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From: Lennart M. <len...@gm...> - 2016-06-28 08:00:38
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Hello, Excellent abstract! And thanks for keeping everything moving along so nicely! Cheers, lnnrt. On 28/06/2016 09:37, Mathias Walzer wrote: > Hi All, > > Do we really have 3000 words? Sounds quite humongous. > Anyways, I added my thoughts to Stefans edit. > In short, I think PSI formats as a mediator between tools and putting the stored metrics into context to help interpretation (CV) also deserves a mention. > > So since our nice meeting in Ghent, the format or better say the WG repository has changed a bit. > As a reminder you find it here: https://github.com/HUPO-PSI/qcML-development. > Repo structure is now cv and schema on top level, development on the format reflecting the metrics will go into schema and qc metric collection, definitions and descriptions go in cv. Previous developments went into legacy. > > I reflected most of the discussions from Ghent into the schema 0_9 and added an example > https://github.com/HUPO-PSI/qcML-development/tree/master/schema/v0_0_9 > Clearly, this will need some testing and some adjustments after that. > > I integrated the collection of metrics we made at the meeting into the repository under cv and sketched a way to structure these within github to ease accessibility. Please view this as only a first iteration of how we will represent the metrics and accompanied data in the repository. > Please see the readme.md for further info. > > best, > mths > > ----- Original Message ----- > From: "Stefan Tenzer" <te...@un...> > To: "Mathias Walzer" <wa...@in...> > Cc: psi...@li... > Sent: Monday, 27 June, 2016 8:58:23 PM > Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei > > Hi Matthias, > > indeed, I got a message saying that I exceeded the size limit of 40 kb. > Best wishes, > > Stefan > > > > > Am 27.06.2016 um 20:54 schrieb Mathias Walzer <wa...@in...>: > >> Hi all, >> >> Stefans mail was caught up in the sourceforge mailinglist filter, although he was already a list-member. >> Not sure as of now, what the cause was, my guess is, that the max. attachment size was exceeded. Also not sure about the sourceforge administration interface functions, but I think I fixed the issue if file size was the issue. >> >> To speed up/build in redundancy to the administration of the list, I would suggest to add more members of the leadership roster. Would you please supply me with your sourceforge account name (, if available,) so I can add you to the list administrators? (Obviously, only those with a sourceforge account registered can do that.) >> >> best, >> mths >> >> ----- Original Message ----- >> From: "Stefan Tenzer" <te...@un...> >> To: "David Tabb, Prof <dt...@su...>" <dt...@su...> >> Cc: psi...@li... >> Sent: Monday, 27 June, 2016 2:57:19 PM >> Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei >> >> >> Dear David, >> >> >> thanks for the updated version - great work! >> I would like to suggest a few minor edits (see attached) >> >> >> Best, >> >> >> Stefan >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> >> ------------------------------------------------------------------------------ >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> >> >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Mathias W. <wa...@in...> - 2016-06-28 07:38:17
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Hi All, Do we really have 3000 words? Sounds quite humongous. Anyways, I added my thoughts to Stefans edit. In short, I think PSI formats as a mediator between tools and putting the stored metrics into context to help interpretation (CV) also deserves a mention. So since our nice meeting in Ghent, the format or better say the WG repository has changed a bit. As a reminder you find it here: https://github.com/HUPO-PSI/qcML-development. Repo structure is now cv and schema on top level, development on the format reflecting the metrics will go into schema and qc metric collection, definitions and descriptions go in cv. Previous developments went into legacy. I reflected most of the discussions from Ghent into the schema 0_9 and added an example https://github.com/HUPO-PSI/qcML-development/tree/master/schema/v0_0_9 Clearly, this will need some testing and some adjustments after that. I integrated the collection of metrics we made at the meeting into the repository under cv and sketched a way to structure these within github to ease accessibility. Please view this as only a first iteration of how we will represent the metrics and accompanied data in the repository. Please see the readme.md for further info. best, mths ----- Original Message ----- From: "Stefan Tenzer" <te...@un...> To: "Mathias Walzer" <wa...@in...> Cc: psi...@li... Sent: Monday, 27 June, 2016 8:58:23 PM Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei Hi Matthias, indeed, I got a message saying that I exceeded the size limit of 40 kb. Best wishes, Stefan Am 27.06.2016 um 20:54 schrieb Mathias Walzer <wa...@in...>: > Hi all, > > Stefans mail was caught up in the sourceforge mailinglist filter, although he was already a list-member. > Not sure as of now, what the cause was, my guess is, that the max. attachment size was exceeded. Also not sure about the sourceforge administration interface functions, but I think I fixed the issue if file size was the issue. > > To speed up/build in redundancy to the administration of the list, I would suggest to add more members of the leadership roster. Would you please supply me with your sourceforge account name (, if available,) so I can add you to the list administrators? (Obviously, only those with a sourceforge account registered can do that.) > > best, > mths > > ----- Original Message ----- > From: "Stefan Tenzer" <te...@un...> > To: "David Tabb, Prof <dt...@su...>" <dt...@su...> > Cc: psi...@li... > Sent: Monday, 27 June, 2016 2:57:19 PM > Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei > > > Dear David, > > > thanks for the updated version - great work! > I would like to suggest a few minor edits (see attached) > > > Best, > > > Stefan > > > > > > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Tenzer, S. <te...@un...> - 2016-06-27 18:58:32
