All,
I'd like to echo all of these concerns and questions. For the end-users
and software/system developers in proteomics, what are the pain points?
What are the current best practices? What can OGF do from a
technology/standards point of view? What can we do from a community-building
point of view? Can the proteomics community articulate (in some way, shape,
or form) a technology roadmap for where they think the field needs to go
in the not-so-distant future?
--Craig
At 05:41 AM 10/29/2007, Richard Sinnott wrote:
>I know lots of people involved in high throughput proteomics, indeed
>Glasgow University has recently had a major centre funded specifically
>in this area. See http://www.gla.ac.uk/rasor/
>
>My point is that having a talk from these people will not help OGF/OGSA
>directly for the reasons I identify below. LSG-RG has to start asking
>questions of the WG's and OGSA efforts in concrete/measurable terms that
>someone in OGSA-BES, JSDL, DAIS, authZ etc etc can understand.
>
>Does the DAIS spec allow me to manage mass spec data? Does it provide
>the security hooks I need? Does JSDL, OGSA-BES provide sufficient
>support for me to process my mass spec data on a range of HPC clusters?
>If not, why not... etc etc
>
>Otherwise we end up with the LSG-RG having no impact whatsoever on the
>rest of the OGF/OGSA efforts - which is ~the case right now. (I struggle
>to see any concrete examples that LSG-RG has thrown at the other groups
>to enhance the OGSA standards - other than the SAML authZ api and lack
>of parameters which we identified a couple of years ago in BRIDGES).
>
>R.
>
>
>
>-----Original Message-----
>From: Angulo, David [mailto:dangulo@cti.depaul.edu]
>Sent: 29 October 2007 13:17
>To: Richard Sinnott; lsg-rg(a)gridforum.org
>Subject: RE: [LSG-RG] [LSG-RG @ OGF] February 2008 Proteomics Meeting
>
>Thanks, Richard, for your comments. You are correct, our purpose is to
>present proteomics / Life Sciences requirements to OGF at large (and
>particular OGF research groups or working groups). To do that, we must
>learn what those requirements are by listening to the experts in the
>area of high throughput proteomics. If you know of any potential
>speakers that have already developed these requirements, we would be
>very happy to have you present their names for consideration; however, I
>assume that our group will need to do this work ourselves.
>
>Dave
>
>David Sigfredo Angulo
>Faculty
>DePaul University
>312-362-5041 dangulo(a)cti.depaul.edu
>
> > -----Original Message-----
> > From: Richard Sinnott [mailto:r.sinnott@nesc.gla.ac.uk]
> > Sent: Monday, October 29, 2007 4:16 AM
> > To: Angulo, David; lsg-rg(a)gridforum.org
> > Subject: RE: [LSG-RG] [LSG-RG @ OGF] February 2008 Proteomics Meeting
> >
> > If we are planning/discussing these via email, then can I suggest that
>
> > the talks are applications of OGF specs/implementations applied to the
>
> > proteomics/mass spec domain. Otherwise, and being my usual being
> > devils advocate, what is the point of having these presentations at
> > OGF and not somewhere else?
> >
> > The LSG-RG SHOULD be about informing OGF and hence OGSA standards
> > (what works and what doesn't etc). It should NOT be about life
> > sciences more generally - there are many conferences out there for
> > that.
> >
> > If nobody is using the OGF specs / implementations in proteomics-land
> > right now (which would not altogether surprise me), then another
> > alternative is to have someone present their proteomics requirements
> > and have OGF/OGSA area directors/WG leaders come in and discuss how
> > their various efforts meet those requirements. I feel that the results
>
> > of this would be much more use to OGF/OGSA as a whole.
> >
> > Thoughts? Flames? ...
