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From: Jones, A. <And...@li...> - 2010-10-12 13:58:38
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Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu...] Sent: 01 October 2010 16:44 To: psi...@li...; mbr...@sy... Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 |
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From: Henk v. d. T. <h.w...@uu...> - 2010-10-13 14:28:49
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Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: > Dear all, > > not good for me -- I will be on a plane during that time. > How about one week later, 10/28 same time? > > Cheers, > Oliver > > On 12.10.2010, at 15:33, Jones, Andy wrote: > >> Hi all, >> >> There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. >> >> How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, >> Cheers >> Andy >> >> >> >> >> >> >> From: Henk van den Toorn [mailto:h.w...@uu...] >> Sent: 01 October 2010 16:44 >> To: psi...@li...; mbr...@sy... >> Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration >> >> Hello all, >> >> Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. >> >> ----------- >> >> >> Dear PSI mzQuantML discussion participants, >> >> Background of APML >> Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. >> >> mzQuantML that Oliver is leading. >> Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. >> >> Essential elements in the schema >> To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. >> >> Thank you for reading. >> >> Warm Regards, >> Mi-Youn >> >> Mi-Youn Brusniak, Ph.D. >> Computational Biology >> Seattle Proteome Center >> mbr...@sy... >> Tel: (206)732-1327 >> >> >> Mi-Youn Brusniak, Ph.D. >> Computational Biology >> Seattle Proteome Center >> mbr...@sy... >> Tel: (206)732-1327 >> ------------------------------------------------------------------------------ >> Beautiful is writing same markup. Internet Explorer 9 supports >> standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. >> Spend less time writing and rewriting code and more time creating great >> experiences on the web. Be a part of the beta today. >> http://p.sf.net/sfu/beautyoftheweb_______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > --- > Oliver Kohlbacher (oli...@un...) > Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen > phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de > > vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard > > > > > > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- *Henk van den Toorn, bioinformatician* Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu... Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
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From: David C. <dc...@ma...> - 2010-10-14 09:11:05
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I'll be away then, so it's unlikely that I'll be able to make it. But
please go ahead without me - I think that my views and Andy's views are
pretty similar.<br>
<br>
David<br>
<br>
Eric Deutsch wrote:
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Not
as convenient for me, but it will be fine, yes.</span></p>
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style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> </span></p>
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Jones,
Andy
[mailto:<a moz-do-not-send="true"
href="mailto:And...@li...">And...@li...</a>]
<br>
<b>Sent:</b> Wednesday, October 13, 2010 7:43 AM<br>
<b>To:</b> Mass spectrometry standard development;
<a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential
element on
mzQuantML consideration</span></p>
</div>
</div>
<p class="MsoNormal"> </p>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: black;">28/10
would also be okay with me, anyone else?</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">cheers</span></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">Andy
</span></p>
</div>
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<p class="MsoNormal" style="margin-bottom: 12pt;"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"> Henk van
den Toorn
[<a moz-do-not-send="true" href="mailto:h.w...@uu...">h.w...@uu...</a>]<br>
<b>Sent:</b> 13 October 2010 15:28<br>
<b>To:</b> Mass spectrometry standard development<br>
<b>Subject:</b> Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential
element on
mzQuantML consideration</span></p>
</div>
<div>
<p class="MsoNormal">Fine by us, Henk & Pieter <br>
<br>
On 12-10-2010 19:08, Oliver Kohlbacher wrote: </p>
<pre>Dear all,</pre>
<pre> </pre>
<pre>not good for me -- I will be on a plane during that time.</pre>
<pre>How about one week later, 10/28 same time?</pre>
<pre> </pre>
<pre>Cheers,</pre>
<pre> Oliver</pre>
<pre> </pre>
<pre>On 12.10.2010, at 15:33, Jones, Andy wrote:</pre>
<pre> </pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Hi all,</pre>
<pre> </pre>
<pre>There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people.</pre>
<pre> </pre>
<pre>How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives,</pre>
<pre>Cheers</pre>