|
Hi Matthias, indeed, I got a message saying that I exceeded the size limit of 40 kb. Best wishes, Stefan Am 27.06.2016 um 20:54 schrieb Mathias Walzer <wa...@in...>: > Hi all, > > Stefans mail was caught up in the sourceforge mailinglist filter, although he was already a list-member. > Not sure as of now, what the cause was, my guess is, that the max. attachment size was exceeded. Also not sure about the sourceforge administration interface functions, but I think I fixed the issue if file size was the issue. > > To speed up/build in redundancy to the administration of the list, I would suggest to add more members of the leadership roster. Would you please supply me with your sourceforge account name (, if available,) so I can add you to the list administrators? (Obviously, only those with a sourceforge account registered can do that.) > > best, > mths > > ----- Original Message ----- > From: "Stefan Tenzer" <te...@un...> > To: "David Tabb, Prof <dt...@su...>" <dt...@su...> > Cc: psi...@li... > Sent: Monday, 27 June, 2016 2:57:19 PM > Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei > > > Dear David, > > > thanks for the updated version - great work! > I would like to suggest a few minor edits (see attached) > > > Best, > > > Stefan > > > > > > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Mathias W. <wa...@in...> - 2016-06-27 18:54:25
|
Hi all, Stefans mail was caught up in the sourceforge mailinglist filter, although he was already a list-member. Not sure as of now, what the cause was, my guess is, that the max. attachment size was exceeded. Also not sure about the sourceforge administration interface functions, but I think I fixed the issue if file size was the issue. To speed up/build in redundancy to the administration of the list, I would suggest to add more members of the leadership roster. Would you please supply me with your sourceforge account name (, if available,) so I can add you to the list administrators? (Obviously, only those with a sourceforge account registered can do that.) best, mths ----- Original Message ----- From: "Stefan Tenzer" <te...@un...> To: "David Tabb, Prof <dt...@su...>" <dt...@su...> Cc: psi...@li... Sent: Monday, 27 June, 2016 2:57:19 PM Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei Dear David, thanks for the updated version - great work! I would like to suggest a few minor edits (see attached) Best, Stefan ------------------------------------------------------------------------------ Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape _______________________________________________ Psidev-qc-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Tenzer, S. <te...@un...> - 2016-06-27 13:32:43
|
<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><div apple-content-edited="true"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"></div> </div> <br><div><div>Am 27.06.2016 um 14:36 schrieb Tabb, David, Prof <<a href="mailto:dt...@su...">dt...@su...</a>> <<a href="mailto:dt...@su...">dt...@su...</a>>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-ZA" link="#0563C1" vlink="#954F72" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div class="WordSection1" style="page: WordSection1;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Hi, all.<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Helpfully, the HUPO 2016 abstract deadline was pushed back to June 30<sup>th</sup>! We have three days to finalize the abstract Ill submit. I am attaching the current draft, which incorporates Rezas feedback (and includes a conclusion and keywords).<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Does anyone have comments on this before I submit it?<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">This is my current understanding of our leadership roster. If there are no further comments, Ill add these to the charter and send it to the execs:<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Chair: David Tabb<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Co-Chair / Website Coordinator: Mathias Walzer<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Co-Chair / Editor: Stefan Tenzer<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Minimum Reporting Requirements: Weimin Zhu and Reza Salek<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Ontology: Martin Eisenacher<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Secretary: Wout Bittremieux<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Weimin, I saw your thoughts about building a database for storage of qcML objects. I like that idea; it ties into the iMonDB work from the Valkenborg group (<a href="https://bitbucket.org/proteinspector/imondb/wiki/Home" style="color: rgb(149, 79, 114); text-decoration: underline;">https://bitbucket.org/proteinspector/imondb/wiki/Home</a>).<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">I am beginning to feel some urgency in getting the announcement whitepaper out (we had said it should go out within three months of the Ghent meeting, which was mid-April). I will try to get some time on that draft shortly. I have been working on a grant to cover qcML activities from an FWO-NRF joint funding program between Belgium and South Africa. Separately, that program has approved funds for Secretary Wout Bittremieux to train down here in South Africa with my group for three months!<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Mathias, could you tell us a bit about the evolution of qcML since the meeting?