> >
> > Rich
> >
> >
> >
> >
> > -----Original Message-----
> > From: lsg-rg-bounces(a)ogf.org [mailto:lsg-rg-bounces@ogf.org] On Behalf
>
> > Of Angulo, David
> > Sent: 28 October 2007 23:40
> > To: lsg-rg(a)gridforum.org
> > Subject: [LSG-RG] [LSG-RG @ OGF] February 2008 Proteomics Meeting
> >
> >
> > Dear all:
> >
> > I would like to apologize for the previous message sent without a
> > proper introduction. My private e-mail message was forwarded to the
> > list without my permission, but hopefully it didn't confuse anyone.
> >
> > 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 will give a background of this group at the end of this message.
> > First, though, let me state the purpose of this message.
> >
> > Our group has been extremely active since 2002, but the visibility of
> > our activities has waned. One suggestion, which we believe is quite
> > on target, was to plan future meetings through our e-mail list
> > (through which you are receiving this message).
> >
> > I would like to start out such an effort by asking for input in
> > planning our next meeting, which will be help in February
> > 2008 in Boston. At the meeting in Seattle last week, the attendees
> > were extremely interested in the proteomics presentations, and the
> > group decided that we would solicit proteomics experts to speak at the
>
> > next meeting.
> >
> > Thus, I would like to extend a call for presentations in proteomics.
> > We would like to specifically look for proteomic mass spectrometry
> > presentations, 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.
> >
> > I'm looking forward to input from all.
> >
> > =================
> > 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:
> > http://www.ogf.org/mailman/listinfo/lsg-rg
> > To see minutes of past LSG-RG meetings and to see other documents
> > about the group, please visit:
> > http://www.ogf.org/gf/group_info/view.php?group=lsg-rg
> > For more information about OGF, including details on the next message,
>
> > please visit:
> > http://www.ogf.org
> > ===========
> >
> > David Sigfredo Angulo
> > Faculty
> > DePaul University
> > 312-362-5041 dangulo(a)cti.depaul.edu
> > --
> > lsg-rg mailing list
> > lsg-rg(a)ogf.org
> > http://www.ogf.org/mailman/listinfo/lsg-rg
> >
>--
> lsg-rg mailing list
> lsg-rg(a)ogf.org
> http://www.ogf.org/mailman/listinfo/lsg-rg
Dear all:
I would like to apologize for the previous message sent without a proper introduction. My private e-mail message was forwarded to the list without my permission, but hopefully it didn't confuse anyone.
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 will give a background of this group at the end of this message. First, though, let me state the purpose of this message.
Our group has been extremely active since 2002, but the visibility of our activities has waned. One suggestion, which we believe is quite on target, was to plan future meetings through our e-mail list (through which you are receiving this message).
I would like to start out such an effort by asking for input in planning our next meeting, which will be help in February 2008 in Boston. At the meeting in Seattle last week, the attendees were extremely interested in the proteomics presentations, and the group decided that we would solicit proteomics experts to speak at the next meeting.
Thus, I would like to extend a call for presentations in proteomics. We would like to specifically look for proteomic mass spectrometry presentations, 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.
I'm looking forward to input from all.
=================
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:
http://www.ogf.org/mailman/listinfo/lsg-rg
To see minutes of past LSG-RG meetings and to see other documents about the group, please visit:
http://www.ogf.org/gf/group_info/view.php?group=lsg-rg
For more information about OGF, including details on the next message, please visit:
http://www.ogf.org
===========
David Sigfredo Angulo
Faculty
DePaul University
312-362-5041 dangulo(a)cti.depaul.edu
We can do this in the abstract, e.g. proteomics has strong HPC, data,
security mgt requirements etc hence needs Grid based solutions. But from
my perspective, we should be looking in more detail at the specific OGF
efforts and how they support proteomics based research (or not) - if
proteomics is the focus of this next meeting that is.
Otherwise we end up with a set of interesting presentations to life
scientists but serve no real benefit to the Grid community at large -
which surely is the point for folk to go to OGF meetings.
