[LSG-RG] [LSG-RG} Meeting on Pharma

Thu Dec 27 06:22:36 CST 2007

RE: [LSG-RG] [LSG-RG} Meeting on PharmaDear Richard,

thank you for your suggestions on the role/mandate of OGF LSG-RG.

In my opinion, the group is not in a situation to deploy a real grid because it does not have the resources to do so. It costs a lot of money to operate a grid and it requires also a very strong management to ensure proper technical choices. 

On the other hand, the group has a unique feature from my point of view: it is a really worldwide group, so it is a fantastic place where people can meet and exchange experience. As most of the technology we are using is open source, it seems to me we can use the group to get to know what is going on in the rest of the world and develop best practices. Learning about success stories and copying what is being done elsewhere is often the best way to avoid traps. 

Regarding standards, we certainly need to work out how to articulate better our relationship to the other OGF working groups. We need also to identify some well defined topics on which some motivated people would be keen to push the work. These people can not be funded by OGF so it means the work they do in OGF must fit within the programme of work of their funding agency. We also need to achieve a certain critical mass of interested people so that RG participants are willing to travel around the world and pay very expensive registration fees to participate to the meetings.  

I think we need to identify topics where there would be interest in Asia, Europe and USA: this way, the work could be presented at almost every OGF meeting. 
If you or any other person has some topic he would like to see addressed in the LSG-RG in relation to standards, it would be very nice to discuss it on the list but I would like to stress again these two points:
    - it should interest members of LSG-RG on at least 2 continents out of Europe, USA and Asia
    - it requires a few committed people to follow it up through

Having some workshops like the one on Pharma is certainly a way to identify common interest topics.

I wish to you and all the list members a merry christmas and happy new year.

Best regards,

Vincent

  ----- Original Message ----- 
  From: Richard Sinnott 
  To: Angulo, David ; Abbas Farazdel ; lsg-rg at gridforum.org 
  Sent: Friday, December 21, 2007 8:49 PM
  Subject: Re: [LSG-RG] [LSG-RG} Meeting on Pharma

  Ok.

  >From my perspective, the LSG-RG "should" be doing the following.

  Build large scale life science Grids applying Grid technologies implementing the standards coming out of the other groups and feeding back concrete requirements to them on what works, what doesn't work, what needs fixing etc. This should be along the lines of the GIN work but focused in particular on the life sciences.

  The kinds of things I envisage are:

  - build an international LSG-RG HPC life science Grid testing out the OGSA-BES, JSDL, GridSAM efforts etc to run large scale BLAST applications, protein docking, building indexes of bio-data sets, other scenarios that are HPC oriented;

  - build an international LSG-RG life science bioinformatics data Grid testing out the work from the OGSA Data Groups (DAIS, DFDL, DMI, GSM, ...etc) for example;

  - build an interational LSG-RG life science Grid focussed on finer grained security - perhaps in the clinical domain, e.g. clinical trials for drug evaluation. Do the AuthN, AuthZ, Shibboleth efforts and standards meet the needs of the LSG-RG community? If not, why not. If yes, then can we document best practice so that others building health Grids in the future know how to do this instead of reinventing wheels?

  These are just some of the things that LSG-RG "should" be doing. There are many more, e.g. building international LSG-RG Grids that test out workflows/interoperability of workflow definition/enactment in the life science domain and feeding experiences back to the workflow groups etc.

  I am keen that we push/fix/finalise the standards and their implementations so we can get on with the science using standards based Grid infrastructures. This can only happen by speaking to groups like AuthZ with concrete requirements about the APIs they are standardising for security and whether they meet the requirements of the life sciences based on case studies/Grids that are applying them in anger.

  Would folk be interested in building these things within the LSG-RG?

  Rich

  PS I note that we at NeSC are working on all of the above in a range of projects in the UK and several new ones that have just been funded by the EU.

  -----Original Message-----
  From: Angulo, David [mailto:dangulo at cti.depaul.edu]
  Sent: Fri 21/12/2007 19:21
  To: Richard Sinnott; Abbas Farazdel; lsg-rg at gridforum.org
  Subject: RE: [LSG-RG] [LSG-RG} Meeting on Pharma

  Thanks, Richard.  Could you post answers, from your perspective, to all these questions, please?