<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Thanks,<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);">Dave<o:p></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><a name="_MailEndCompose"><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);"> </span></a></div><div><div style="border-style: solid none none; border-top-color: rgb(225, 225, 225); border-top-width: 1pt; padding: 3pt 0cm 0cm;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;"><span class="Apple-converted-space"> </span>Reza Salek [<a href="mailto:rez...@eb..." style="color: rgb(149, 79, 114); text-decoration: underline;">mailto:rez...@eb...</a>]<span class="Apple-converted-space"> </span><br><b>Sent:</b><span class="Apple-converted-space"> </span>Wednesday, 25 May 2016 14:26<br><b>To:</b><span class="Apple-converted-space"> </span>Tabb, David, Prof <<a href="mailto:dt...@su..." style="color: rgb(149, 79, 114); text-decoration: underline;">dt...@su...</a>><br><b>Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:psi...@li..." style="color: rgb(149, 79, 114); text-decoration: underline;">psi...@li...</a><br><b>Subject:</b><span class="Apple-converted-space"> </span>Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei<o:p></o:p></span></div></div></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Hi David,<o:p></o:p></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Some minor edits, with my metabolomics hat on, reads well.<o:p></o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Best Wishes, <o:p></o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Reza<o:p></o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;"><o:p> </o:p></div></div></div></div><span><20160525-HUPO-qcML-abstract.docx></span>------------------------------------------------------------------------------<br>Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San<br>Francisco, CA to explore cutting-edge tech and listen to tech luminaries<br>present their vision of the future. This family event has something for<br>everyone, including kids. Get more information and register today.<br><a href="http://sdm.link/attshape_______________________________________________" style="color: rgb(149, 79, 114); text-decoration: underline;">http://sdm.link/attshape_______________________________________________</a><br>Psidev-qc-dev mailing list<br><a href="mailto:Psi...@li..." style="color: rgb(149, 79, 114); text-decoration: underline;">Psi...@li...</a><br><a href="https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev" style="color: rgb(149, 79, 114); text-decoration: underline;">https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev</a></div></blockquote></div><br></div></body></html> |
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From: Tabb, D. P. <dt...@su...> - 2016-06-27 12:49:22
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Hi, all. Helpfully, the HUPO 2016 abstract deadline was pushed back to June 30th! We have three days to finalize the abstract I'll submit. I am attaching the current draft, which incorporates Reza's feedback (and includes a conclusion and keywords). Does anyone have comments on this before I submit it? This is my current understanding of our leadership roster. If there are no further comments, I'll add these to the charter and send it to the execs: Chair: David Tabb Co-Chair / Website Coordinator: Mathias Walzer Co-Chair / Editor: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu and Reza Salek Ontology: Martin Eisenacher Secretary: Wout Bittremieux Weimin, I saw your thoughts about building a database for storage of qcML objects. I like that idea; it ties into the iMonDB work from the Valkenborg group (https://bitbucket.org/proteinspector/imondb/wiki/Home). I am beginning to feel some urgency in getting the announcement whitepaper out (we had said it should go out within three months of the Ghent meeting, which was mid-April). I will try to get some time on that draft shortly. I have been working on a grant to cover qcML activities from an FWO-NRF joint funding program between Belgium and South Africa. Separately, that program has approved funds for Secretary Wout Bittremieux to train down here in South Africa with my group for three months! Mathias, could you tell us a bit about the evolution of qcML since the meeting? Thanks, Dave From: Reza Salek [mailto:rez...@eb...] Sent: Wednesday, 25 May 2016 14:26 To: Tabb, David, Prof <dt...@su...> Cc: psi...@li... Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei Hi David, Some minor edits, with my metabolomics hat on, reads well. Best Wishes, Reza |
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From: weimin z. <wmz...@gm...> - 2016-05-27 10:18:30
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sorry, I missed this email thread. to re-phrase my commitment: yes, I confirm to take the role in miape-like qc document. any solid timeline to have the first version to roll out? - weimin On Fri, May 27, 2016 at 5:54 PM, Martin Eisenacher <mar...@ru... > wrote: > Hi! > > > > I can do the Ontology Coord., > > if we come to the conclusion that it fits into the current PSI-MS/-PI > ontology, Gerhard should be the executive. > > > > Bye from Bochum > > Martin > > > > > > *--* > > *PD DR. MARTIN EISENACHER* > > *Department Leader* > > *DEPARTMENT Medical Bioinformatics* > > *Medizinisches Proteom-Center* > > *Ruhr-University Bochum* > > *Building *ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum > > *Fon *+49 (0)234 32-29288 | *Fax *+49 (0)234 32-14554 > > *E-mail *mar...@ru... > > www.medizinisches-proteom-center.de > > > > [image: > http://www.ruhr-uni-bochum.de/cd/extern/logo/Logo_RUB_BLAU_srgb.jpg] > > > > ANNOUNCEMENT de.NBI summer school September 2016: > > *Analysis of Mass-Spectrometric Data - * > > *Big Data Bioinformatics in Proteomics and Metabolomics* > > http://www.denbi.de/index.php/11-training-cat/95-lss2016 > > > > > > > > *Von:* Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] > *Gesendet:* Mittwoch, 18. Mai 2016 14:18 > *An:* psi...