<pre>Andy</pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre>From: Henk van den Toorn [<a moz-do-not-send="true"
href="mailto:h.w...@uu...">mailto:h.w...@uu...</a>] </pre>
<pre>Sent: 01 October 2010 16:44</pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a>; <a
moz-do-not-send="true" href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration</pre>
<pre> </pre>
<pre>Hello all,</pre>
<pre> </pre>
<pre>Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list.</pre>
<pre> </pre>
<pre>-----------</pre>
<pre> </pre>
<pre> </pre>
<pre>Dear PSI mzQuantML discussion participants,</pre>
<pre> </pre>
<pre>Background of APML</pre>
<pre>Corra (<a moz-do-not-send="true"
href="http://www.biomedcentral.com/1471-2105/9/542" target="_blank">http://www.biomedcentral.com/1471-2105/9/542</a>) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (<a
moz-do-not-send="true"
href="http://sourceforge.net/projects/corra/files/" target="_blank">http://sourceforge.net/projects/corra/files/</a> ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008.</pre>
<pre> </pre>
<pre>mzQuantML that Oliver is leading.</pre>
<pre>Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies.</pre>
<pre> </pre>
<pre>Essential elements in the schema</pre>
<pre>To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community.</pre>
<pre> </pre>
<pre>Thank you for reading.</pre>
<pre> </pre>
<pre>Warm Regards,</pre>
<pre>Mi-Youn</pre>
<pre> </pre>
<pre>Mi-Youn Brusniak, Ph.D.</pre>
<pre>Computational Biology</pre>
<pre>Seattle Proteome Center</pre>
<pre><a moz-do-not-send="true"
href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Tel: (206)732-1327</pre>
<pre> </pre>
<pre> </pre>
<pre>Mi-Youn Brusniak, Ph.D.</pre>
<pre>Computational Biology</pre>
<pre>Seattle Proteome Center</pre>
<pre><a moz-do-not-send="true"
href="mailto:mbr...@sy...">mbr...@sy...</a></pre>
<pre>Tel: (206)732-1327</pre>
<pre>------------------------------------------------------------------------------</pre>
<pre>Beautiful is writing same markup. Internet Explorer 9 supports</pre>
<pre>standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.</pre>
<pre>Spend less time writing and rewriting code and more time creating great</pre>
<pre>experiences on the web. Be a part of the beta today.</pre>
<pre><a moz-do-not-send="true"
href="http://p.sf.net/sfu/beautyoftheweb_______________________________________________"
target="_blank">http://p.sf.net/sfu/beautyoftheweb_______________________________________________</a></pre>
<pre>Psidev-ms-dev mailing list</pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev"
target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev</a></pre>
</blockquote>
<pre>---</pre>
<pre>Oliver Kohlbacher (<a moz-do-not-send="true"
href="mailto:oli...@un...">oli...@un...</a>)</pre>
<pre>Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen</pre>
<pre>phone: +49-7071-29-70457 <a moz-do-not-send="true"
href="http://www-bs.informatik.uni-tuebingen.de" target="_blank">http://www-bs.informatik.uni-tuebingen.de</a> </pre>
<pre> </pre>
<pre>vCard at: <a moz-do-not-send="true"
href="http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard"
target="_blank">http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard</a></pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre> </pre>
<pre>------------------------------------------------------------------------------</pre>
<pre>Beautiful is writing same markup. Internet Explorer 9 supports</pre>
<pre>standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.</pre>
<pre>Spend less time writing and rewriting code and more time creating great</pre>
<pre>experiences on the web. Be a part of the beta today.</pre>
<pre><a moz-do-not-send="true"
href="http://p.sf.net/sfu/beautyoftheweb" target="_blank">http://p.sf.net/sfu/beautyoftheweb</a></pre>
<pre>_______________________________________________</pre>
<pre>Psidev-ms-dev mailing list</pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev"
target="_blank">https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev</a></pre>
<p class="MsoNormal" style="margin-bottom: 12pt;"> </p>
<div>
<p class="MsoNormal">-- </p>
<p class="MsoNormal" style="text-align: center;" align="center">-------------------------------------------------------------------------------------------------------<br>
<b>Henk van den Toorn, bioinformatician</b><br>
<span style="font-size: 11pt; color: rgb(16, 16, 221);">Biomolecular
Mass Spectrometry and
Proteomics Group</span><br>
Bijvoet Center for Biomolecular Research and<br>
Utrecht Institute for Pharmaceutical Sciences<br>
Utrecht University<br>
Padualaan, 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
<br>
E-mail: <a moz-do-not-send="true" href="mailto:h.w...@uu...">h.w...@uu...</a><br>
Tel: +31 30 253 6758<br>
Fax: +31 30 253 6919<br>
--------------------------------------------------------------------------------------------------</p>
</div>
</div>
</div>
</div>
<pre wrap="">
<hr size="4" width="90%">
------------------------------------------------------------------------------
Beautiful is writing same markup. Internet Explorer 9 supports
standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3.
