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.
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
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
-------------------------------------------------------------
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/
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>
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>
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>
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>
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
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.euwww.biopredyn.eu