@li... > *Betreff:* Re: [Psidev-qc-dev] Organizational roundup > > > > Hi, folks. > > > > I would like some feedback on this slate so that we can finalize our > charter before I leave for the United States next Tuesday. If you would > like to completely alter the associations of names with positions, that’s > absolutely fine. I do want some feedback before I tell HUPO this is what > we’re going to try, though. > > > > I would really value some emails such as, “yes, I am willing to fill that > role” or “no, that doesn’t sound like a good role for me.” > > > > Thank you! > > Dave > > > > *From:* Tabb, David, Prof <dt...@su...> [mailto:dt...@su... > <dt...@su...>] > *Sent:* Friday, 06 May 2016 08:35 > *To:* psi...@li... > *Subject:* [Psidev-qc-dev] Organizational roundup > > > > Hello, all! > > > > I am thrilled to have worked with you all at Ghent on April 19th! It is > very refreshing to work with a group so willing to contribute to this new > effort. > > > > For a first goal, I would like to nominate some roles for the core group > of individuals who volunteered at the meeting. I am using roles borrowed > from this grid: http://www.psidev.info/roles. > > > > Chair: David Tabb > > Website/Co-Chair: Mathias Walzer > > Editor/Co-Chair: Stefan Tenzer > > Minimum Reporting Requirements: Weimin Zhu > > Ontology: Martin Eisenacher > > Secretary: Wout Bittremieux > > > > My rationale looks like this: > > We range considerably in our experience as researchers. I understand that > senior folks are going to have deeply split attention (my slow reply after > Ghent reflects one example; I was teaching a solo four-day blitz in > bioinformatics to the Honours students down here). I know that we must > have the enthusiasm and energy of the younger folks to drive this project > to 1.0. I propose myself as chair because I value time very deeply, and I > intend to keep our meetings on-point and short! J > > > > I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I > appreciate his establishing the GitHub site so rapidly. His initial > development of the draft format is an impressive beginning upon which we > can build. I think he will be an able co-chair. Given his attention to > GitHub, I think he will be well-placed to ensure our group is > well-represented on the HUPO-PSI website. > > > > Stefan Tenzer has volunteered to co-chair, and I appreciated the > contributions he was able to make in the morning of our session. I think > he will be a solid member of the team. I have also volunteered him as the > editor for our team, which is a role that may require considerable effort > since it involves document process management ( > http://www.psidev.info/groups/psi-editors). > > > > Weimin Zhu has plenty of valuable experience from the mzData effort, and I > think he would have good thoughts on which aspects of quality reporting are > essential to a minimal report. > > > > Martin Eisenacher seems to have highly relevant experience in format > specificiation and ontology management. If he is willing to serve as our > Ontology lead, we will be fortunate! > > > > Wout Bittremieux has already made great contributions to the software > library aspect of the qcML format. I hope he will be willing to work on > our meeting reports (and assist in the construction of our various > manuscripts). > > > > If you would like to request a modified role or propose an altogether > different roster, I would be happy to hear it. I have not been > organizationally involved with HUPO-PSI in the past, so I may not have the > most useful experience for framing such a candidate slate. > > > > Yes, I will attend ASMS in San Antonio, and I think that’s a great > deadline for immediate goals. I would like to knock together an outline > for the perspective/announcement. > > > > Mathias, I liked your idea about sending an invite/announcement to the > other HUPO-PSI groups. > > > > We should start soon on identifying the major use cases for qcML and the > applicability of various metrics to that purpose. I particularly want to > look at experimental types that are currently uncovered by quality metrics > (such as top-down and DIA). > > > > Thank you all for your willingness to take part in this push! > > Dave > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and protocols > are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > |
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From: Martin E. <mar...@ru...> - 2016-05-27 09:54:38
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Hi! I can do the Ontology Coord., if we come to the conclusion that it fits into the current PSI-MS/-PI ontology, Gerhard should be the executive. Bye from Bochum Martin -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Ruhr-University Bochum Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554 E-mail <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de ANNOUNCEMENT de.NBI summer school September 2016: Analysis of Mass-Spectrometric Data - Big Data Bioinformatics in Proteomics and Metabolomics <http://www.denbi.de/index.php/11-training-cat/95-lss2016> http://www.denbi.de/index.php/11-training-cat/95-lss2016 Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] Gesendet: Mittwoch, 18. Mai 2016 14:18 An: psi...@li... Betreff: Re: [Psidev-qc-dev] Organizational roundup Hi, folks. I would like some feedback on this slate so that we can finalize our charter before I leave for the United States next Tuesday. If you would like to completely alter the associations of names with positions, thats absolutely fine. I do want some feedback before I tell HUPO this is what were going to try, though. I would really value some emails such as, yes, I am willing to fill that role or no, that doesnt sound like a good role for me. Thank you! Dave From: Tabb, David, Prof <dt...@su... <mailto:dt...@su...> > [mailto:dt...@su...] Sent: Friday, 06 May 2016 08:35 To: psi...@li... <mailto:psi...@li...> Subject: [Psidev-qc-dev] Organizational roundup Hello, all! I am thrilled to have worked with you all at Ghent on April 19th! It is very refreshing to work with a group so willing to contribute to this new effort. For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles. Chair: David Tabb Website/Co-Chair: Mathias Walzer Editor/Co-Chair: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu Ontology: Martin Eisenacher Secretary: Wout Bittremieux My rationale looks like this: We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! J I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management (http://www.psidev.info/groups/psi-editors). Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. Yes, I will attend ASMS in San Antonio, and I think thats a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). Thank you all for your willingness to take part in this push! Dave |