Note I have taken the liberty of copying these discussions to the wider
LSG-RG email list, since email discussions behind closed doors is one of
the issues this group needs to stop. More than happy for folk to
disagree with me...
Cheers,
R.
________________________________
From: Abbas Farazdel [mailto:farazdel@us.ibm.com]
Sent: 27 October 2007 21:17
To: Richard Sinnott
Cc: Vincent Breton; Angulo, David; fumikazu(a)gsc.riken.jp; Richard
Sinnott
Subject: RE: Proposed message
I assume the focus of the presentations should address the following
questions and not just covering merely proteomics): 1) How grid
computing can be used to help proteomics scientists and professionals to
achieve breakthrough science or shorter time-to-solution; and 2) Are
there any requirements in the area of proteomics that presently is not
addressed by OGF groups but should be addressed.
Best Regards,
Dr. Abbas Farazdel
Blue Gene Solutions Executive - Petascale Computing
IBM Systems & Technology Group
Office: +1 845 433 1652 (t/l-293); Mobile: +1 845 216 4066
Fax: +1 845 491 3569
Email: farazdel(a)us.ibm.com <mailto:farazdel@us.ibm.com>
http://www.ibm.com/servers/deepcomputing/bluegene.html
<http://www.ibm.com/servers/deepcomputing/bluegene.html>
"Richard Sinnott" <ros(a)dcs.gla.ac.uk>
10/27/2007 02:03 PM
To
"Angulo, David" <dangulo(a)cti.depaul.edu>, <fumikazu(a)gsc.riken.jp>, Abbas
Farazdel/Poughkeepsie/IBM@IBMUS, "Vincent Breton"
<breton(a)clermont.in2p3.fr>
cc
<r.sinnott(a)nesc.gla.ac.uk>
Subject
RE: Proposed message
As long as the proteomics presentations are aligned with the work
on-going within the OGF standards/implementations of those standards
etc, then I am all for this. From my own perspective, LSG-RG should be
telling people what works with OGF specs and what doesn't. Thus we
should be asking is anyone out there in LSG-RG land using the
imlementations of DAIS, ByteIO, OGSA-BES, authZ, etc etc.
There are many other life science conferences/workshops where folk can
talk about proteomics more generally etc. Having talks about
non-specific OGF related applications in the life science domain for me
does not make much sense.
Thoughts?
R.
PS Please use the r.sinnott(a)nesc.gla.ac.uk as I no longer get emails
directly forwarded from my DCS account.
-----Original Message-----
From: Angulo, David [mailto:dangulo@cti.depaul.edu
<mailto:dangulo@cti.depaul.edu> ]
Sent: Sat 27/10/2007 17:15
To: Fumikazu KONISHI <fumikazu(a)gsc.riken.jp>; Abbas Farazdel; Vincent
Breton; Richard Sinnott
Subject: Proposed message
Dear all:
Please give feedback before Sunday, 5PM Chicago Time (CST). At that
time, if I have no feedback, I will send this message.
========================
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 will give a background of this group at the end of this message.
First, though, let me state the purpose of this message.
Our group has been extremely active since 2002, but the visibility of
our activities has waned. One suggestion, which we believe is quite on
target, was to plan future meetings through our e-mail list (through
which you are receiving this message).
I would like to start out such an effort by asking for input in planning
our next meeting, which will be help in February 2008 in Boston. At the
meeting in Seattle last week, the attendees were extremely interested in
the proteomics presentations, and the group decided that we would
solicit proteomics experts to speak at the next meeting.
Thus, I would like to extend a call for presentations in proteomics. We
would like to specifically look for proteomic mass spectrometry
presentations, 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.
I'm looking forward to input from all.
