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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 16 May

[Wout B. <wo...@uw...>]

Dear colleagues,

You can find the meeting notes of yesterday's teleconference here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190516_telco.md

I would especially like to point out the discussion on Julian's open 
pull request. We should be able to merge this pull request soon.

Best,
Wout

On 2019-05-14 16:44, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, May 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
> Cape Town, 7h00 Seattle, 22h00 Beijing).
> 
> You can connect to our teleconference on Google Hangouts through the 
> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
> 
> I missed last month's teleconference, so I'm open to anyone suggesting 
> agenda items to follow up on the stuff that was discussed then.
> 
> I will try to finalize my example file with internal references using 
> JSON pointers and update the JSON schema to allow a list of units, and 
> communicate that to the mailing list tomorrow (Wednesday).
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 16 May

[Julian U. <jul...@ru...>]

Hi all,


I unfortunately won't make it to today's call.


Best,

Julian


On 15.05.19 14:38, Tabb, David, Prof [dt...@su...] wrote:
> Hi, all.
>
> Mathias, I'll need you to chair this one; I am tied up in a School of
> Data Science and Computational Thinking meeting just then.
>
> I keep thinking the schema is finalized, but then I haven't seen the
> example data structures decided upon at the HUPO-PSI meeting.  I also
> thought we were en route to a new CV version number, but I was unable to
> do my "homework" for that task.
>
> Thanks,
> Dave
>
> On 5/15/2019 1:44 AM, Wout Bittremieux wrote:
>> Dear colleagues,
>>
>> This is a reminder that our next teleconference is scheduled for
>> Thursday, May 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe /
>> Cape Town, 7h00 Seattle, 22h00 Beijing).
>>
>> You can connect to our teleconference on Google Hangouts through the
>> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
>>
>> I missed last month's teleconference, so I'm open to anyone suggesting
>> agenda items to follow up on the stuff that was discussed then.
>>
>> I will try to finalize my example file with internal references using
>> JSON pointers and update the JSON schema to allow a list of units, and
>> communicate that to the mailing list tomorrow (Wednesday).
>>
>> Thanks,
>> Wout
>>
>>
>> _______________________________________________
>> Psidev-qc-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
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> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 16 May

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

Hi, all.

Mathias, I'll need you to chair this one; I am tied up in a School of
Data Science and Computational Thinking meeting just then.

I keep thinking the schema is finalized, but then I haven't seen the
example data structures decided upon at the HUPO-PSI meeting.  I also
thought we were en route to a new CV version number, but I was unable to
do my "homework" for that task.

Thanks,
Dave

On 5/15/2019 1:44 AM, Wout Bittremieux wrote:
> Dear colleagues,
>
> This is a reminder that our next teleconference is scheduled for
> Thursday, May 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe /
> Cape Town, 7h00 Seattle, 22h00 Beijing).
>
> You can connect to our teleconference on Google Hangouts through the
> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
>
> I missed last month's teleconference, so I'm open to anyone suggesting
> agenda items to follow up on the stuff that was discussed then.
>
> I will try to finalize my example file with internal references using
> JSON pointers and update the JSON schema to allow a list of units, and
> communicate that to the mailing list tomorrow (Wednesday).
>
> Thanks,
> Wout
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev


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[Psidev-qc-dev] Upcoming teleconference Thursday 16 May

[Wout B. <wo...@uw...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, May 16th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
Cape Town, 7h00 Seattle, 22h00 Beijing).

You can connect to our teleconference on Google Hangouts through the 
following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

I missed last month's teleconference, so I'm open to anyone suggesting 
agenda items to follow up on the stuff that was discussed then.

I will try to finalize my example file with internal references using 
JSON pointers and update the JSON schema to allow a list of units, and 
communicate that to the mailing list tomorrow (Wednesday).

Thanks,
Wout

Re: [Psidev-qc-dev] HUPO-PSI communication of quality parameters

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

Hi, Meena.

Rather than aiming for comprehensive support for mzQC in MSstats from the word "go," I would suggest we try a pilot implementation of mzQC in MSstats first.  An item that is very high on my wishlist is to see a workflow for targeted quantitation supporting mzQC from our very first release, and of course you have already developed one in MSstats.  From a look at the quick reference at http://msstats.org/msstatsqc/, it appears you emphasize four metrics for the analytes in question:

  *   Retention Time
  *   Total Peak Area
  *   Full Width at Half Maximum
  *   Peak Asymmetry

Are these metrics always computed one peptide at a time, or does the software routinely target a number of peptides from a predefined set?  Does it work from a Skyline document to determine which transitions are to be monitored?  I understand that the reference ranges for these metrics are determined on the basis of a guide set, so necessarily one would want to store that information along with the experimental metrics.