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From: Reza S. <rez...@eb...> - 2016-05-25 12:26:12
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Hi David, Some minor edits, with my metabolomics hat on, reads well. Best Wishes, Reza > On 25 May 2016, at 09:00, David L. Tabb <dav...@va...> wrote: > > Hi, all. I'm boarding. See attached draft > > On 5/25/2016 9:30 AM, David L. Tabb wrote: >> Hello, all! >> >> I have learned that HUPO expects abstracts by today, and we do not yet have a submission in place for the new qcML working group (due to disorganization on my part, primarily). Here's what the format expects: >> >> total max. 3000 characters >> >> Sections: >> title: max 150 characters >> Introduction and Objectives >> Methods >> Results and discussion >> Conclusion >> Keywords >> I am about to board a flight from London to Dallas, having just arrived here from Cape Town, so I am jet-lagged and sleep-deprived. Just the same, I will submit a manuscript once I arrive at Kansas City if nobody else can do it first (I just created an account for myself at the website, actually). Are any of us attending the meeting in Taipei? I hope you will volunteer to present on our behalf, if so! I may be able to combine Taipei with a half-planned trip to Beijing, but that will probably involve some contortions. I don't have a budget handy to attend this meeting. >> >> I also hoped to send out a message to this list summarizing the current status of the leadership roles each of us has filled, but yesterday became pretty messy as I prepared for my departure for an extended visit to the United States. I see that Reza has volunteered to help us with minimal information in the area of metabolomics. Stefan gave a well-considered response to the editor role, saying that he was willing to help us navigate the document process. Wout is happy to serve as secretary. Dirk wrote affirming the need for qcML roles outside shotgun proteomics. Mathias liked the idea of co-chairing and spurring us along with our web resources. I'd still like to see a response from Weimin Zhu and Martin Eisenacher confirming their willingness to take on tasks. >> >> Okay, the lines to board are starting to form. I hope to see amazing things when next I connect to the network! >> Dave >> >> >> ------------------------------------------------------------------------------ >> Mobile security can be enabling, not merely restricting. Employees who >> bring their own devices (BYOD) to work are irked by the imposition of MDM >> restrictions. Mobile Device Manager Plus allows you to control only the >> apps on BYO-devices by containerizing them, leaving personal data untouched! >> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j <https://ad.doubleclick.net/ddm/clk/304595813;131938128;j> >> >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... <mailto:Psi...@li...> >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev <https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev> > > <20160525-HUPO-qcML-abstract.docx>------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: David L. T. <dav...@va...> - 2016-05-25 08:15:24
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Hi, all. I'm boarding. See attached draft On 5/25/2016 9:30 AM, David L. Tabb wrote: > Hello, all! > > I have learned that HUPO expects abstracts by today, and we do not yet > have a submission in place for the new qcML working group (due to > disorganization on my part, primarily). Here's what the format expects: > > total max. 3000 characters > > Sections: > > * title: max 150 characters > * Introduction and Objectives > * Methods > * Results and discussion > * Conclusion > * Keywords > > I am about to board a flight from London to Dallas, having just > arrived here from Cape Town, so I am jet-lagged and sleep-deprived. > Just the same, I will submit a manuscript once I arrive at Kansas City > if nobody else can do it first (I just created an account for myself > at the website, actually). Are any of us attending the meeting in > Taipei? I hope you will volunteer to present on our behalf, if so! I > may be able to combine Taipei with a half-planned trip to Beijing, but > that will probably involve some contortions. I don't have a budget > handy to attend this meeting. > > I also hoped to send out a message to this list summarizing the > current status of the leadership roles each of us has filled, but > yesterday became pretty messy as I prepared for my departure for an > extended visit to the United States. I see that Reza has volunteered > to help us with minimal information in the area of metabolomics. > Stefan gave a well-considered response to the editor role, saying that > he was willing to help us navigate the document process. Wout is > happy to serve as secretary. Dirk wrote affirming the need for qcML > roles outside shotgun proteomics. Mathias liked the idea of > co-chairing and spurring us along with our web resources. *I'd still > like to see a response from Weimin Zhu and Martin Eisenacher > confirming their willingness to take on tasks*. > > Okay, the lines to board are starting to form. I hope to see amazing > things when next I connect to the network! > Dave > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: weimin z. <wmz...@gm...> - 2016-05-25 07:49:55