David Sigfredo Angulo
Faculty
DePaul University
312-362-5041 dangulo(a)cti.depaul.edu
One further note to all: Chris Oehmen is associated with Washington State and is from PNNL (Pacific Northwest National Lab)
dave
David Sigfredo Angulo
Faculty
DePaul University
312-362-5041 dangulo(a)cti.depaul.edu
> -----Original Message-----
> From: Angulo, David
> Sent: Tuesday, October 16, 2007 5:23 PM
> To: lsg-rg(a)gridforum.org
> Cc: 'Abbas Farazdel'; 'Oehmen, Christopher S'; 'John Boyle';
> 'Julie Wulf-Knoerzer'
> Subject: LSG-RG talks on Thursday at OGF 21
>
> Dear all:
>
> Life Science Grid Research Group has two scheduled sessions
> at OGF this week. Both are in Discovery B on Thursday, Oct.
> 18. The first is at 9AM the second at 11AM.
>
> Besides an open discussion and group business, we will have
> two presentations:
>
>
> You can find slides in the LSG-RG section of gridforum.org
>
>
>
> John Boyle of the Institute for Systems Biology will talk in
> the first session
>
> Title: Requirements for a research enterprise for systems biology
>
> Abstract: In systems biology, and many other areas of
> research, there is a need for the interoperability of tools
> and data sources which were not originally designed to be
> ntegrated. Due to the interdisciplinary nature of systems
> biology, and its association with high throughput
> experimental platforms, there is an additional need to
> continually integrate new technologies. This problem is
> confounded by the fact that as scientists work in isolated
> groups, integration is rarely a consideration when building
> the required software tools. This talk will discuss a
> light-weight software architecture, based upon a common
> identity system and dynamically discovered interoperable
> services, used at the ISB through which scientists can both
> get access to and analyze the plethora of experimentally
> derived data. The shortcomings of this architecture will be
> discussed, as well as the need for the adoption of a new type
> of data infrastructure which is able to fulfill the
> requirements of the next generation of high throughput
> experiment technologies.
>
>
>
> Chris Oehmen of Washington State will talk in the second session
>
> Title: High-throughput sequence analysis challenges: what
> the Grid can do for us
>
> Abstract: Exponentially growing sequence data is driving a
> revolution in bioinformatics and biology in general but the
> demand for compute resources is quickly outpacing the
> capacity of conventional platforms. Taking advantage of the
> unique capabilities of the grid means new algorithms and
> programming paradigms are needed. We present some challenges
> and a vision of high-performance bioinformatics using grid technology.
>
>
>
>
> David Sigfredo Angulo
> Faculty
> DePaul University
> 312-362-5041 dangulo(a)cti.depaul.edu
Dear all:
Life Science Grid Research Group has two scheduled sessions at OGF this week. Both are in Discovery B on Thursday, Oct. 18. The first is at 9AM the second at 11AM.
Besides an open discussion and group business, we will have two presentations:
You can find slides in the LSG-RG section of gridforum.org
John Boyle of the Institute for Systems Biology will talk in the first session
Title: Requirements for a research enterprise for systems biology
Abstract: In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources which were not originally designed to be ntegrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. This problem is confounded by the fact that as scientists work in isolated groups, integration is rarely a consideration when building the required software tools. This talk will discuss a light-weight software architecture, based upon a common identity system and dynamically discovered interoperable services, used at the ISB through which scientists can both get access to and analyze the plethora of experimentally derived data. The shortcomings of this architecture will be discussed, as well as the need for the adoption of a new type of data infrastructure which is able to fulfill the requirements of the next generation of high throughput experiment technologies.
Chris Oehmen of Washington State will talk in the second session
Title: High-throughput sequence analysis challenges: what the Grid can do for us
Abstract: Exponentially growing sequence data is driving a revolution in bioinformatics and biology in general but the demand for compute resources is quickly outpacing the capacity of conventional platforms. Taking advantage of the unique capabilities of the grid means new algorithms and programming paradigms are needed. We present some challenges and a vision of high-performance bioinformatics using grid technology.
David Sigfredo Angulo
Faculty
DePaul University
312-362-5041 dangulo(a)cti.depaul.edu