  Dave

  ________________________________
  From: Richard Sinnott [mailto:r.sinnott at nesc.gla.ac.uk]
  Sent: Thursday, December 20, 2007 4:56 PM
  To: Abbas Farazdel; Angulo, David; lsg-rg at gridforum.org
  Subject: RE: [LSG-RG] [LSG-RG} Meeting on Pharma

  I'll be devils advocate - for a change!!! ;o)

  What is this group attempting to achieve? Is it to explore software per se used in the life sciences or is it to work within OGF to help improve the standards and best practice in building Grids for the life sciences? These need not be orthogonal but I am not sure how presentations by commercial software providers will help the OGF work as a whole. I could be wrong of course - they may be all be implementing standards/technologies which have a direct bearing on the Grid and OGF activities. Being my usual cynical self, I am not sure that this is the case though.

  I note that there are many venues for commercial software providers to present their wares.

  I guess these comments could be applied to many/all research groups at OGF.

  Thoughts?

  Rich

  ________________________________
  From: lsg-rg-bounces at ogf.org [mailto:lsg-rg-bounces at ogf.org] On Behalf Of Abbas Farazdel
  Sent: 20 December 2007 20:34
  To: Angulo, David; lsg-rg at gridforum.org
  Subject: Re: [LSG-RG] [LSG-RG} Meeting on Pharma

  I suggest the presentation topic to be "Pharmaceutical R&D" instead of "Pharmacology" so that we would have a bigger umbrella to cover areas of interest. In particular, I suggest "In-silico Pharmaceutical R&D" (e.g., in-silico clinical development with simulated patients) which is of considerable interest to pharma companies for pre-clinical development and even patient care situations.

  Some of the Independent Software Vendor companies in this area are Gene Network Sciences, Immunetrics, Entelos, GenStruct, Optimata, Genomatica, and Pharsight. In fact we can have people from these companies or the customers of these companies present at the workshop. What do you think?

  Best Regards,

  Dr. Abbas Farazdel
  Blue Gene Solutions Executive - Petascale Computing
  IBM Systems & Technology Group
  Tel:        +1 603 707 6377
  Mobile:  +1 603 707 6377
  Fax:       +1 845 491 3569
  Email: farazdel at us.ibm.com<mailto:farazdel at us.ibm.com>

  http://www.ibm.com/servers/deepcomputing/bluegene.html

  "Angulo, David" <dangulo at cti.depaul.edu>
  Sent by: lsg-rg-bounces at ogf.org

  12/20/2007 02:02 PM

  To

  "lsg-rg at gridforum.org" <lsg-rg at gridforum.org>

  cc

  Subject

  [LSG-RG] [LSG-RG} Meeting on Pharma

  Dear all:

  This is an e-mail message regarding the Life Science Grid Research Group (LSG-RG) in the Open Grid Forum (OGF), formerly the Global Grid Forum (GGF).

  I sent out last month asking for input regarding a proposed meeting regarding proteomics for the next OGF meeting in Boston in February.  The leadership of OGF would like to make a workshop for Pharma, and they have asked us to participate with them in this effort.

  Thus, I would like to extend a call for presentations in Pharmacology.  We would like to specifically look for presentations relating to those areas in Pharmacology that involve intensive computational power, extensive communications, or massive amounts of data, but all will be considered.  I would like the membership of this e-mail list to help us in the solicitation of speakers, and would like to solicit your input into what topics and/or speakers we should pursue.

  Here are some suggested speakers

  * Piotr Sliz, PhD, Bioinformatics Specialist II, Howard Hughes Medical Institute
  * Steve Litster, Novartis Institutes of BioMedical Research
  * Timothy Wagner, Bristol-Myers Squibb Company
  * Jeffrey Mathers, Pharmaceutical Research & Development
  * Sanjoy Ray, Merck
  * Peter S. Shenkin, Schrodinger
  * WISDOM, Vincent Breton CNRS
  * Bridge, Martin Hofmann fron SCAI Fraunhofer
  * Share, Tony Solomonides from Univ West England
  * Ian Penny of Pfizer

  I'm looking forward to input from all.  Please post notices by 12/26/07

  =================
  The LSG-RG (Life Science Grid Research Group) is a group in OGF (Open Grid Forum) which was formed with the purpose of developing best practices in the area of the Life Sciences in the intersection with Grid Computing.  The group also serves the purpose of interfacing with the other group in OGF and ensuring that all standards created by OGF take into account the requirements of applications in the Life Sciences.

  To Subscribe to the LSG-RG mailing list or to see archives messages, please visit:
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  To see minutes of past LSG-RG meetings and to see other documents about the group, please visit:
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  For more information about OGF, including details on the next message, please visit:
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  ===========

  David Sigfredo Angulo
  Faculty
  DePaul University
  312-362-5041  dangulo at cti.depaul.edu

  David Sigfredo Angulo
  Faculty
  DePaul University
  312-362-5041  dangulo at cti.depaul.edu
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