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Dear David and all, sorry for the late reply, I have also been running about for meetings. to answer David's question: 1. I will be participating taiwan meeting, so I am happy to represent the QC group if nobody else goes; 2. whatever the unfilled role is fine with me, or happy to serve as co-chair if PSI charter allows. 3. task to undertake: it seems that each essential components of qc standard are taken care of: format, MIAPI-like document and CV/ontolog. I probably can work out a database schema based on qcML, and implement it as qc group's database. David: let me know if you decide to visit Beijing. cheers, weimin On Wed, May 25, 2016 at 3:30 PM, David L. Tabb <dav...@va...> wrote: > Hello, all! > > I have learned that HUPO expects abstracts by today, and we do not yet > have a submission in place for the new qcML working group (due to > disorganization on my part, primarily). Here's what the format expects: > > total max. 3000 characters > > Sections: > > - title: max 150 characters > - Introduction and Objectives > - Methods > - Results and discussion > - Conclusion > - Keywords > > I am about to board a flight from London to Dallas, having just arrived > here from Cape Town, so I am jet-lagged and sleep-deprived. Just the same, > I will submit a manuscript once I arrive at Kansas City if nobody else can > do it first (I just created an account for myself at the website, > actually). Are any of us attending the meeting in Taipei? I hope you will > volunteer to present on our behalf, if so! I may be able to combine Taipei > with a half-planned trip to Beijing, but that will probably involve some > contortions. I don't have a budget handy to attend this meeting. > > I also hoped to send out a message to this list summarizing the current > status of the leadership roles each of us has filled, but yesterday became > pretty messy as I prepared for my departure for an extended visit to the > United States. I see that Reza has volunteered to help us with minimal > information in the area of metabolomics. Stefan gave a well-considered > response to the editor role, saying that he was willing to help us navigate > the document process. Wout is happy to serve as secretary. Dirk wrote > affirming the need for qcML roles outside shotgun proteomics. Mathias > liked the idea of co-chairing and spurring us along with our web > resources. *I'd still like to see a response from Weimin Zhu and Martin > Eisenacher confirming their willingness to take on tasks*. > > Okay, the lines to board are starting to form. I hope to see amazing > things when next I connect to the network! > Dave > > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data > untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > |
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From: David L. T. <dav...@va...> - 2016-05-25 07:30:43
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Hello, all! I have learned that HUPO expects abstracts by today, and we do not yet have a submission in place for the new qcML working group (due to disorganization on my part, primarily). Here's what the format expects: total max. 3000 characters Sections: * title: max 150 characters * Introduction and Objectives * Methods * Results and discussion * Conclusion * Keywords I am about to board a flight from London to Dallas, having just arrived here from Cape Town, so I am jet-lagged and sleep-deprived. Just the same, I will submit a manuscript once I arrive at Kansas City if nobody else can do it first (I just created an account for myself at the website, actually). Are any of us attending the meeting in Taipei? I hope you will volunteer to present on our behalf, if so! I may be able to combine Taipei with a half-planned trip to Beijing, but that will probably involve some contortions. I don't have a budget handy to attend this meeting. I also hoped to send out a message to this list summarizing the current status of the leadership roles each of us has filled, but yesterday became pretty messy as I prepared for my departure for an extended visit to the United States. I see that Reza has volunteered to help us with minimal information in the area of metabolomics. Stefan gave a well-considered response to the editor role, saying that he was willing to help us navigate the document process. Wout is happy to serve as secretary. Dirk wrote affirming the need for qcML roles outside shotgun proteomics. Mathias liked the idea of co-chairing and spurring us along with our web resources. *I'd still like to see a response from Weimin Zhu and Martin Eisenacher confirming their willingness to take on tasks*. Okay, the lines to board are starting to form. I hope to see amazing things when next I connect to the network! Dave |
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From: Mathias W. <wa...@in...> - 2016-05-23 09:58:50