I believe that a first step for us is to understand the structure of quality metrics output by your targeted quant module.  If it's a simple table where each row is peptide and each column is one of the four fields above, that's obviously not going to be very stressful to model.  We have also made provision to report distributions, for example the quartiles of total peak area.  With that output structure in hand, we would guide you in defining the metrics within our controlled vocabulary and prototype what kind of text we would expect in the corresponding JSON.  Does that sound like a good point of entry?

I see as well that you have implemented a variety of ways to visualize and analyze the QC data (longitudinal control charts, decision maps, river and radar plots, change points).  How specifically have these been coded to reflect the data structures of MSstats itself?  Would it be possible for your code to be modified to read mzQC objects created by other tools, such as QuaMeter IDFree?  This type of interoperability is a big motivator for us in creating a standard QC communication format.

Thanks so much!
Dave

On 4/30/2019 9:48 PM, Choi, Meena wrote:
Hi David,

First of all, I'm sorry for my late response. We started two weeks course from yesterday and are getting settled :)

Timo from OpenMS tean also reminded me. Yes, I'm happy to join. Thank you for inviting me.
Please let me know what I should do next.

Thank you!
- Meena

On Tue, Apr 23, 2019 at 5:12 AM Tabb, David, Prof [dt...@su...<mailto:dt...@su...>] <dt...@su...<mailto:dt...@su...>> wrote:

Hi, Meena.  I hope that you enjoyed a good holiday weekend!


I am writing in connection with my work on mzQC, a file format for communicating quality information about biological mass spec data.  Our working group for mzQC formed after the 2016 HUPO-PSI Workshop at Ghent.  Our goal is to design a format for passing qc data from metric generation tools (like QuaMeter IDFree) to metric analysis tools (like outlier detectors) and metric storage databases.  Wouldn't it be nice to be able to perform outlier detection from many different metric generators?  At first, we intended to use an XML-based format, like qcML, but we have shifted to a lightweight JSON format instead.


When we publish mzQC, we want to have a well-established "ecosystem" of tools that can speak the mzQC format.  Your MSstats toolkit already has a solid track record, so we would love to work with you to enable mzQC output.  We're just about done with the file specification, so the course to that implementation would probably look like this:


1) Together we select a particular analysis workflow to adapt for this purpose (MSstats can handle lots of different types of experiments, so we might select a most common route to model in the first case).

2) We add terms to our controlled vocabulary that relate to the different metrics that your software outputs.

3) Your team adds the JSON output capability, and we ensure our mzQC readers can validate the JSON your code outputs.


Would something like this be feasible in the next twelve months or so?


I know that's it's always hard to find the time for features like this, but we hope that our work on streamlining the format requirements will make this a relatively easy task.


Thanks,
Dave

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--
Meena Choi
Associate Research Scientist
Khoury College of Computer Sciences
Northeastern University

Re: [Psidev-qc-dev] HUPO-PSI communication of quality parameters

[Choi, M. <m....@no...>]

Hi David,

First of all, I'm sorry for my late response. We started two weeks course from yesterday and are getting settled :)

Timo from OpenMS tean also reminded me. Yes, I'm happy to join. Thank you for inviting me.
Please let me know what I should do next.

Thank you!
- Meena

On Tue, Apr 23, 2019 at 5:12 AM Tabb, David, Prof [dt...@su...<mailto:dt...@su...>] <dt...@su...<mailto:dt...@su...>> wrote:

Hi, Meena.  I hope that you enjoyed a good holiday weekend!


I am writing in connection with my work on mzQC, a file format for communicating quality information about biological mass spec data.  Our working group for mzQC formed after the 2016 HUPO-PSI Workshop at Ghent.  Our goal is to design a format for passing qc data from metric generation tools (like QuaMeter IDFree) to metric analysis tools (like outlier detectors) and metric storage databases.  Wouldn't it be nice to be able to perform outlier detection from many different metric generators?  At first, we intended to use an XML-based format, like qcML, but we have shifted to a lightweight JSON format instead.


When we publish mzQC, we want to have a well-established "ecosystem" of tools that can speak the mzQC format.  Your MSstats toolkit already has a solid track record, so we would love to work with you to enable mzQC output.  We're just about done with the file specification, so the course to that implementation would probably look like this:


1) Together we select a particular analysis workflow to adapt for this purpose (MSstats can handle lots of different types of experiments, so we might select a most common route to model in the first case).