Spend less time writing and rewriting code and more time creating great
experiences on the web. Be a part of the beta today.
<a class="moz-txt-link-freetext" href="http://p.sf.net/sfu/beautyoftheweb">http://p.sf.net/sfu/beautyoftheweb</a></pre>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
Psidev-pi-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>
Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
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From: Jones, A. <And...@li...> - 2010-10-14 10:53:55
|
Hi all, Seems difficult to find a slot :) Doodle poll created, can you complete with availability: http://www.doodle.com/nqe59tnb7bmzce7q Cheers Andy From: David Creasy [mailto:dc...@ma...] Sent: 14 October 2010 10:11 To: psi...@li... Cc: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration I'll be away then, so it's unlikely that I'll be able to make it. But please go ahead without me - I think that my views and Andy's views are pretty similar. David Eric Deutsch wrote: Not as convenient for me, but it will be fine, yes. From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>] Sent: Wednesday, October 13, 2010 7:43 AM To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration 28/10 would also be okay with me, anyone else? cheers Andy ________________________________ From: Henk van den Toorn [h.w...@uu...<mailto:h.w...@uu...>] Sent: 13 October 2010 15:28 To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu...] Sent: 01 October 2010 16:44 To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...> Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb_______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- Henk van den Toorn, bioinformatician Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu...<mailto:h.w...@uu...> Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- ________________________________ ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ________________________________ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma...<mailto:dc...@ma...> http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Jones, A. <And...@li...> - 2010-10-19 13:00:24
|
Hi all, It looks like 28th Oct at 4pm UK time (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136) is the best slot for most people, so let’s go with that. Juan, would you be able to find someone else to start the call for us, using the EBI line? I’ll send round an agenda for discussion early next week, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 14 October 2010 11:54 To: 'Mass spectrometry standard development'; 'psi...@li...' Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Hi all, Seems difficult to find a slot :) Doodle poll created, can you complete with availability: http://www.doodle.com/nqe59tnb7bmzce7q Cheers Andy From: David Creasy [mailto:dc...@ma...] Sent: 14 October 2010 10:11 To: psi...@li... Cc: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration I'll be away then, so it's unlikely that I'll be able to make it. But please go ahead without me - I think that my views and Andy's views are pretty similar. David Eric Deutsch wrote: Not as convenient for me, but it will be fine, yes. From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>] Sent: Wednesday, October 13, 2010 7:43 AM To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration 28/10 would also be okay with me, anyone else? cheers Andy ________________________________ From: Henk van den Toorn [h.w...@uu...<mailto:h.w...@uu...>] Sent: 13 October 2010 15:28 To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu...] Sent: 01 October 2010 16:44 To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...> Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb_______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- Henk van den Toorn, bioinformatician Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu...<mailto:h.w...@uu...> Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- ________________________________ ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ________________________________ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma...<mailto:dc...@ma...> http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Florian <fl...@eb...> - 2010-10-19 13:13:57
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Hi Andy, I am sure we will find someone here at the EBI to start the phone conf. Either Richard or myself should be around to do this. Cheers, Florian On 19/10/2010 14:00, Jones, Andy wrote: > Hi all, > > It looks like 28^th Oct at 4pm UK time > (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136 > <http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136>) > is the best slot for most people, so let’s go with that. > > Juan, would you be able to find someone else to start the call for us, > using the EBI line? I’ll send round an agenda for discussion early next > week, > > Best wishes > > Andy > > *From:* Jones, Andy [mailto:And...@li...] > *Sent:* 14 October 2010 11:54 > *To:* 'Mass spectrometry standard development'; > 'psi...