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Hi all, thank you David, I for my part like it and am willing to take my role. regarding the metrics for 'new' tech, I will hopefully soon put something up on github, that will make it easy to oversee what we already have defined and easy to suggest/draft new metrics. (https://github.com/HUPO-PSI/qcML-development/pull/21) best, mths ----- Original Message ----- From: "Valkenborg Dirk" <dir...@vi...> To: "David Tabb, Prof <dt...@su...>" <dt...@su...>, psi...@li... Sent: Wednesday, 18 May, 2016 8:36:51 PM Subject: Re: [Psidev-qc-dev] Organizational roundup Looks good for me and I definitely agree that we need to extent the QC/QA to DIA, top-down and SRM. Regards, Dirk From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] Sent: woensdag 18 mei 2016 14:18 To: psi...@li... Subject: Re: [Psidev-qc-dev] Organizational roundup Hi, folks. I would like some feedback on this slate so that we can finalize our charter before I leave for the United States next Tuesday. If you would like to completely alter the associations of names with positions, that’s absolutely fine. I do want some feedback before I tell HUPO this is what we’re going to try, though. I would really value some emails such as, “yes, I am willing to fill that role” or “no, that doesn’t sound like a good role for me.” Thank you! Dave From: Tabb, David, Prof < dt...@su... > [ mailto:dt...@su... ] Sent: Friday, 06 May 2016 08:35 To: psi...@li... Subject: [Psidev-qc-dev] Organizational roundup Hello, all! I am thrilled to have worked with you all at Ghent on April 19 th ! It is very refreshing to work with a group so willing to contribute to this new effort. For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles . Chair: David Tabb Website/Co-Chair: Mathias Walzer Editor/Co-Chair: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu Ontology: Martin Eisenacher Secretary: Wout Bittremieux My rationale looks like this: We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! J I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management ( http://www.psidev.info/groups/psi-editors ). Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. Yes, I will attend ASMS in San Antonio, and I think that’s a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). Thank you all for your willingness to take part in this push! Dave Indien deze e-mail een bevestiging is voor een vergadering bij VITO, dan dient u de afgedrukte versie aan de bewaking te tonen om toegang te krijgen tot de privéweg naar VITO. If this mail is a meeting confirmation at VITO, the printed version needs to be presented to the security in order to gain access to the private road leading to VITO. VITO Disclaimer: http://www.vito.be/e-maildisclaimer ------------------------------------------------------------------------------ Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j _______________________________________________ Psidev-qc-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Valkenborg D. <dir...@vi...> - 2016-05-18 18:59:24
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Looks good for me and I definitely agree that we need to extent the QC/QA to DIA, top-down and SRM. Regards, Dirk From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] Sent: woensdag 18 mei 2016 14:18 To: psi...@li... Subject: Re: [Psidev-qc-dev] Organizational roundup Hi, folks. I would like some feedback on this slate so that we can finalize our charter before I leave for the United States next Tuesday. If you would like to completely alter the associations of names with positions, that's absolutely fine. I do want some feedback before I tell HUPO this is what we're going to try, though. I would really value some emails such as, "yes, I am willing to fill that role" or "no, that doesn't sound like a good role for me." Thank you! Dave From: Tabb, David, Prof <dt...@su...<mailto:dt...@su...>> [mailto:dt...@su...] Sent: Friday, 06 May 2016 08:35 To: psi...@li...<mailto:psi...@li...> Subject: [Psidev-qc-dev] Organizational roundup Hello, all! I am thrilled to have worked with you all at Ghent on April 19th! It is very refreshing to work with a group so willing to contribute to this new effort. For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles. Chair: David Tabb Website/Co-Chair: Mathias Walzer Editor/Co-Chair: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu Ontology: Martin Eisenacher Secretary: Wout Bittremieux My rationale looks like this: We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! :) I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management (http://www.psidev.info/groups/psi-editors). Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. Yes, I will attend ASMS in San Antonio, and I think that's a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). Thank you all for your willingness to take part in this push! Dave Indien deze e-mail een bevestiging is voor een vergadering bij VITO, dan dient u de afgedrukte versie aan de bewaking te tonen om toegang te krijgen tot de priv?weg naar VITO. If this mail is a meeting confirmation at VITO, the printed version needs to be presented to the security in order to gain access to the private road leading to VITO. VITO Disclaimer: http://www.vito.be/e-maildisclaimer |
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From: Bittremieux W. <wou...@ua...> - 2016-05-18 15:12:30
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Hi Dave, My apologies for not explicitly confirming sooner. I'll gladly take up the role of secretary, and I have no further remarks about the role distribution. Kind regards, Wout > On 18 May 2016, at 14:17, Tabb, David, Prof <dt...@su...> <dt...@su...> wrote: > > Hi, folks. > > I would like some feedback on this slate so that we can finalize our charter before I leave for the United States next Tuesday. If you would like to completely alter the associations of names with positions, that’s absolutely fine. I do want some feedback before I tell HUPO this is what we’re going to try, though. > > I would really value some emails such as, “yes, I am willing to fill that role” or “no, that doesn’t sound like a good role for me.” > > Thank you! > Dave > > From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] > Sent: Friday, 06 May 2016 08:35 > To: psi...