psidev-ms-dev

[Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Randy J. <rkj...@in...>]

The PSI-MS biweekly call is scheduled for 10:00 EST at the usual call-i=
n=20
number. Please sent an e-mail to Kent Laursen=20
(Ken...@ge...) if you need dialing instructions for the =
call.

The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially se=
t=20
at the last meeting:

1. MCP response - This is essential since the reply is required by 15=20
Oct 2005
2. Review of feedback on the Requirements Survey
3. Review of mission statement
4. Approval of working groups and recommendations for chairs & spec tea=
ms.

On this last point, the recommendation for working groups looks like th=
is:

1) MI
2) Mass spec (mzData Spec)
3) Separations (Prep, Columns, Gels)
4) Protein Modifications
5) Informatics/Identification/Analysis (analysisXML spec)
6) GPS (deliverable Document is the Object Model used by all WGs)
7) Extensions, CV=92s & Ontology Methodology
8) Reporting Recommendations (MIAPE documents)

Each group needs at least two chairs who are committed to keeping the=20
communication active and providing reports.

According to the minutes, the draft of the document process should have=
=20
been completed, but is still underway with good feedback being provided=
=20
by several members (but not enough time to do all the editing yet). We=20
will discuss the state of these documents and the overall process if=20
time allows.

Thanks,
Randy Julian

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Angel P. <an...@ma...>]

First stab at a mission statement:

"The PSI Mass Spectrometry (PSI-MS) standards group consists of academic 
and industry researchers, software developers and instrument 
manufacturers. The goal of the group is to provide vendor-neutral 
standard formats for representing mass spectrometry experimental data 
and the results derived through analysis of those data. A secondary goal 
of the group is to foster adoption of the format by highlighting efforts 
made by vendors and individuals that utilize the format in their products."

 We could go on from here to highlight the current efforts and releases, 
as well as provide the mechanisms whereby we get things done. In 
addition we may want to touch on the boundaries with other PSI groups.
Angel

 Randy Julian wrote:

> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual 
> call-in number. Please sent an e-mail to Kent Laursen 
> (Ken...@ge...) if you need dialing instructions for the 
> call.
>
> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially 
> set at the last meeting:
>
> 1. MCP response - This is essential since the reply is required by 15 
> Oct 2005
> 2. Review of feedback on the Requirements Survey
> 3. Review of mission statement
> 4. Approval of working groups and recommendations for chairs & spec 
> teams.
>
> On this last point, the recommendation for working groups looks like 
> this:
>
> 1) MI
> 2) Mass spec (mzData Spec)
> 3) Separations (Prep, Columns, Gels)
> 4) Protein Modifications
> 5) Informatics/Identification/Analysis (analysisXML spec)
> 6) GPS (deliverable Document is the Object Model used by all WGs)
> 7) Extensions, CV’s & Ontology Methodology
> 8) Reporting Recommendations (MIAPE documents)
>
> Each group needs at least two chairs who are committed to keeping the 
> communication active and providing reports.
>
> According to the minutes, the draft of the document process should 
> have been completed, but is still underway with good feedback being 
> provided by several members (but not enough time to do all the editing 
> yet). We will discuss the state of these documents and the overall 
> process if time allows.
>
> Thanks,
> Randy Julian
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Pierre-Alain B. <pie...@is...>]

Thanks Angel.
I would add, even if we decide that MIAPE is a group on its own, that=20
the MS working group also generates the corresponding MIAPE modules,=20
which are high-level (end-user and software-vendor) minimal requirements=20
to be supported by the formats

Pierre-Alain

Angel Pizarro wrote:

> First stab at a mission statement:
>
> "The PSI Mass Spectrometry (PSI-MS) standards group consists of=20
> academic and industry researchers, software developers and instrument=20
> manufacturers. The goal of the group is to provide vendor-neutral=20
> standard formats for representing mass spectrometry experimental data=20
> and the results derived through analysis of those data. A secondary=20
> goal of the group is to foster adoption of the format by highlighting=20
> efforts made by vendors and individuals that utilize the format in=20
> their products."
>
> We could go on from here to highlight the current efforts and=20
> releases, as well as provide the mechanisms whereby we get things=20
> done. In addition we may want to touch on the boundaries with other=20
> PSI groups.
> Angel
>
> Randy Julian wrote:
>
>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual=20
>> call-in number. Please sent an e-mail to Kent Laursen=20
>> (Ken...@ge...) if you need dialing instructions for=20
>> the call.
>>
>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially=20
>> set at the last meeting:
>>
>> 1. MCP response - This is essential since the reply is required by 15=20
>> Oct 2005
>> 2. Review of feedback on the Requirements Survey
>> 3. Review of mission statement
>> 4. Approval of working groups and recommendations for chairs & spec=20
>> teams.
>>
>> On this last point, the recommendation for working groups looks like=20
>> this:
>>
>> 1) MI
>> 2) Mass spec (mzData Spec)
>> 3) Separations (Prep, Columns, Gels)
>> 4) Protein Modifications
>> 5) Informatics/Identification/Analysis (analysisXML spec)
>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>> 7) Extensions, CV=92s & Ontology Methodology
>> 8) Reporting Recommendations (MIAPE documents)
>>
>> Each group needs at least two chairs who are committed to keeping the=20
>> communication active and providing reports.
>>
>> According to the minutes, the draft of the document process should=20
>> have been completed, but is still underway with good feedback being=20
>> provided by several members (but not enough time to do all the=20
>> editing yet). We will discuss the state of these documents and the=20
>> overall process if time allows.
>>
>> Thanks,
>> Randy Julian
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads,=20
>> discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussion=
s,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