@li...' > *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on > mzQuantML consideration > > Hi all, > > Seems difficult to find a slot J Doodle poll created, can you complete > with availability: http://www.doodle.com/nqe59tnb7bmzce7q > > Cheers > > Andy > > *From:* David Creasy [mailto:dc...@ma...] > *Sent:* 14 October 2010 10:11 > *To:* psi...@li... > *Cc:* Mass spectrometry standard development > *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on > mzQuantML consideration > > I'll be away then, so it's unlikely that I'll be able to make it. But > please go ahead without me - I think that my views and Andy's views are > pretty similar. > > David > > Eric Deutsch wrote: > > Not as convenient for me, but it will be fine, yes. > > *From:* Jones, Andy [mailto:And...@li... > <mailto:And...@li...>] > *Sent:* Wednesday, October 13, 2010 7:43 AM > *To:* Mass spectrometry standard development; > psi...@li... > <mailto:psi...@li...> > *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on > mzQuantML consideration > > 28/10 would also be okay with me, anyone else? > > cheers > > Andy > > ------------------------------------------------------------------------ > > *From:* Henk van den Toorn [h.w...@uu... > <mailto:h.w...@uu...>] > *Sent:* 13 October 2010 15:28 > *To:* Mass spectrometry standard development > *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on > mzQuantML consideration > > Fine by us, Henk & Pieter > > On 12-10-2010 19:08, Oliver Kohlbacher wrote: > > Dear all, > > > > not good for me -- I will be on a plane during that time. > > How about one week later, 10/28 same time? > > > > Cheers, > > Oliver > > > > On 12.10.2010, at 15:33, Jones, Andy wrote: > > > > Hi all, > > > > There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. > > > > How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, > > Cheers > > Andy > > > > > > > > > > > > > > From: Henk van den Toorn [mailto:h.w...@uu...] > > Sent: 01 October 2010 16:44 > > To:psi...@li... <mailto:psi...@li...>;mbr...@sy... <mailto:mbr...@sy...> > > Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration > > > > Hello all, > > > > Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. > > > > ----------- > > > > > > Dear PSI mzQuantML discussion participants, > > > > Background of APML > > Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. > > > > mzQuantML that Oliver is leading. > > Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. > > > > Essential elements in the schema > > To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. > > > > Thank you for reading. > > > > Warm Regards, > > Mi-Youn > > > > Mi-Youn Brusniak, Ph.D. > > Computational Biology > > Seattle Proteome Center > > mbr...@sy... <mailto:mbr...@sy...> > > Tel: (206)732-1327 > > > > > > Mi-Youn Brusniak, Ph.D. > > Computational Biology > > Seattle Proteome Center > > mbr...@sy... <mailto:mbr...@sy...> > > Tel: (206)732-1327 > > ------------------------------------------------------------------------------ > > Beautiful is writing same markup. Internet Explorer 9 supports > > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > > Spend less time writing and rewriting code and more time creating great > > experiences on the web. Be a part of the beta today. > > http://p.sf.net/sfu/beautyoftheweb_______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > --- > > Oliver Kohlbacher (oli...@un... <mailto:oli...@un...>) > > Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen > > phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de > > > > vCard at:http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > > Beautiful is writing same markup. Internet Explorer 9 supports > > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > > Spend less time writing and rewriting code and more time creating great > > experiences on the web. Be a part of the beta today. > > http://p.sf.net/sfu/beautyoftheweb > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > -- > > ------------------------------------------------------------------------------------------------------- > *Henk van den Toorn, bioinformatician* > Biomolecular Mass Spectrometry and Proteomics Group > Bijvoet Center for Biomolecular Research and > Utrecht Institute for Pharmaceutical Sciences > Utrecht University > Padualaan, 8 > 3584 CH Utrecht > The Netherlands > > E-mail: h.w...@uu... <mailto:h.w...@uu...> > Tel: +31 30 253 6758 > Fax: +31 30 253 6919 > -------------------------------------------------------------------------------------------------- > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > ------------------------------------------------------------------------------ > > Beautiful is writing same markup. Internet Explorer 9 supports > > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > > Spend less time writing and rewriting code and more time creating great > > experiences on the web. Be a part of the beta today. > > http://p.sf.net/sfu/beautyoftheweb > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > -- > > David Creasy > > Matrix Science > > 64 Baker Street > > London W1U 7GB, UK > > Tel: +44 (0)20 7486 1050 > > Fax: +44 (0)20 7224 1344 > > > > dc...