2) We add terms to our controlled vocabulary that relate to the different metrics that your software outputs.

3) Your team adds the JSON output capability, and we ensure our mzQC readers can validate the JSON your code outputs.


Would something like this be feasible in the next twelve months or so?


I know that's it's always hard to find the time for features like this, but we hope that our work on streamlining the format requirements will make this a relatively easy task.


Thanks,
Dave

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Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.sun.ac.za%2Femaildisclaimer&data=02%7C01%7Cm.choi%40northeastern.edu%7Cfd154f97e4e14e33d6b108d6c7cbc599%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C636916075355905673&sdata=KHMJBCXK%2FV5WG1ZAgCKcrpY7Et4BWRPLlkxr1b%2B2Ojc%3D&reserved=0>


--
Meena Choi
Associate Research Scientist
Khoury College of Computer Sciences
Northeastern University

Re: [Psidev-qc-dev] qcML

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

Hi, Chris.

Yes, that's right!  We've had three annual meetings in support of our "mzQC" effort (renamed from "qcML" when we shifted to JSON from XML), and we hope to publish a schema for the format in the coming year.

We are *definitely* interested in developers of existing QC packages to incorporate support of the format.  Supporting you in exporting mzQC from PTXQC will help us to iron out places that could hinder developers from using the format.  I am cc'ing the QC working group; I might suggest you join the list and/or take part in our monthly phone calls.  The schema and controlled vocabular are developed through our GitHub project: https://github.com/HUPO-PSI/mzQC

I really loved those meetings back in La Jolla.  I met such interesting people there!  Will I see you at ASMS this year?

Thanks,
Dave


On 4/29/2019 5:56 PM, Bielow, Chris wrote:
Hi David,

We met briefly at Recomb satellite 2010 (or 2011) in La Jolla, but that’s ages ago :)
I heard from Timo (cc) during the recent OpenMS developer meeting that you are driving the development of a json-based qc data format – to be published soonish.

Since I’m actively developing QC in OpenMS at the moment with downstream use of the PTXQC R package, could mzQC be integrated in the latter to increase momentum?
I’m currently extending PTXQC to accept mzTab. It should not be hard to create qc data in JSON format from that – the data is basically processing in the package anyway. Just needs to be written out as an intermediate step.
If you think this would be a good fit, just let me know. We can also skype etc if that makes things a bit easier.

Cheers
Chris


--
Dr. Chris Bielow

Bioinformatics Solution Center (BSC)
www.bsc.fu-berlin.de<http://www.bsc.fu-berlin.de>
Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin
Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de



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Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/04

[Wout B. <wo...@uw...>]

Thanks for the summary Dave. I've added this to the repository as well 
to keep all meeting notes in the same place: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190418_telco.md

Our next teleconference will be May 16th. I'm back in action, 
invigorated after a nice holiday, so I'll talk to all of you then.

Best,
Wout

On 2019-04-18 07:54, Tabb, David, Prof [dt...@su...] wrote:
> Hi, all.  My immediate memories from the last hour give this report on the to-do roster:
> 
> - Paul: Finalize and share the example mzQC snippet containing SWATH metrics in a matrix.
> 
> Paul has sent around an example of mzQC for SWATH metrics in a message today.
> Paul also created an example of an iRT-based data table metric, but we are unsure of its present whereabouts.
> 
> - Timo/Mathias/Wout: Finalize and share the example mzQC file demonstrating internal references.
> 
> We are currently unsure about this implementation because it uses a proposed but not formally accepted JSON mechanism.
> 
> - Dave/Timo: Contact Meena Choi in April about mzQC export in MSstats/MSstatsQC. Timo can address this in person with her when he's visiting Boston next month for the computational proteomics course.
> - Dave: Contact Oliver Fiehn to inquire how we can support GC-MS metabolomics in mzQC and advertise this to the metabolomics community.
> 
> Dave has set aside time on April 23rd for this purpose.
> 
> - Mathias: Align source data for CVs with Yasset's metadata efforts.
> 
> Mathias suggested this wasn't completed.
> 
> And LOGO!  I sent an image to the Google Hangout that Paul Brack created to humor my silly concept for the mzQC logo.  I like it, yes, even the 3D version!
> 
> We had a bit more discussion about synchronizing schema and cv versions (Julian added a pull request for a new CV number).  Dave pledged to update his JSON example for Lizex's 1091_Pool_start IDFree metrics on April 30th.
> 
> WOUT, what day is our next telecon?
> 
> Now let's go eat chocolate and jelly beans!
> 
> Thanks,
> Dave
> 
> 
> -----Original Message-----
> From: Wout Bittremieux <wo...@uw...>
> Sent: Tuesday, April 9, 2019 9:36 PM
> To: psi...@li...
> Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 18/04
> 
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for Thursday, April 18th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape Town, 7h00 Seattle, 22h00 Beijing).
> 
> I will be on holiday from tomorrow until the end of next week and won't be able to send the regular notification or attend the meeting, hence this early reminder.
> 
> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
> 
> I propose the following agenda items to follow up on the action points from the spring meeting
> (https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190318_CapeTown.md):
> 
> - Paul: Finalize and share the example mzQC snippet containing SWATH metrics in a matrix.
> - Timo/Mathias/Wout: Finalize and share the example mzQC file demonstrating internal references.
> - Dave/Timo: Contact Meena Choi in April about mzQC export in MSstats/MSstatsQC. Timo can address this in person with her when he's visiting Boston next month for the computational proteomics course.
> - Dave: Contact Oliver Fiehn to inquire how we can support GC-MS metabolomics in mzQC and advertise this to the metabolomics community.
> - Mathias: Align source data for CVs with Yasset's metadata efforts.
> (- Wout: Update the JSON schema to have a list of units.)
> (- Wout: Add new checks to the semantic validator (#51).)
> 
> (Unfortunately I haven't had time yet to address these final two action items. I have a small example file implementing internal references using JSON pointers, but it's not fully ready to be shared yet.)
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
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> 