--=20
--
 Dr. Pierre-Alain Binz
 Swiss Institute of Bioinformatics
 Proteome Informatics Group
 1, Rue Michel Servet
 CH-1211 Geneve 4
 Switzerland
 - - - - - - - - - - - - - - - - -
 Tel: +41-22-379 50 50
 Fax: +41-22-379 58 58
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Angel P. <an...@ma...>]

Pierre-Alain Binz wrote:

> Thanks Angel.
> I would add, even if we decide that MIAPE is a group on its own, that 
> the MS working group also generates the corresponding MIAPE modules, 
> which are high-level (end-user and software-vendor) minimal 
> requirements to be supported by the formats
>
Good point. Revised:

The PSI Mass Spectrometry (PSI-MS) standards group consists of academic 
and industry researchers, software developers and instrument 
manufacturers. The goals of the group are: to provide a set of minimal 
reporting requirements which augment the \link{ MIAPE reporting 
guidelines }with respect to mass spectrometry experiments; to provide 
vendor-neutral standard formats for representing mass spectrometry 
experimental data and the results derived through analysis of those 
data;  to foster adoption of the format by highlighting efforts made by 
vendors and individuals that utilize the format in their \link{ products }.

-angel

> Pierre-Alain
>
> Angel Pizarro wrote:
>
>> First stab at a mission statement:
>>
>> "The PSI Mass Spectrometry (PSI-MS) standards group consists of 
>> academic and industry researchers, software developers and instrument 
>> manufacturers. The goal of the group is to provide vendor-neutral 
>> standard formats for representing mass spectrometry experimental data 
>> and the results derived through analysis of those data. A secondary 
>> goal of the group is to foster adoption of the format by highlighting 
>> efforts made by vendors and individuals that utilize the format in 
>> their products."
>>
>> We could go on from here to highlight the current efforts and 
>> releases, as well as provide the mechanisms whereby we get things 
>> done. In addition we may want to touch on the boundaries with other 
>> PSI groups.
>> Angel
>>
>> Randy Julian wrote:
>>
>>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual 
>>> call-in number. Please sent an e-mail to Kent Laursen 
>>> (Ken...@ge...) if you need dialing instructions for 
>>> the call.
>>>
>>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially 
>>> set at the last meeting:
>>>
>>> 1. MCP response - This is essential since the reply is required by 
>>> 15 Oct 2005
>>> 2. Review of feedback on the Requirements Survey
>>> 3. Review of mission statement
>>> 4. Approval of working groups and recommendations for chairs & spec 
>>> teams.
>>>
>>> On this last point, the recommendation for working groups looks like 
>>> this:
>>>
>>> 1) MI
>>> 2) Mass spec (mzData Spec)
>>> 3) Separations (Prep, Columns, Gels)
>>> 4) Protein Modifications
>>> 5) Informatics/Identification/Analysis (analysisXML spec)
>>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>>> 7) Extensions, CV’s & Ontology Methodology
>>> 8) Reporting Recommendations (MIAPE documents)
>>>
>>> Each group needs at least two chairs who are committed to keeping 
>>> the communication active and providing reports.
>>>
>>> According to the minutes, the draft of the document process should 
>>> have been completed, but is still underway with good feedback being 
>>> provided by several members (but not enough time to do all the 
>>> editing yet). We will discuss the state of these documents and the 
>>> overall process if time allows.
>>>
>>> Thanks,
>>> Randy Julian
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads, 
>>> discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads, 
>> discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>


-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Chris T. <chr...@eb...>]

Hi all. First of all, really great job on the pairwise=20
comparisons. Nice clinical laying out of the issues.

And on the MIAPE 'ownership' thing; clearly the MS workgroup own=20
both MIAPE: MS and MSI and are the responsible body in this=20
interaction with MCP.