@ma... <mailto:dc...@ma...> > > http://www.matrixscience.com > > > > Matrix Science Ltd. is registered in England and Wales > > Company number 3533898 > > > > ------------------------------------------------------------------------------ > Download new Adobe(R) Flash(R) Builder(TM) 4 > The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly > Flex(R) Builder(TM)) enable the development of rich applications that run > across multiple browsers and platforms. Download your free trials today! > http://p.sf.net/sfu/adobe-dev2dev > > > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Jones, A. <And...@li...> - 2010-10-25 10:29:01
|
Hi all, Just to confirm, we will have a conference call this Thurs at 4pm UK time: http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136 Agenda: 1. Scope and remit for mzQuantML (i.e. for first release features in or out) 2. Review current examples in the googlecode: http://code.google.com/p/mzquantml/ 3. Short discussion about status of mzIdentML (paper and implementations) 4. Plan for future development and calls 5. AOB Let me know if you’d like to add anything to the agenda. Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 Florian / Juan, I hope the call details are still correct, let me know if anything has changed. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 19 October 2010 14:00 To: 'Mass spectrometry standard development'; 'psi...@li...' Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Hi all, It looks like 28th Oct at 4pm UK time (http://www.timeanddate.com/worldclock/fixedtime.html?day=25&month=10&year=2010&hour=16&min=0&sec=0&p1=136) is the best slot for most people, so let’s go with that. Juan, would you be able to find someone else to start the call for us, using the EBI line? I’ll send round an agenda for discussion early next week, Best wishes Andy From: Jones, Andy [mailto:And...@li...] Sent: 14 October 2010 11:54 To: 'Mass spectrometry standard development'; 'psi...@li...' Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Hi all, Seems difficult to find a slot :) Doodle poll created, can you complete with availability: http://www.doodle.com/nqe59tnb7bmzce7q Cheers Andy From: David Creasy [mailto:dc...@ma...] Sent: 14 October 2010 10:11 To: psi...@li... Cc: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration I'll be away then, so it's unlikely that I'll be able to make it. But please go ahead without me - I think that my views and Andy's views are pretty similar. David Eric Deutsch wrote: Not as convenient for me, but it will be fine, yes. From: Jones, Andy [mailto:And...@li...<mailto:And...@li...>] Sent: Wednesday, October 13, 2010 7:43 AM To: Mass spectrometry standard development; psi...@li...<mailto:psi...@li...> Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration 28/10 would also be okay with me, anyone else? cheers Andy ________________________________ From: Henk van den Toorn [h.w...@uu...<mailto:h.w...@uu...>] Sent: 13 October 2010 15:28 To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu...] Sent: 01 October 2010 16:44 To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...> Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb_______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- Henk van den Toorn, bioinformatician Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu...<mailto:h.w...@uu...> Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- ________________________________ ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb ________________________________ _______________________________________________ Psidev-pi-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma...<mailto:dc...@ma...> http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Henk v. d. T. <h.w...@uu...> - 2010-10-12 14:42:06
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Hi Andy, That's a good idea, and the time is fine for us! Pieter and Henk On 12-10-2010 15:33, Jones, Andy wrote: > > Hi all, > > There has been some interesting discussions on the scope of mzQuantML > and some work been done on use cases fulfilling the first draft we > built after the Sept development meeting. I’d like to arrange a > conference call to discuss the main issues. It appears that the most > convenient time for people in different locations is usually 4pm UK > time. I would like to take on board as many opinions as possible so > let’s try find a time that is suitable for most people. > > How would Thurs 21^st Oct at 4pm UK (8am West coast, 11am East Coast) > suit people? If not please suggest some alternatives, > > Cheers > > Andy > > *From:* Henk van den Toorn [mailto:h.w...@uu...] > *Sent:* 01 October 2010 16:44 > *To:* psi...@li...; mbr...