[Psidev-qc-dev] HUPO-PSI communication of quality parameters

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

Hi, Meena.  I hope that you enjoyed a good holiday weekend!


I am writing in connection with my work on mzQC, a file format for communicating quality information about biological mass spec data.  Our working group for mzQC formed after the 2016 HUPO-PSI Workshop at Ghent.  Our goal is to design a format for passing qc data from metric generation tools (like QuaMeter IDFree) to metric analysis tools (like outlier detectors) and metric storage databases.  Wouldn't it be nice to be able to perform outlier detection from many different metric generators?  At first, we intended to use an XML-based format, like qcML, but we have shifted to a lightweight JSON format instead.


When we publish mzQC, we want to have a well-established "ecosystem" of tools that can speak the mzQC format.  Your MSstats toolkit already has a solid track record, so we would love to work with you to enable mzQC output.  We're just about done with the file specification, so the course to that implementation would probably look like this:


1) Together we select a particular analysis workflow to adapt for this purpose (MSstats can handle lots of different types of experiments, so we might select a most common route to model in the first case).

2) We add terms to our controlled vocabulary that relate to the different metrics that your software outputs.

3) Your team adds the JSON output capability, and we ensure our mzQC readers can validate the JSON your code outputs.


Would something like this be feasible in the next twelve months or so?


I know that's it's always hard to find the time for features like this, but we hope that our work on streamlining the format requirements will make this a relatively easy task.


Thanks,
Dave

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Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/04

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

Hi, all.  My immediate memories from the last hour give this report on the to-do roster:

- Paul: Finalize and share the example mzQC snippet containing SWATH metrics in a matrix.

Paul has sent around an example of mzQC for SWATH metrics in a message today.
Paul also created an example of an iRT-based data table metric, but we are unsure of its present whereabouts.

- Timo/Mathias/Wout: Finalize and share the example mzQC file demonstrating internal references.

We are currently unsure about this implementation because it uses a proposed but not formally accepted JSON mechanism.

- Dave/Timo: Contact Meena Choi in April about mzQC export in MSstats/MSstatsQC. Timo can address this in person with her when he's visiting Boston next month for the computational proteomics course.
- Dave: Contact Oliver Fiehn to inquire how we can support GC-MS metabolomics in mzQC and advertise this to the metabolomics community.

Dave has set aside time on April 23rd for this purpose.

- Mathias: Align source data for CVs with Yasset's metadata efforts.

Mathias suggested this wasn't completed.

And LOGO!  I sent an image to the Google Hangout that Paul Brack created to humor my silly concept for the mzQC logo.  I like it, yes, even the 3D version!

We had a bit more discussion about synchronizing schema and cv versions (Julian added a pull request for a new CV number).  Dave pledged to update his JSON example for Lizex's 1091_Pool_start IDFree metrics on April 30th.

WOUT, what day is our next telecon?

Now let's go eat chocolate and jelly beans!

Thanks,
Dave


-----Original Message-----
From: Wout Bittremieux <wo...@uw...>
Sent: Tuesday, April 9, 2019 9:36 PM
To: psi...@li...
Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 18/04

Dear colleagues,

This is a reminder that our next teleconference is scheduled for Thursday, April 18th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape Town, 7h00 Seattle, 22h00 Beijing).

