! Best wishes, Veronica Veronica Raker, Ph.D. Scientific Project Manager International and Scientific Affairs Center for Genomic Regulation C/ Dr. Aiguader, 88 08003 Barcelona Tel. +34 933160374 www.4DCellFate.eu www.biopredyn.eu

11 years, 11 months

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