@sy... > *Subject:* [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on > mzQuantML consideration > > Hello all, > > Sorry for cross-forwarding (is that a word?), but I noticed this > message was sent to the ms-dev mailinglist while I guess it should > have gone to the mzQuantML (psidev-pi) mailing list. > > ----------- > > > Dear PSI mzQuantML discussion participants, > > Background of APML > > Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in > 2008 with APML (Annotated Putative peptide Markup Language) that > enables using several different ms1 peak extraction and alignment > modules. After publication, Damon May, who is a lead developer on > MSInspect from Fred Hutchinson Cancer Research Center, initiated to > use APML for broader use for MsInspect and LabKey as well as Parag > Mallick group in Los Angeles. After review and merging all > institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 > schema and java written parsers > (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch > introduced APML v2.0 to PSI in 2008. > > mzQuantML that Oliver is leading. > > Recent my visit to Oliver Kohlbacher group in University of Tubingen > and meeting with Peter Horvatovich from University of Groningen in > HUPO Sydney, The mzQuantML schema and availability of its parser and > validator can be an important contribution to bioinformatician and > computational biologists, who develop or process MS1 based dataset for > biological system studies. > > Essential elements in the schema > > To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) > are using APML v2.0, it would be nice (or rather essential) to have > some of elements that can capture essential dataset to reproduce or > reprocessing (e.g., statistical analysis on quantification etc). Thus, > without further explanation, I have absolute agreement on Dr. > Kohlbacher comments on “complexity is expected” posted on Sep 13 to > this mailing list. The “feature” element is an absolute “must” for > MS1 based pipeline. In my experience and perspective of continuous > usage of Corra for several biomarker discovery projects, we need the > feature element for mzQuantML and it will help for broad future > mzQuantML schema in proteomics community. > > Thank you for reading. > > Warm Regards, > > Mi-Youn > > Mi-Youn Brusniak, Ph.D. > > Computational Biology > > Seattle Proteome Center > > mbr...@sy... <mailto:mbr...@sy...> > > Tel: (206)732-1327 > > Mi-Youn Brusniak, Ph.D. > > Computational Biology > > Seattle Proteome Center > > mbr...@sy... <mailto:mbr...@sy...> > > Tel: (206)732-1327 > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2& L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > > > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- *Henk van den Toorn, bioinformatician* Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu... Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
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From: Oliver K. <oli...@un...> - 2010-10-12 17:09:05
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Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: > Hi all, > > There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. > > How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, > Cheers > Andy > > > > > > > From: Henk van den Toorn [mailto:h.w...@uu...] > Sent: 01 October 2010 16:44 > To: psi...@li...; mbr...@sy... > Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration > > Hello all, > > Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. > > ----------- > > > Dear PSI mzQuantML discussion participants, > > Background of APML > Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. > > mzQuantML that Oliver is leading. > Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. > > Essential elements in the schema > To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. > > Thank you for reading. > > Warm Regards, > Mi-Youn > > Mi-Youn Brusniak, Ph.D. > Computational Biology > Seattle Proteome Center > mbr...@sy... > Tel: (206)732-1327 > > > Mi-Youn Brusniak, Ph.D. > Computational Biology > Seattle Proteome Center > mbr...@sy... > Tel: (206)732-1327 > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb_______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard |
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From: Eric D. <ede...@sy...> - 2010-10-13 16:53:57
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Not as convenient for me, but it will be fine, yes. *From:* Jones, Andy [mailto:And...@li...] *Sent:* Wednesday, October 13, 2010 7:43 AM *To:* Mass spectrometry standard development; psi...@li... *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration 28/10 would also be okay with me, anyone else? cheers Andy ------------------------------ *From:* Henk van den Toorn [h.w...@uu...] *Sent:* 13 October 2010 15:28 *To:* Mass spectrometry standard development *Subject:* Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu... <h.w...@uu...>] Sent: 01 October 2010 16:44 To: psi...@li...; mbr...@sy... Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy... Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy... Tel: (206)732-1327 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb_______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- *Henk van den Toorn, bioinformatician* Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu... Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