I will be on holiday from tomorrow until the end of next week and won't be able to send the regular notification or attend the meeting, hence this early reminder.

You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

I propose the following agenda items to follow up on the action points from the spring meeting
(https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190318_CapeTown.md):

- Paul: Finalize and share the example mzQC snippet containing SWATH metrics in a matrix.
- Timo/Mathias/Wout: Finalize and share the example mzQC file demonstrating internal references.
- Dave/Timo: Contact Meena Choi in April about mzQC export in MSstats/MSstatsQC. Timo can address this in person with her when he's visiting Boston next month for the computational proteomics course.
- Dave: Contact Oliver Fiehn to inquire how we can support GC-MS metabolomics in mzQC and advertise this to the metabolomics community.
- Mathias: Align source data for CVs with Yasset's metadata efforts.
(- Wout: Update the JSON schema to have a list of units.)
(- Wout: Add new checks to the semantic validator (#51).)

(Unfortunately I haven't had time yet to address these final two action items. I have a small example file implementing internal references using JSON pointers, but it's not fully ready to be shared yet.)

Thanks,
Wout


_______________________________________________
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[Psidev-qc-dev] 2d metric toy examples

[Paul B. <pau...@ma...>]

Hi all,

Here's the first stab at modelling a few 2d SWATH metrics - see attached.

Paul

[Psidev-qc-dev] Upcoming teleconference Thursday 18/04

[Wout B. <wo...@uw...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, April 18th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
Cape Town, 7h00 Seattle, 22h00 Beijing).

I will be on holiday from tomorrow until the end of next week and won't 
be able to send the regular notification or attend the meeting, hence 
this early reminder.

You can connect to our teleconference on Google Hangouts through the 
following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

I propose the following agenda items to follow up on the action points 
from the spring meeting 
(https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190318_CapeTown.md):

- Paul: Finalize and share the example mzQC snippet containing SWATH 
metrics in a matrix.
- Timo/Mathias/Wout: Finalize and share the example mzQC file 
demonstrating internal references.
- Dave/Timo: Contact Meena Choi in April about mzQC export in 
MSstats/MSstatsQC. Timo can address this in person with her when he's 
visiting Boston next month for the computational proteomics course.
- Dave: Contact Oliver Fiehn to inquire how we can support GC-MS 
metabolomics in mzQC and advertise this to the metabolomics community.
- Mathias: Align source data for CVs with Yasset's metadata efforts.
(- Wout: Update the JSON schema to have a list of units.)
(- Wout: Add new checks to the semantic validator (#51).)

(Unfortunately I haven't had time yet to address these final two action 
items. I have a small example file implementing internal references 
using JSON pointers, but it's not fully ready to be shared yet.)

Thanks,
Wout

[Psidev-qc-dev] Meeting notes PSI spring meeting Cape Town

[Wout B. <wo...@uw...>]

Dear colleagues,

I want to thank you all for your valuable contributions during the 
terrific PSI spring meeting this week. I had a great time and I hope 
everyone else did so as well.

You can find the meeting notes here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190318_CapeTown.md

We discussed a lot of stuff, so please feel free to add anything that I 
might have missed to the notes.

Below I'm also reiterating the action points we identified to keep the 
momentum going:

- Wout: Update the JSON schema to have a list of units.
- Wout: Add new checks to the semantic validator (#51).
- Paul: Finalize and share the example mzQC snippet containing SWATH 
metrics in a matrix.
- Timo/Mathias/Wout: Finalize and share the example mzQC file 
demonstrating internal references.
- Dave/Timo: Contact Meena Choi in April about mzQC export in 
MSstats/MSstatsQC. Timo can address this in person with her when he's 
visiting Boston next month for the computational proteomics course.
- Dave: Contact Oliver Fiehn to inquire how we can support GC-MS 
metabolomics in mzQC and advertise this to the metabolomics community.
- Mathias: Align source data for CVs with Yasset's metadata efforts.

Check the notes for context and more information.

Finally, I want to invite everyone who hasn't subscribed to our mailing 
list yet to do so. That way you can keep up with the working group's 
efforts, get notifications about our monthly teleconferences, etc.
You can subscribe to the mailing list here: 
https://sourceforge.net/projects/psidev/lists/psidev-qc-dev

Best,
Wout

Re: [Psidev-qc-dev] [Psidev-pi-dev] Training materials

[Horvatovich, P.L. <p.l...@ru...>]

Dear Andy and All,

Unfortunately, I will be not attending the meeting but would be interested
both for any tutorial materials and/or or materials (slides documents etc)
summarising the outcome of the meeting.