@li... > Subject: [Psidev-qc-dev] Organizational roundup > > Hello, all! > > I am thrilled to have worked with you all at Ghent on April 19th! It is very refreshing to work with a group so willing to contribute to this new effort. > > For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles. > > Chair: David Tabb > Website/Co-Chair: Mathias Walzer > Editor/Co-Chair: Stefan Tenzer > Minimum Reporting Requirements: Weimin Zhu > Ontology: Martin Eisenacher > Secretary: Wout Bittremieux > > My rationale looks like this: > We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! J > > I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. > > Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management (http://www.psidev.info/groups/psi-editors). > > Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. > > Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! > > Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). > > If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. > > Yes, I will attend ASMS in San Antonio, and I think that’s a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. > > Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. > > We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). > > Thank you all for your willingness to take part in this push! > Dave > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Tabb, D. P. <dt...@su...> - 2016-05-18 12:17:54
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Hi, folks. I would like some feedback on this slate so that we can finalize our charter before I leave for the United States next Tuesday. If you would like to completely alter the associations of names with positions, that's absolutely fine. I do want some feedback before I tell HUPO this is what we're going to try, though. I would really value some emails such as, "yes, I am willing to fill that role" or "no, that doesn't sound like a good role for me." Thank you! Dave From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] Sent: Friday, 06 May 2016 08:35 To: psi...@li... Subject: [Psidev-qc-dev] Organizational roundup Hello, all! I am thrilled to have worked with you all at Ghent on April 19th! It is very refreshing to work with a group so willing to contribute to this new effort. For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles. Chair: David Tabb Website/Co-Chair: Mathias Walzer Editor/Co-Chair: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu Ontology: Martin Eisenacher Secretary: Wout Bittremieux My rationale looks like this: We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! :) I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management (http://www.psidev.info/groups/psi-editors). Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. Yes, I will attend ASMS in San Antonio, and I think that's a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). Thank you all for your willingness to take part in this push! Dave |
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From: Tabb, D. P. <dt...@su...> - 2016-05-06 06:54:36
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Hello, all! I am thrilled to have worked with you all at Ghent on April 19th! It is very refreshing to work with a group so willing to contribute to this new effort. For a first goal, I would like to nominate some roles for the core group of individuals who volunteered at the meeting. I am using roles borrowed from this grid: http://www.psidev.info/roles. Chair: David Tabb Website/Co-Chair: Mathias Walzer Editor/Co-Chair: Stefan Tenzer Minimum Reporting Requirements: Weimin Zhu Ontology: Martin Eisenacher Secretary: Wout Bittremieux My rationale looks like this: We range considerably in our experience as researchers. I understand that senior folks are going to have deeply split attention (my slow reply after Ghent reflects one example; I was teaching a solo four-day blitz in bioinformatics to the Honours students down here). I know that we must have the enthusiasm and energy of the younger folks to drive this project to 1.0. I propose myself as chair because I value time very deeply, and I intend to keep our meetings on-point and short! :) I enjoyed the enthusiasm Mathias Walzer shows for this effort, and I appreciate his establishing the GitHub site so rapidly. His initial development of the draft format is an impressive beginning upon which we can build. I think he will be an able co-chair. Given his attention to GitHub, I think he will be well-placed to ensure our group is well-represented on the HUPO-PSI website. Stefan Tenzer has volunteered to co-chair, and I appreciated the contributions he was able to make in the morning of our session. I think he will be a solid member of the team. I have also volunteered him as the editor for our team, which is a role that may require considerable effort since it involves document process management (http://www.psidev.info/groups/psi-editors). Weimin Zhu has plenty of valuable experience from the mzData effort, and I think he would have good thoughts on which aspects of quality reporting are essential to a minimal report. Martin Eisenacher seems to have highly relevant experience in format specificiation and ontology management. If he is willing to serve as our Ontology lead, we will be fortunate! Wout Bittremieux has already made great contributions to the software library aspect of the qcML format. I hope he will be willing to work on our meeting reports (and assist in the construction of our various manuscripts). If you would like to request a modified role or propose an altogether different roster, I would be happy to hear it. I have not been organizationally involved with HUPO-PSI in the past, so I may not have the most useful experience for framing such a candidate slate. Yes, I will attend ASMS in San Antonio, and I think that's a great deadline for immediate goals. I would like to knock together an outline for the perspective/announcement. Mathias, I liked your idea about sending an invite/announcement to the other HUPO-PSI groups. We should start soon on identifying the major use cases for qcML and the applicability of various metrics to that purpose. I particularly want to look at experimental types that are currently uncovered by quality metrics (such as top-down and DIA). Thank you all for your willingness to take part in this push! Dave |
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