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From: Jones, A. <And...@li...> - 2010-10-13 14:43:50
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28/10 would also be okay with me, anyone else? cheers Andy ________________________________ From: Henk van den Toorn [h.w...@uu...] Sent: 13 October 2010 15:28 To: Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on mzQuantML consideration Fine by us, Henk & Pieter On 12-10-2010 19:08, Oliver Kohlbacher wrote: Dear all, not good for me -- I will be on a plane during that time. How about one week later, 10/28 same time? Cheers, Oliver On 12.10.2010, at 15:33, Jones, Andy wrote: Hi all, There has been some interesting discussions on the scope of mzQuantML and some work been done on use cases fulfilling the first draft we built after the Sept development meeting. I’d like to arrange a conference call to discuss the main issues. It appears that the most convenient time for people in different locations is usually 4pm UK time. I would like to take on board as many opinions as possible so let’s try find a time that is suitable for most people. How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit people? If not please suggest some alternatives, Cheers Andy From: Henk van den Toorn [mailto:h.w...@uu...] Sent: 01 October 2010 16:44 To: psi...@li...<mailto:psi...@li...>; mbr...@sy...<mailto:mbr...@sy...> Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML consideration Hello all, Sorry for cross-forwarding (is that a word?), but I noticed this message was sent to the ms-dev mailinglist while I guess it should have gone to the mzQuantML (psidev-pi) mailing list. ----------- Dear PSI mzQuantML discussion participants, Background of APML Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 with APML (Annotated Putative peptide Markup Language) that enables using several different ms1 peak extraction and alignment modules. After publication, Damon May, who is a lead developer on MSInspect from Fred Hutchinson Cancer Research Center, initiated to use APML for broader use for MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After review and merging all institutions’ needs for capturing MS1 dataset, we introduced APML v2.0 schema and java written parsers (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch introduced APML v2.0 to PSI in 2008. mzQuantML that Oliver is leading. Recent my visit to Oliver Kohlbacher group in University of Tubingen and meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, The mzQuantML schema and availability of its parser and validator can be an important contribution to bioinformatician and computational biologists, who develop or process MS1 based dataset for biological system studies. Essential elements in the schema To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are using APML v2.0, it would be nice (or rather essential) to have some of elements that can capture essential dataset to reproduce or reprocessing (e.g., statistical analysis on quantification etc). Thus, without further explanation, I have absolute agreement on Dr. Kohlbacher comments on “complexity is expected” posted on Sep 13 to this mailing list. The “feature” element is an absolute “must” for MS1 based pipeline. In my experience and perspective of continuous usage of Corra for several biomarker discovery projects, we need the feature element for mzQuantML and it will help for broad future mzQuantML schema in proteomics community. Thank you for reading. Warm Regards, Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy...<mailto:mbr...@sy...> Tel: (206)732-1327 ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb_______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev --- Oliver Kohlbacher (oli...@un...<mailto:oli...@un...>) Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University Tuebingen phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Psidev-ms-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- ------------------------------------------------------------------------------------------------------- Henk van den Toorn, bioinformatician Biomolecular Mass Spectrometry and Proteomics Group Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences Utrecht University Padualaan, 8 3584 CH Utrecht The Netherlands E-mail: h.w...@uu...<mailto:h.w...@uu...> Tel: +31 30 253 6758 Fax: +31 30 253 6919 -------------------------------------------------------------------------------------------------- |
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From: Laurent G. <lg...@ca...> - 2010-10-13 14:50:02