With best regards,

Peter Horvatovich

On Tue, Mar 12, 2019 at 12:30 PM Jones, Andy <And...@li...>
wrote:

> Hi all,
>
>
>
> Apologies for the cross-posting. The PSI meeting kicks off next Monday in
> Cape Town and hoping to see lots of you there. We are going to have lots of
> local participation from individuals new to PSI processes and standards,
> and as such, we have decided to give various tutorials in different slots
> to bring people up to speed.
>
>
>
> If you have any slides introducing one of the core PSI standards, data
> submission to a public repository or some other relevant aspect of data
> sharing, please send them over to me (off the mailing list), and I will add
> them to a shared drive that various people can access when we’re in Cape
> Town, so that we can be flexible at who gives a tutorial dependent on
> availability during the meeting.
>
>
>
> Best wishes
>
> Andy
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>


-- 

Peter Horvatovich
Associate Professor

University of Groningen
Faculty of Sciences and Engineering
Groningen Research Institute of Pharmacy
Analytical Biochemistry

Building 3226, Room 6.9
Antonius Deusinglaan 1
9713 AV Groningen
Internal Zip Code XB20
P.O. Box 196
9700 AD Groningen
The Netherlands

Telephone: +31-(0)50-363 3341
Fax: +31 (0)50 363 7582
Mobile: +31 (0)6 2459 7203
Email: p.l...@ru...
Homepage: www.biomac.nl

[Psidev-qc-dev] Training materials

[Jones, A. <And...@li...>]

Hi all,

Apologies for the cross-posting. The PSI meeting kicks off next Monday in Cape Town and hoping to see lots of you there. We are going to have lots of local participation from individuals new to PSI processes and standards, and as such, we have decided to give various tutorials in different slots to bring people up to speed.

If you have any slides introducing one of the core PSI standards, data submission to a public repository or some other relevant aspect of data sharing, please send them over to me (off the mailing list), and I will add them to a shared drive that various people can access when we're in Cape Town, so that we can be flexible at who gives a tutorial dependent on availability during the meeting.

Best wishes
Andy

[Psidev-qc-dev] Updated draft of MIAPE-QC

[Jinmeng J. <jia...@16...>]

Hi all,
The attached is the draft of current MIAPE-QC.
You can also find it through the following link:
https://github.com/Jinmeng-QC/MIAPE-QC/blob/master/MIAPE-QC_draft.md


Please feel free to let me know if you have any further question.


Best,
Jinmeng


--

Jinmeng, Jia
Ph.D. candidate,Tieliu Shi's Lab
Center for Bioinformatics and Computational Biology
Shanghai Key Laboratory of Regulatory Biology
Institute of Biomedical Sciences and School of Life Sciences
East China Normal University
Minhang Campus: 500 Dongchuan RD., Shanghai 200241

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 21/02

[Wout B. <wo...@uw...>]

Dear colleagues,

You can find the meeting notes of today's teleconference here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190221_telco.md

I hope to see all of you in Cape Town next month!

Best,
Wout

On 2/19/19 4:00 PM, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, February 21st, at 14h00 GMT (14h00 London, 15h00 Western 
> Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing).
> 
> You can connect to our teleconference on Google Hangouts through the 
> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
> 
> I propose the following agenda item:
> 
> - Getting ready for the spring meeting!
> 
> If you haven't done so yet, you can find information on how to register 
> for the spring meeting here: http://psidev.info/hupo-psi-meeting-2019
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Upcoming teleconference Thursday 21/02

[Wout B. <wo...@uw...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, February 21st, at 14h00 GMT (14h00 London, 15h00 Western 
Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing).

You can connect to our teleconference on Google Hangouts through the 
following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

I propose the following agenda item:

- Getting ready for the spring meeting!

If you haven't done so yet, you can find information on how to register 
for the spring meeting here: http://psidev.info/hupo-psi-meeting-2019

Thanks,
Wout

[Psidev-qc-dev] HUPO PSI recommendation document, PSI Extended FASTA Format (PEFF) 60-days public review

[Sylvie Ricard-B. <syl...@un...>]

Dear colleague, dear member of the Proteomics community,

The HUPO Proteomics Standards Initiative (PSI) develops standards for 
documentation and storage of Proteomics data (see http://www.psidev.info 
for an overview of activities).

