psidev-qc-dev — PSI-QC working group mailinglist

Re: [Psidev-qc-dev] PSI QC Announcement Draft

[Lennart M. <len...@vi...>]

Hello,


I took the liberty of going through the text (which is great!), and made 
a few additions, adding three references in the process.

I also put a comment at line 257-260, where i suggest a change in a 
sentence that probably needs a look from whoever wrote the original.


Cheers,

lnnrt.

On 19/08/2016 20:00, Reza Salek wrote:
> Hello Daivd, all.
>
>
>> On 1 Aug 2016, at 17:16, Tabb, David, Prof <dt...@su...
>> <mailto:dt...@su...>> <dt...@su... <mailto:dt...@su...>>
>> wrote:
>>
>> Hi, all.
>>
>> I hope that our full team is now on the QC Dev mailing list.  I should
>> probably figure out how to get the roster from SourceForge.
>>
>> I hope by now everyone has had a look at the draft of the QC
>> Announcement draft at Overleaf
>> (https://www.overleaf.com/5671898jfvtyd).  *Wout* did some key work
>> getting us off the ground with an initial draft, and I think a few of
>> us have made contributions to that draft, as well.
>>
>> *Reza*, I would like to request that you help us with some
>> concreteness in metabolomics experimental methods.
>
> I have added several paragraphs to the manuscript,  covering role and
> types of QC and QA samples in metabolomics. Also added tools, that I
> hope would support qcML, as well added the initiative within the
> Metabolomics Society that can support or we are coordinating with (Task
> groups). Please have a looking and let me know if more details are
> needed. I will be on holiday next week but back in September.
>
>
>> We already mention a variety of techniques in proteomics into which we
>> hope to expand QC (SRM, iTRAQ, DIA, MALDI).
>
> specially target and un-target methods but not much different from
> proteomics
>> We haven’t done the same for metabolomics.  Presumably data-dependent
>> acquisition is not the dominant paradigm for metabolomics experiments;
>
> A work in progress ….
>
> Best Wishes
> Reza
>
>> we would like to sketch out methods in metabolomic mass spectrometry
>> that we hope to keep in mind as QC moves forward.
>>
>> I wanted to single out *Dave* for failing to navigate the HUPO 2016
>> abstract submission site.  We learned two weeks after abstracts were
>> due that the abstract I thought had been submitted had not, in fact,
>> been sent (one must hit the submission button once, wait for the
>> refresh, and then a second time).  Thankfully, *Eric* *Deutsch* caught
>> the mistake when searching for our abstract for inclusion in his
>> panel!  We were able to do a late submission courtesy of folks in the
>> HUPO office.  I’m sorry for the foul-up, folks.
>>
>> Thank you for all your good work!
>> Dave
>>
>> P.S. I ran QuaMeter today on a pile of RAW files to untangle a mystery
>> about the origin of some files collected before the uniform naming
>> strategy went into effect.  How useful!
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Psidev-qc-dev mailing list
>> Psi...@li...
>> <mailto:Psi...@li...>
>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
>
>
> ------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] PSI QC Announcement Draft

[Reza S. <rez...@eb...>]

Hello Daivd, all.


> On 1 Aug 2016, at 17:16, Tabb, David, Prof <dt...@su...> <dt...@su...> wrote:
> 
> Hi, all.
>  
> I hope that our full team is now on the QC Dev mailing list.  I should probably figure out how to get the roster from SourceForge.
>  
> I hope by now everyone has had a look at the draft of the QC Announcement draft at Overleaf (https://www.overleaf.com/5671898jfvtyd <https://www.overleaf.com/5671898jfvtyd>).  Wout did some key work getting us off the ground with an initial draft, and I think a few of us have made contributions to that draft, as well.
>  
> Reza, I would like to request that you help us with some concreteness in metabolomics experimental methods. 

I have added several paragraphs to the manuscript,  covering role and types of QC and QA samples in metabolomics. Also added tools, that I hope would support qcML, as well added the initiative within the Metabolomics Society that can support or we are coordinating with (Task groups). Please have a looking and let me know if more details are needed. I will be on holiday next week but back in September.


> We already mention a variety of techniques in proteomics into which we hope to expand QC (SRM, iTRAQ, DIA, MALDI). 

specially target and un-target methods but not much different from proteomics
> We haven’t done the same for metabolomics.  Presumably data-dependent acquisition is not the dominant paradigm for metabolomics experiments;

A work in progress ….