But... I would like nonetheless to comment on the cover=20
letter/document. As I say I think the comparison is very clear=20
in the actual comparison documents themselves (MS/MSI/MCP) but=20
the cover letter is too long and doesn't make the main point=20
clearly enough up front. It is good to lay out the various=20
aspects of our work, but what should be clear throughout is that=20
the issue is the overlap between MIAPE and MCP. The first page=20
or so talks about using PSI formats to supply data to meet=20
journal quality measures, but doesn't actually mention or define=20
MIAPE. The first clear mention of MIAPE is halfway down page 2...

Towards the end the message becomes clearer, but is still=20
embedded in a lot of verbiage and discussion of our other work=20
(which is essentially irrelevant and potentially confusing).=20
Overall I think the premises and proposed resolution need to be=20
up front, almost in an abstract-style front end summary,=20
followed by clear supporting arguments and (minimally) detailed=20
proposals. The background info about formats etc. needs to be=20
drastically cut back and generally it needs tightening.

We will obviously chat about this shortly; I would be happy to=20
contribute some time to redrafting this document in the light of=20
discussions this afternoon if that appeals..?

Cheers, Chris.


Angel Pizarro wrote:
> Pierre-Alain Binz wrote:
>=20
>> Thanks Angel.
>> I would add, even if we decide that MIAPE is a group on its own, that=20
>> the MS working group also generates the corresponding MIAPE modules,=20
>> which are high-level (end-user and software-vendor) minimal=20
>> requirements to be supported by the formats
>>
> Good point. Revised:
>=20
> The PSI Mass Spectrometry (PSI-MS) standards group consists of academic=
=20
> and industry researchers, software developers and instrument=20
> manufacturers. The goals of the group are: to provide a set of minimal=20
> reporting requirements which augment the \link{ MIAPE reporting=20
> guidelines }with respect to mass spectrometry experiments; to provide=20
> vendor-neutral standard formats for representing mass spectrometry=20
> experimental data and the results derived through analysis of those=20
> data;  to foster adoption of the format by highlighting efforts made by=
=20
> vendors and individuals that utilize the format in their \link{ product=
s }.
>=20
> -angel
>=20
>> Pierre-Alain
>>
>> Angel Pizarro wrote:
>>
>>> First stab at a mission statement:
>>>
>>> "The PSI Mass Spectrometry (PSI-MS) standards group consists of=20
>>> academic and industry researchers, software developers and instrument=
=20
>>> manufacturers. The goal of the group is to provide vendor-neutral=20
>>> standard formats for representing mass spectrometry experimental data=
=20
>>> and the results derived through analysis of those data. A secondary=20
>>> goal of the group is to foster adoption of the format by highlighting=
=20
>>> efforts made by vendors and individuals that utilize the format in=20
>>> their products."
>>>
>>> We could go on from here to highlight the current efforts and=20
>>> releases, as well as provide the mechanisms whereby we get things=20
>>> done. In addition we may want to touch on the boundaries with other=20
>>> PSI groups.
>>> Angel
>>>
>>> Randy Julian wrote:
>>>
>>>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual=20
>>>> call-in number. Please sent an e-mail to Kent Laursen=20
>>>> (Ken...@ge...) if you need dialing instructions for=20
>>>> the call.
>>>>
>>>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially=
=20
>>>> set at the last meeting:
>>>>
>>>> 1. MCP response - This is essential since the reply is required by=20
>>>> 15 Oct 2005
>>>> 2. Review of feedback on the Requirements Survey
>>>> 3. Review of mission statement
>>>> 4. Approval of working groups and recommendations for chairs & spec=20
>>>> teams.
>>>>
>>>> On this last point, the recommendation for working groups looks like=
=20
>>>> this:
>>>>
>>>> 1) MI
>>>> 2) Mass spec (mzData Spec)
>>>> 3) Separations (Prep, Columns, Gels)
>>>> 4) Protein Modifications
>>>> 5) Informatics/Identification/Analysis (analysisXML spec)
>>>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>>>> 7) Extensions, CV=92s & Ontology Methodology
>>>> 8) Reporting Recommendations (MIAPE documents)
>>>>
>>>> Each group needs at least two chairs who are committed to keeping=20
>>>> the communication active and providing reports.
>>>>
>>>> According to the minutes, the draft of the document process should=20
>>>> have been completed, but is still underway with good feedback being=20
>>>> provided by several members (but not enough time to do all the=20
>>>> editing yet). We will discuss the state of these documents and the=20
>>>> overall process if time allows.
>>>>
>>>> Thanks,
>>>> Randy Julian
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by:
>>>> Power Architecture Resource Center: Free content, downloads,=20
>>>> discussions,
>>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>> _______________________________________________
>>>> Psidev-ms-dev mailing list
>>>> Psi...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads,=20
>>> discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>
>=20
>=20

--=20
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~