The PSI Mass Spectrometry Standards Working Group has submitted to the 
PSI document process a proposal for a PSI standard, the PSI Extended 
FASTA Format (PEFF). With the growing interest in proteogenomics, PEFF 
neatly addresses in a standardized manner the growing problem challenge 
of how to encode and use not just the protein sequences, but also the 
many known annotations on those protein sequences.
After having passed a 30-day review of the PSI steering group with minor 
changes, the proposed document version 1.0.0 DRAFT now goes through 
*60-days public comments and external review phase until* *March 25th, 
2019*).

The specification document and three example files 
(PEFF_Tiny_Valid.peff, SmallTestDB-PEFF1.0.peff and 
PEFF_AnnotID_Insulin_Valid.peff) are attached to this e-mail and are 
available in the PEFF GitHub repository https://github.com/HUPO-PSI/PEFF
Athough not included in this submission bundle, PEFF 1.0 files 
(according to the current draft specification) can already be downloaded 
from the neXtProt knowledge base, 
e.g.ftp://ftp.nextprot.org/pub/current_release/peff/
or through the web interface
https://www.nextprot.org/entry/NX_P00738/ (then select download link in 
upper right and choose PEFF)
https://api.nextprot.org/export/entry/NX_P00738.peff

Furthermore, software supporting PEFF is already being developed. The 
widely used Comet search engine supports the current draft of PEFF as 
described here http://comet-ms.sourceforge.net/release/release_201701/ 
(search on page for PEFF)

We invite both positive and negative comments on the relevance, 
correctness and clarity of the proposal (e.g. is the standard 
comprehensively described and are the examples in agreement with the 
specification?) as a whole or of specific parts of it.

Please feel free to forward this message to potentially interested 
colleagues. There is no requirement that people commenting should have 
had any prior contact with the PSI.

Please send comments by e-mail to syl...@un....

I thank you very much in advance for your valuable time and contribution.

Best regards.

Professor Sylvie RICARD-BLUM - PSI Editor
Pericellular and Extracellular Supramolecular Assemblies
UMR 5246 CNRS - University Lyon 1
Institute of Molecular and Supramolecular Chemistry and Biochemistry
University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex, France
Phone: +33(0)4 72 44 82 32
E-mail: syl...@un...
http://www.icbms.fr
The French Society for Matrix Biology http://www.sfbmec.fr
The International Society for Matrix Biology http://ismb.org

[Psidev-qc-dev] PSI2019

[Jones, A. <And...@li...>]

Hi all,
A polite reminder to register for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019 if you are interested in data sharing for proteomics. We are also planning to run some training activities as part of the meeting, so that new participants can learn about existing standards and related software.

There is no cost to register for the meeting, although participants must pay their own travel and hotel costs. Please forward this on to anyone who you think might be interested in attending – we are always keen to attract new participants.

Best wishes
Andy

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 17/01

[Jinmeng J. <jia...@16...>]

Hi everyone, 

I have a group meeting to attend latter. I will join the teleconference if the meeting ends early.
My apologies.




Best,

Jinmeng







At 2019-01-15 08:32:27, "Wout Bittremieux" <wo...@uw...> wrote:
>Dear colleagues,
>
>This is a reminder that our next teleconference is scheduled for 
>Thursday, January 17th, at 14h00 GMT (14h00 London, 15h00 Western 
>Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing).
>
>You can connect to our teleconference on Google Hangouts through the 
>following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
>
>I propose the following agenda items:
>
>Spring meeting preparation:
>- Brief overview of the current status: JSON format/schema, CV, MIAPE-QC
>- Tasks to take care of before the spring meeting
>- Spring meeting agenda
>
>As a reminder, you can find all the information about the spring meeting 
>and how to register here: http://psidev.info/hupo-psi-meeting-2019
>
>Thanks,
>Wout
>
>
>_______________________________________________
>Psidev-qc-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev







--

Jinmeng, Jia
Ph.D. candidate,Tieliu Shi's Lab
Center for Bioinformatics and Computational Biology
Shanghai Key Laboratory of Regulatory Biology
Institute of Biomedical Sciences and School of Life Sciences
East China Normal University
Minhang Campus: 500 Dongchuan RD., Shanghai 200241

[Psidev-qc-dev] Upcoming teleconference Thursday 17/01

[Wout B. <wo...@uw...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, January 17th, at 14h00 GMT (14h00 London, 15h00 Western 
Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing).

You can connect to our teleconference on Google Hangouts through the 
following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2

I propose the following agenda items:

Spring meeting preparation:
- Brief overview of the current status: JSON format/schema, CV, MIAPE-QC
- Tasks to take care of before the spring meeting
- Spring meeting agenda

As a reminder, you can find all the information about the spring meeting 
and how to register here: http://psidev.info/hupo-psi-meeting-2019

Thanks,
Wout

Re: [Psidev-qc-dev] QC workshop at ASMS?