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Fine for me. Laurent 2010/10/13 Jones, Andy <And...@li...>: > 28/10 would also be okay with me, anyone else? > cheers > Andy > ________________________________ > From: Henk van den Toorn [h.w...@uu...] > Sent: 13 October 2010 15:28 > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] [Psidev-pi-dev] Fwd: Essential element on > mzQuantML consideration > > Fine by us, Henk & Pieter > > On 12-10-2010 19:08, Oliver Kohlbacher wrote: > > Dear all, > > not good for me -- I will be on a plane during that time. > How about one week later, 10/28 same time? > > Cheers, > Oliver > > On 12.10.2010, at 15:33, Jones, Andy wrote: > > Hi all, > > There has been some interesting discussions on the scope of mzQuantML and > some work been done on use cases fulfilling the first draft we built after > the Sept development meeting. I’d like to arrange a conference call to > discuss the main issues. It appears that the most convenient time for people > in different locations is usually 4pm UK time. I would like to take on board > as many opinions as possible so let’s try find a time that is suitable for > most people. > > How would Thurs 21st Oct at 4pm UK (8am West coast, 11am East Coast) suit > people? If not please suggest some alternatives, > Cheers > Andy > > > > > > > From: Henk van den Toorn [mailto:h.w...@uu...] > Sent: 01 October 2010 16:44 > To: psi...@li...; mbr...@sy... > Subject: [Psidev-pi-dev] Fwd: [Psidev-ms-dev] Essential element on mzQuantML > consideration > > Hello all, > > Sorry for cross-forwarding (is that a word?), but I noticed this message was > sent to the ms-dev mailinglist while I guess it should have gone to the > mzQuantML (psidev-pi) mailing list. > > ----------- > > > Dear PSI mzQuantML discussion participants, > > Background of APML > Corra (http://www.biomedcentral.com/1471-2105/9/542) is published in 2008 > with APML (Annotated Putative peptide Markup Language) that enables using > several different ms1 peak extraction and alignment modules. After > publication, Damon May, who is a lead developer on MSInspect from Fred > Hutchinson Cancer Research Center, initiated to use APML for broader use for > MsInspect and LabKey as well as Parag Mallick group in Los Angeles. After > review and merging all institutions’ needs for capturing MS1 dataset, we > introduced APML v2.0 schema and java written parsers > (http://sourceforge.net/projects/corra/files/ ) . Then Eric Deutsch > introduced APML v2.0 to PSI in 2008. > > mzQuantML that Oliver is leading. > Recent my visit to Oliver Kohlbacher group in University of Tubingen and > meeting with Peter Horvatovich from University of Groningen in HUPO Sydney, > The mzQuantML schema and availability of its parser and validator can be an > important contribution to bioinformatician and computational biologists, who > develop or process MS1 based dataset for biological system studies. > > Essential elements in the schema > To the best of my knowledge, we (ISB, FHCRC, Labkey, Peter’s group) are > using APML v2.0, it would be nice (or rather essential) to have some of > elements that can capture essential dataset to reproduce or reprocessing > (e.g., statistical analysis on quantification etc). Thus, without further > explanation, I have absolute agreement on Dr. Kohlbacher comments on > “complexity is expected” posted on Sep 13 to this mailing list. The > “feature” element is an absolute “must” for MS1 based pipeline. In my > experience and perspective of continuous usage of Corra for several > biomarker discovery projects, we need the feature element for mzQuantML and > it will help for broad future mzQuantML schema in proteomics community. > > Thank you for reading. > > Warm Regards, > Mi-Youn > > Mi-Youn Brusniak, Ph.D. > Computational Biology > Seattle Proteome Center > mbr...@sy... > Tel: (206)732-1327 > > > Mi-Youn Brusniak, Ph.D. > Computational Biology > Seattle Proteome Center > mbr...@sy... > Tel: (206)732-1327 > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb_______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > --- > Oliver Kohlbacher (oli...@un...) > Professor, Center for Bioinformatics Tuebingen, Eberhard Karls University > Tuebingen > phone: +49-7071-29-70457 http://www-bs.informatik.uni-tuebingen.de > > vCard at: http://www-bs.informatik.uni-tuebingen.de/People/kohlbach/vCard > > > > > > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > -- > ------------------------------------------------------------------------------------------------------- > Henk van den Toorn, bioinformatician > Biomolecular Mass Spectrometry and Proteomics Group > Bijvoet Center for Biomolecular Research and > Utrecht Institute for Pharmaceutical Sciences > Utrecht University > Padualaan, 8 > 3584 CH Utrecht > The Netherlands > > E-mail: h.w...@uu... > Tel: +31 30 253 6758 > Fax: +31 30 253 6919 > -------------------------------------------------------------------------------------------------- > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > -- Laurent Gatto Cambridge Centre For Proteomics http://www.bio.cam.ac.uk/proteomics |
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