Best Wishes
Reza

> we would like to sketch out methods in metabolomic mass spectrometry that we hope to keep in mind as QC moves forward.
>  
> I wanted to single out Dave for failing to navigate the HUPO 2016 abstract submission site.  We learned two weeks after abstracts were due that the abstract I thought had been submitted had not, in fact, been sent (one must hit the submission button once, wait for the refresh, and then a second time).  Thankfully, Eric Deutsch caught the mistake when searching for our abstract for inclusion in his panel!  We were able to do a late submission courtesy of folks in the HUPO office.  I’m sorry for the foul-up, folks.
>  
> Thank you for all your good work!
> Dave
>  
> P.S. I ran QuaMeter today on a pile of RAW files to untangle a mystery about the origin of some files collected before the uniform naming strategy went into effect.  How useful!
> ------------------------------------------------------------------------------
> _______________________________________________
> 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>

[Psidev-qc-dev] PSI QC Announcement Draft

[Tabb, D. P. <dt...@su...>]

Hi, all.

I hope that our full team is now on the QC Dev mailing list.  I should probably figure out how to get the roster from SourceForge.

I hope by now everyone has had a look at the draft of the QC Announcement draft at Overleaf (https://www.overleaf.com/5671898jfvtyd).  Wout did some key work getting us off the ground with an initial draft, and I think a few of us have made contributions to that draft, as well.

Reza, I would like to request that you help us with some concreteness in metabolomics experimental methods.  We already mention a variety of techniques in proteomics into which we hope to expand QC (SRM, iTRAQ, DIA, MALDI).  We haven't done the same for metabolomics.  Presumably data-dependent acquisition is not the dominant paradigm for metabolomics experiments; we would like to sketch out methods in metabolomic mass spectrometry that we hope to keep in mind as QC moves forward.

I wanted to single out Dave for failing to navigate the HUPO 2016 abstract submission site.  We learned two weeks after abstracts were due that the abstract I thought had been submitted had not, in fact, been sent (one must hit the submission button once, wait for the refresh, and then a second time).  Thankfully, Eric Deutsch caught the mistake when searching for our abstract for inclusion in his panel!  We were able to do a late submission courtesy of folks in the HUPO office.  I'm sorry for the foul-up, folks.

Thank you for all your good work!
Dave

P.S. I ran QuaMeter today on a pile of RAW files to untangle a mystery about the origin of some files collected before the uniform naming strategy went into effect.  How useful!

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Mathias W. <wa...@in...>]

Hi Martin,

Problem is, I have no access to psi's drupal/server.
Can you create such site and give me access? 

best, 
 mths

----- Original Message -----
From: "Martin Eisenacher" <mar...@ru...>
To: dt...@su..., "Mathias Walzer" <wa...@in...>
Cc: psi...@li...
Sent: Thursday, 30 June, 2016 2:05:41 PM
Subject: AW: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi David,

group charter also looks good for me.
I have added only one comment in the attached doc.
regarding the WG page on psidev.info:

"I could add a group page, but cannot link it 
on http://www.psidev.info/groups ; hopefully Mathias can.
We can choose an alias here!, 
e.g. www.psidev.info/quality-control "

I am also not sure, whether there exist WG roles in the Drupal,
do you know, Mathias?

The charter could be at least placed on such a page...

  Best regards
     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



ANNOUNCEMENT de.NBI workshop hosted by the BioInfra.Prot service center
Differential analysis of proteomic data using R
https://www.denbi.de/index.php/22-training-cat/training-courses/101-r 



-----Ursprüngliche Nachricht-----
Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Gesendet: Donnerstag, 30. Juni 2016 09:57
An: psi...@li...
Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tabb, D. P. <dt...@su...>]

Good thinking on both counts.  I will probably list Mathias first as it appears he may be able to attend and present this work personally!

Thanks,
dave

-----Original Message-----
From: Martin Eisenacher [mailto:mar...@ru...] 
Sent: Thursday, 30 June 2016 14:12
To: Tabb, David, Prof <dt...@su...>; psi...@li...
Subject: AW: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi David,

everything great, but I believe, Mathias should be last author instead of me. Or you last and Mathias / Wout first...

As keyword also "standardization" or "standard format"?

  Best regards
     Martin


-----Ursprüngliche Nachricht-----
Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...]
Gesendet: Donnerstag, 30. Juni 2016 11:49
An: psi...@li...
Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, all.

The attached PDF shows how the release candidate HUPO abstract looks in the website.

Did I leave anyone out?  I used the list of people in leadership roles from the working group charter, and the order is the same as the names appear there.

Did I appropriately translate each university name into English?  Did I use your preferred affiliation?

At present, I am only sure that Weimin Zhu will be in attendance, and he has volunteered as our presenter.  I have listed myself as corresponding and Weimin as our presenter.

Is the category okay?  We're in 41: Bioinformatics and Computational Proteomics.

Does anyone have more keywords to include?

Are there any objections to my hitting the submit button?  I will probably do so after lunch without further comment.

Thanks,
Dave

-----Original Message-----
From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...]
Sent: Thursday, 30 June 2016 09:57
To: psi...@li...
Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Martin E. <mar...@ru...>]

Hi David,

everything great, but I believe, Mathias should be last author
instead of me. Or you last and Mathias / Wout first...

As keyword also "standardization" or "standard format"?

  Best regards
     Martin


-----Ursprüngliche Nachricht-----
Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Gesendet: Donnerstag, 30. Juni 2016 11:49
An: psi...@li...
Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, all.

The attached PDF shows how the release candidate HUPO abstract looks in the website.

Did I leave anyone out?  I used the list of people in leadership roles from the working group charter, and the order is the same as the names appear there.

Did I appropriately translate each university name into English?  Did I use your preferred affiliation?

At present, I am only sure that Weimin Zhu will be in attendance, and he has volunteered as our presenter.  I have listed myself as corresponding and Weimin as our presenter.

Is the category okay?  We're in 41: Bioinformatics and Computational Proteomics.

Does anyone have more keywords to include?

Are there any objections to my hitting the submit button?  I will probably do so after lunch without further comment.

Thanks,
Dave

-----Original Message-----
From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Sent: Thursday, 30 June 2016 09:57
To: psi...@li...
Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Martin E. <mar...@ru...>]

Hi David,

group charter also looks good for me.
I have added only one comment in the attached doc.
regarding the WG page on psidev.info:

"I could add a group page, but cannot link it 
on http://www.psidev.info/groups ; hopefully Mathias can.
We can choose an alias here!, 
e.g. www.psidev.info/quality-control "

I am also not sure, whether there exist WG roles in the Drupal,
do you know, Mathias?

The charter could be at least placed on such a page...

  Best regards
     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



ANNOUNCEMENT de.NBI workshop hosted by the BioInfra.Prot service center
Differential analysis of proteomic data using R
https://www.denbi.de/index.php/22-training-cat/training-courses/101-r 



-----Ursprüngliche Nachricht-----
Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Gesendet: Donnerstag, 30. Juni 2016 09:57
An: psi...@li...
Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tabb, D. P. <dt...@su...>]

Hi, all.

The attached PDF shows how the release candidate HUPO abstract looks in the website.

Did I leave anyone out?  I used the list of people in leadership roles from the working group charter, and the order is the same as the names appear there.

Did I appropriately translate each university name into English?  Did I use your preferred affiliation?

At present, I am only sure that Weimin Zhu will be in attendance, and he has volunteered as our presenter.  I have listed myself as corresponding and Weimin as our presenter.

Is the category okay?  We're in 41: Bioinformatics and Computational Proteomics.

Does anyone have more keywords to include?

Are there any objections to my hitting the submit button?  I will probably do so after lunch without further comment.

Thanks,
Dave

-----Original Message-----
From: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Sent: Thursday, 30 June 2016 09:57
To: psi...@li...
Subject: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tabb, D. P. <dt...@su...>]

Hi, everyone.  Thank you for the feedback on the abstract!  I have combined edits into the attached copy.  This is what I intend to submit later today, unless I see more feedback here.

I saw that Mathias had added a couple of significant points that I ended up omitting from the abstract to keep it concise (3000 characters rather than words, IIRC), but I do not want them to be lost:

1) By keeping our tools small, we can build more flexible pipelines.  Standard formats are the glue allowing for this modularity.

2) The ontology work is essential to the success of this project, both in keeping a HUPO-PSI "flavour" but also in relating terms among formats.

(Mathias used different words; I hope I've done the meaning justice.)

In any case, let me know what you think of this copy, and hopefully we'll get this in around lunchtime.

Thanks,
Dave

P.S. I am also attaching the Group Charter draft.  Does anyone have additional comments on this?

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Mathias W. <wa...@in...>]

Hi!
Hi!

> @Mathias: Mentioning of the OpenMS team okay?
Mmmh, good point Martin is raising, do we want to mention other organisations/development teams?
Maybe as cite in the modify existing suites part? I don't know, what do you think David?

Do we need anything else?

best,


> 
> 
> 
> Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...]
> Gesendet: Montag, 27. Juni 2016 14:37
> An: psi...@li...
> Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016
> in Taipei
> 
> 
> 
> Hi, all.
> 
> 
> 
> Helpfully, the HUPO 2016 abstract deadline was pushed back to June 30
> th ! 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
> 
> 
> 
> ------------------------------------------------------------------------------
> 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
>

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Martin E. <mar...@ru...>]

Hi all!

 

My suggestions added as tracked changes.

@Mathias: Mentioning of the OpenMS team okay?

 

Many thanks for the abstract, David!

 

  Best regards

     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 workshop hosted by the BioInfra.Prot service center

Differential analysis of proteomic data using R

 <https://www.denbi.de/index.php/22-training-cat/training-courses/101-r>
https://www.denbi.de/index.php/22-training-cat/training-courses/101-r 

 

 

 

Von: Tabb, David, Prof <dt...@su...> [mailto:dt...@su...] 
Gesendet: Montag, 27. Juni 2016 14:37
An: psi...@li...
Betreff: Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in
Taipei

 

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... <mailto:dt...@su...> >
Cc: psi...@li...
<mailto: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

 

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Lennart M. <len...@gm...>]

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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Mathias W. <wa...@in...>]

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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tenzer, S. <te...@un...>]

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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Mathias W. <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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tenzer, S. <te...@un...>]

<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 &lt;<a href="mailto:dt...@su...">dt...@su...</a>&gt; &lt;<a href="mailto:dt...@su...">dt...@su...</a>&gt;:</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);">&nbsp;</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>!&nbsp; We have three days to finalize the abstract I’ll submit.&nbsp; I am attaching the current draft, which incorporates Reza’s 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);">&nbsp;</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);">&nbsp;</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.&nbsp; If there are no further comments, I’ll 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);">&nbsp;</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);">&nbsp;</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.&nbsp; 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);">&nbsp;</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).&nbsp; I will try to get some time on that draft shortly.&nbsp; I have been working on a grant to cover qcML activities from an FWO-NRF joint funding program between Belgium and South Africa.&nbsp; 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);">&nbsp;</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);">&nbsp;</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);">&nbsp;</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">&nbsp;</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">&nbsp;</span><br><b>Sent:</b><span class="Apple-converted-space">&nbsp;</span>Wednesday, 25 May 2016 14:26<br><b>To:</b><span class="Apple-converted-space">&nbsp;</span>Tabb, David, Prof &lt;<a href="mailto:dt...@su..." style="color: rgb(149, 79, 114); text-decoration: underline;">dt...@su...</a>&gt;<br><b>Cc:</b><span class="Apple-converted-space">&nbsp;</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">&nbsp;</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>&nbsp;</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>&nbsp;</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>&nbsp;</o:p></div></div><div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;">Best Wishes,&nbsp;<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>&nbsp;</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>&nbsp;</o:p></div></div></div></div><span>&lt;20160525-HUPO-qcML-abstract.docx&gt;</span>------------------------------------------------------------------------------<br>Attend Shape: An AT&amp;T Tech Expo July 15-16. Meet us at AT&amp;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>

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Tabb, D. P. <dt...@su...>]

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

Re: [Psidev-qc-dev] Organizational roundup

[weimin z. <wmz...@gm...>]

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
>
>

Re: [Psidev-qc-dev] Organizational roundup

[Martin E. <mar...@ru...>]

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, 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!  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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[Reza S. <rez...@eb...>]

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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[David L. T. <dav...@va...>]

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

Re: [Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[weimin z. <wmz...@gm...>]

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
>
>

[Psidev-qc-dev] Work for TODAY: Abstract for HUPO 2016 in Taipei

[David L. T. <dav...@va...>]

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

Re: [Psidev-qc-dev] Organizational roundup

[Mathias W. <wa...@in...>]

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! 

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Re: [Psidev-qc-dev] Organizational roundup

[Valkenborg D. <dir...@vi...>]

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.

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