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

Hi, all.

It might make sense to create a persistent HUPO-PSI evening workshop
rather than one specific to PSI-QC.

I'm sorry to reply slowly; I've only returned from honeymoon on Tuesday
evening!

Dave

On 1/7/2019 7:58 PM, Wout Bittremieux wrote:
> Dear colleagues,
>
> I hope everyone had a good holiday period and is ready for all the
> exciting QC stuff we have planned for 2019.
>
> I would like to bring the option to organize a workshop at the
> upcoming ASMS conference in June to your attention again. If we want
> to do this we'll have to submit an application by early next week.
>
> Writing the actual application isn't a huge amount of work, but we
> need to properly know in advance how we'd like to fill the workshop,
> how to engage participants, potential guest speakers and discussion
> facilitators, ...
> See the initial mail below for some more details.
>
> I would like to ask you to communicate your thoughts on organizing a
> workshop to the working group as soon as possible this week.
>
> Best,
> Wout
>
> On 12/20/18 2:37 PM, Wout Bittremieux wrote:
>> Dear colleagues,
>>
>> This morning we discussed whether we should try to organize a
>> workshop at the upcoming ASMS conference in June to present the mzQC
>> version 1.0 and discuss other QC-related topics.
>>
>> The procedure to organize a workshop seems pretty simple, only a 250
>> word description is needed to apply:
>> https://applications-and-award-nominations.formstack.com/forms/asms_workshop_2019
>>
>>
>> A disadvantage is that we're not a special interest group (SIG) and
>> precedence will be given to workshop topics proposed by the
>> established SIGs.
>>
>> The deadline for the workshop applications is January 15th, and we'll
>> only have our next teleconference later that week. So we'll have to
>> decide via mail whether we want to organize a workshop or not.
>>
>> Therefore I would like to invite everyone to give their opinion about
>> this.
>> - Do you think it will be useful to organize a workshop at ASMS?
>> - What topics should we address? In which format? (Workshops are less
>> formal than regular talks, it's important to engage the audience.)
>> - Will you attend the ASMS conference?
>>
>> As the deadline to propose a workshop topic is relatively soon,
>> please share your thoughts with the working group as soon as possible.
>>
>> Best,
>> Wout
>>
>>
>> _______________________________________________
>> Psidev-qc-dev mailing list
>> 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


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[Psidev-qc-dev] Registration for Cape Town meeting in March

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

Hi, all.

Has everyone registered for the March 18-20 HUPO-PSI meeting at Cape
Town?  Please do so, if you have not already!

Thanks,
Dave

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Re: [Psidev-qc-dev] QC workshop at ASMS?

[Wout B. <wo...@bi...>]

Dear colleagues,

I hope everyone had a good holiday period and is ready for all the 
exciting QC stuff we have planned for 2019.

I would like to bring the option to organize a workshop at the upcoming 
ASMS conference in June to your attention again. If we want to do this 
we'll have to submit an application by early next week.

Writing the actual application isn't a huge amount of work, but we need 
to properly know in advance how we'd like to fill the workshop, how to 
engage participants, potential guest speakers and discussion 
facilitators, ...
See the initial mail below for some more details.

I would like to ask you to communicate your thoughts on organizing a 
workshop to the working group as soon as possible this week.

Best,
Wout

On 12/20/18 2:37 PM, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This morning we discussed whether we should try to organize a workshop 
> at the upcoming ASMS conference in June to present the mzQC version 1.0 
> and discuss other QC-related topics.
> 
> The procedure to organize a workshop seems pretty simple, only a 250 
> word description is needed to apply: 
> https://applications-and-award-nominations.formstack.com/forms/asms_workshop_2019 
> 
> 
> A disadvantage is that we're not a special interest group (SIG) and 
> precedence will be given to workshop topics proposed by the established 
> SIGs.
> 
> The deadline for the workshop applications is January 15th, and we'll 
> only have our next teleconference later that week. So we'll have to 
> decide via mail whether we want to organize a workshop or not.
> 
> Therefore I would like to invite everyone to give their opinion about this.
> - Do you think it will be useful to organize a workshop at ASMS?
> - What topics should we address? In which format? (Workshops are less 
> formal than regular talks, it's important to engage the audience.)
> - Will you attend the ASMS conference?
> 
> As the deadline to propose a workshop topic is relatively soon, please 
> share your thoughts with the working group as soon as possible.
> 
> Best,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev