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

[Psidev-qc-dev] Upcoming teleconference March 9

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,



We have our next teleconference today, Wednesday March 9, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).



You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https:/uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!0tysUTnV4ccDLUmo8oc_kWC7emejckAibPgQndQG74XWXKmGdqWvL8GUigGkzeRSoHxOIQ$>

(Password: 012575)


Agenda items:

  *   PSI Spring Meeting 2022 (Hinxton, UK & remote) planning.
  *   mzQC software updates.
  *   Time permitting: CV integration, manuscript.


Apologies for the late notification email; I was traveling today and yesterday.



Best,

Wout

[Psidev-qc-dev] Items for May meeting agenda

[David T. <dav...@pa...>]

Hi, guys.

Which topics would you like to ensure we cover in the May meeting at Hinxton?  I've asked to combine our group with the larger MS / Proteome Informatics groups, so we will probably have a relatively compact period of time given over to just quality control topics.

If you want a room just for our discussions, we should ask sooner rather than later.  My feeling is that most of the mzQC business is concluding well.

Thanks,
Dave

[Psidev-qc-dev] Upcoming teleconference 23/02

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday February 23, at 7h00 Pacific Time (15h00 London, 16h00 Western Europe).

As remarked last time, I have attached a calendar invite to keep better track of when our meetings happen.

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   mzQC software support: updates.
  *   CV integration: next batch(es) of terms.
  *   Manuscript: identify relevant use cases and development champions.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 09/02

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,



We have our next teleconference tomorrow, Wednesday February 9, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).



You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https:/uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!0tysUTnV4ccDLUmo8oc_kWC7emejckAibPgQndQG74XWXKmGdqWvL8GUigGkzeRSoHxOIQ$>

(Password: 012575)



Agenda items:

  *   Specification document: finalize specification document<https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit?usp=sharing> and response to reviewers<https://docs.google.com/document/d/14mC7sDjPpeg7uFVZSaPv799CgSHqKMmzKuv-rLepuhc/edit?usp=sharing> for resubmission to the PSI document process.
  *   Discuss strategy and new batch of CV terms for integration into the PSI-MS CV.
  *   Status and strategy of mzQC implementing tools & validator: brief update.
  *   Review manuscript outline<https://urldefense.com/v3/__https:/docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit__;!!JFdNOqOXpB6UZW0!5Q4IDr-aYhrO5Yx3yViqi7KQG241jgV4nxBt8HxqBIr8ig71NKrNzKVl4fGWNz0$> and establish writing strategy.



Best,

Wout

[Psidev-qc-dev] Upcoming teleconference 26/01

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,



We have our next teleconference tomorrow, Wednesday January 26, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).



You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!0tysUTnV4ccDLUmo8oc_kWC7emejckAibPgQndQG74XWXKmGdqWvL8GUigGkzeRSoHxOIQ$>

(Password: 012575)



Agenda items:

  *   Finalize CV merging PR<https://github.com/HUPO-PSI/mzQC/pull/165>. Discussion of duration metrics.
  *   Status and strategy of mzQC implementing tools.
  *   Review manuscript outline<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit> and establish writing strategy.


Best,

Wout

[Psidev-qc-dev] Upcoming teleconference 12/01

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,



We have our next teleconference tomorrow, Wednesday January 12, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).



You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!0tysUTnV4ccDLUmo8oc_kWC7emejckAibPgQndQG74XWXKmGdqWvL8GUigGkzeRSoHxOIQ$>

(Password: 012575)



Agenda items:

  *   Status update specification document going through the PSI document process.
  *   Review first batch of CV terms for inclusion in PSI-MS-CV.<https://github.com/HUPO-PSI/mzQC/pull/165>
  *   Review manuscript outline<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit> and writing strategy.


Best,

Wout

[Psidev-qc-dev] Interest in joining the HUPO-PSI QC working group

[David Jimenez-M. <dav...@st...>]

Hi there,

I am writing to express my interest in joining the HUPO-PSI QC working group. I learned about it at the last ASMS conference, in a workshop by Wout Bittremieux and David Tabb.

I have experience in proteomics data analysis. In fact, I developed and maintain a Bioconductor R package call artMS<http://artms.org/>, which provides, as one of the core functionalities, extensive QA/QC. In addition to this, I am part of the multi-omics MoTrPAC consortium<https://motrpac-data.org/dashboard>, where I lead the QC/QA working group.

What would I need to do to be part of this HUPO-PSI QC WG?

Thanks a lot!
David

----
David Jimenez-Morales, PhD

Senior Research Engineer

Stanford University School of Medicine

Department of Medicine/Division of Cardiovascular Medicine

Center for Academic Medicine

453 Quarry Road

Palo Alto, CA 94304

http://web.stanford.edu/people/david.jimenez-morales


________________________________
From: David Jimenez-Morales
Sent: Wednesday, December 8, 2021 12:27 PM
To: wbi...@he... <wbi...@he...>; dt...@su... <dt...@su...>
Subject: Interest in joining the HUPO-PSI QC working group

Hi Wout and David,

I attended your excellent workshop "Quality Control for Proteomics and Metabolomics" at the ASMS meeting.

Wout, I talked to you briefly after the session (I hope you remember) and expressed interest in joining the HUPO-PSI QC working group. I found very interesting the initiative on defining community standards for ms-based proteomics. The questions that I have for you is, how should I do it?


Please, let me know. Looking forward to joining the group and get to know more about this initiative.

Thanks
David


----
David Jimenez-Morales, PhD

Senior Research Engineer

Stanford University School of Medicine

Department of Medicine/Division of Cardiovascular Medicine

Center for Academic Medicine

453 Quarry Road

Palo Alto, CA 94304

http://web.stanford.edu/people/david.jimenez-morales

[Psidev-qc-dev] Upcoming teleconference 8/12

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday December 8, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Finalize ASMS workshop report.
  *   Open PR in the PSI-MS-CV repository to start merging in our CV.
  *   Resubmit specification document to review process.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 24/11

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday November 24, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   ASMS survey feedback and reporting.
  *   PSI Spring workshop sneak peek.
  *   MS and QC CV integration: PR 145<https://github.com/HUPO-PSI/mzQC/pull/145>, related issues & PRs, specification document<https://docs.google.com/document/d/132F3MBgDJgtFlXxDZhpJ1oHGbKL8pT6dk9fvL55L5_M/edit>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 10/11

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday November 10, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!2SexQqpIt6lcOsq4yVY7meWtQEb6AgSN-lKZGphG426FhxUOjvEsvkqHPQWYMpohTgqFIw$>
(Password: 012575)

Agenda items:

  *   Brief recap ASMS workshop (Dave, Wout)
  *   MS and QC CV integration: issue 141<https://github.com/HUPO-PSI/mzQC/issues/141> and related smaller issues (CV term ambiguity & requests), PR 145<https://github.com/HUPO-PSI/mzQC/pull/145> (Mathias, everyone)
  *   Progress and planning of the manuscript (Mathias, Wout)

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 27/10

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday October 27, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!2SexQqpIt6lcOsq4yVY7meWtQEb6AgSN-lKZGphG426FhxUOjvEsvkqHPQWYMpohTgqFIw$>
(Password: 012575)

Agenda items:

  *   ASMS workshop: Final preparations!
  *   MS and QC CV integration: Lots of activity on GitHub.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 13/10

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the notes of yesterday's meeting here<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20211013_telco.md>.

Please note that (i) you can add relevant bingo terms for the ASMS workshop here<https://docs.google.com/spreadsheets/d/1L5UUHCsv4Uugsccd37_cgoCbWfilBNhcmw9lB5oUzic/edit?usp=sharing>, and (ii) the next steps<https://github.com/HUPO-PSI/mzQC/issues/141> to merge our CV in the MS CV.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, October 12, 2021 19:19
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 13/10

Dear colleagues,

We have our next teleconference tomorrow, Wednesday October 13, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!2SexQqpIt6lcOsq4yVY7meWtQEb6AgSN-lKZGphG426FhxUOjvEsvkqHPQWYMpohTgqFIw$>
(Password: 012575)

Agenda items:

  *   ASMS workshop: workshop material<https://docs.google.com/document/d/1frOR9Z1BZE5ELzl0XznQsPqZWE0IzEEnK9hvsZ87Lds/edit?usp=sharing>, bingo<https://docs.google.com/spreadsheets/d/1L5UUHCsv4Uugsccd37_cgoCbWfilBNhcmw9lB5oUzic/edit?usp=sharing>, software demo videos.
  *   MS and QC CV integration<https://github.com/HUPO-PSI/mzQC/issues/141>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 13/10

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday October 13, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!2SexQqpIt6lcOsq4yVY7meWtQEb6AgSN-lKZGphG426FhxUOjvEsvkqHPQWYMpohTgqFIw$>
(Password: 012575)

Agenda items:

  *   ASMS workshop: workshop material<https://docs.google.com/document/d/1frOR9Z1BZE5ELzl0XznQsPqZWE0IzEEnK9hvsZ87Lds/edit?usp=sharing>, bingo<https://docs.google.com/spreadsheets/d/1L5UUHCsv4Uugsccd37_cgoCbWfilBNhcmw9lB5oUzic/edit?usp=sharing>, software demo videos.
  *   MS and QC CV integration<https://github.com/HUPO-PSI/mzQC/issues/141>.

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 29/09

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday September 29, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09<https://urldefense.com/v3/__https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09__;!!LLK065n_VXAQ!2SexQqpIt6lcOsq4yVY7meWtQEb6AgSN-lKZGphG426FhxUOjvEsvkqHPQWYMpohTgqFIw$>
(Password: 012575)

Agenda items:

  *   ASMS workshop: Debate + hesitant PI, software demo videos, QC bingo.
  *   MS and QC CV integration<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210917_telco.md> (if time permits)

Best,
Wout

Re: [Psidev-qc-dev] [Psidev-ms-vocab] QC-CV -> MS-CV

[Eric D. <ede...@sy...>]

Hi everyone, I sent out the Zoom link to a private list of recipients so
as not to post the Zoom link here on these lists. If you did not get a
Zoom link from me and want to attend, please email me and I'll send you
the Zoom link.

Thanks,
Eric


-----Original Message-----
From: walzer <wa...@eb...>
Sent: Thursday, September 16, 2021 3:39 AM
To: psi...@li...;
psi...@li...
Subject: Re: [Psidev-ms-vocab] QC-CV -> MS-CV

Hello Everyone,
thanks for the swift completion of the doodle, this Friday seems like the
most viable option. On that date, there will be another call for some of
you, that has graciously been postponed for half an hour, to make some
time for us.
So we're going to make it short and snappy, slotting 30min. on

Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST

to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will
follow shortly.

later,
   mths

On 2021-09-13 12:55, walzer wrote:
> Hello Everyone,
>
> I just started a doodle to find a date (and a channel on HUPO-PSI
> slack for the topic, but since not everyone is there, I'll also post
> here).
> B'cs of timezone spread Wout suggested we'd start with the USI
> timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST
> https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you
> think we need to add new dates/times)
>
> best,
>   mths
>
> On 2021-08-17 17:49, Mathias Walzer wrote:
>> Dear PSI-MS CV community,
>>
>> I am writing on behalf of the PSI-QC working group, as we want to get
>> our QC-CV 'into the fold'. Before that however, we thought it'd be
>> best to start a conversation on how.
>> We have been developing a separate CV initially to have some freedoms
>> on what/how things work out best for the mzQC format, which relies
>> heavily on CV control.
>> Our CV holds the metric definitions, relations and few additional
>> 'organisational' terms, so far <300 entries, for which we chose the
>> QC
>>
>> prefix (naturally). We ditched the `xref: value-type` declarations in
>> favour of defining term values with full CV terms and relations,
>> which
>>
>> works nicely with the format.
>> The mzQC format is, unlike most PSI formats, JSON based. One of the
>> goals in the design was to bring the format closer to the last miles
>> of analysis
>> (R/pandas/web) but also as something that works between any steps of
>> a MS based study workflow (lightweight with high automation
>> potential). If you want to know more, check out our specification
>> document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we have
>> to cover a vast range of QC/MS related topics in the CV. For that,
>> we've devised a set of templates and rules for adding new
>> term/metrics via GitHub issues. To keep better track of the entries,
>> Nils created a GitHub workflow for obo-to-markup conversion to
>> enhance browsability. QC-CV is not standalone, we base as much as
>> possible on existing definitions, so we
>>
>> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
>> So, overall I think QC-CV would fit in nicely, either as big PR or
>> piece-wise. As for the merge, maybe we can follow the same playbook
>> as the PEFF integration did?
>> What do you think?
>>
>> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
>> gargantuan PR, we should talk.
>>
>> Best,
>>
>> --
>> Mathias Walzer
>> European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome
>> Campus, Hinxton, Cambridge, UK
>> Office: +44 (0)1223 494 2610
>> E-mail: wa...@eb...


_______________________________________________
Psidev-ms-vocab mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-ms-vocab

Re: [Psidev-qc-dev] QC-CV -> MS-CV

[walzer <wa...@eb...>]

Hello Everyone,
thanks for the swift completion of the doodle, this Friday seems like 
the most viable option. On that date, there will be another call for 
some of you, that has graciously been postponed for half an hour, to 
make some time for us.
So we're going to make it short and snappy, slotting 30min. on

Sep 17,Fri, 8 am PST/ 11am EDT / 4pm BST / 5pm CEST

to discuss the QC-CV and how to merge with MS-CV. Zoom/google link will 
follow shortly.

later,
   mths

On 2021-09-13 12:55, walzer wrote:
> Hello Everyone,
> 
> I just started a doodle to find a date (and a channel on HUPO-PSI
> slack for the topic, but since not everyone is there, I'll also post
> here).
> B'cs of timezone spread Wout suggested we'd start with the USI
> timeslot Fridays 8 am PST/ 11am EDT / 4pm BST / 5pm CEST
> https://doodle.com/poll/c76bbv6in2h8ywv3 (admin link in slack if you
> think we need to add new dates/times)
> 
> best,
>   mths
> 
> On 2021-08-17 17:49, Mathias Walzer wrote:
>> Dear PSI-MS CV community,
>> 
>> I am writing on behalf of the PSI-QC working group, as we want to get
>> our
>> QC-CV 'into the fold'. Before that however, we thought it'd be best to
>> start a
>> conversation on how.
>> We have been developing a separate CV initially to have some freedoms
>> on
>> what/how things work out best for the mzQC format, which relies
>> heavily on
>> CV control.
>> Our CV holds the metric definitions, relations and few additional
>> 'organisational' terms, so far <300 entries, for which we chose the QC
>> 
>> prefix (naturally). We ditched the `xref: value-type` declarations in
>> favour of defining term values with full CV terms and relations, which
>> 
>> works nicely with the format.
>> The mzQC format is, unlike most PSI formats, JSON based. One of the
>> goals
>> in the design was to bring the format closer to the last miles of
>> analysis
>> (R/pandas/web) but also as something that works between any steps of a
>> MS
>> based study workflow (lightweight with high automation potential). If
>> you
>> want to know more, check out our specification document draft
>> (https://hupo-psi.github.io/mzQC/). For mzQC, we
>> have to cover a vast range of QC/MS related topics in the CV. For
>> that,
>> we've devised a set of templates and rules for adding new term/metrics
>> via
>> GitHub issues. To keep better track of the entries, Nils created a
>> GitHub
>> workflow for obo-to-markup conversion to enhance browsability. QC-CV
>> is not
>> standalone, we base as much as possible on existing definitions, so we
>> 
>> imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
>> So, overall I think QC-CV would fit in nicely, either as big PR or
>> piece-wise. As for the merge, maybe we can follow the same playbook as
>> the
>> PEFF integration did?
>> What do you think?
>> 
>> TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
>> gargantuan PR, we should talk.
>> 
>> Best,
>> 
>> --
>> Mathias Walzer
>> European Bioinformatics Institute (EMBL-EBI)
>> Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
>> Office: +44 (0)1223 494 2610
>> E-mail: wa...@eb...

Re: [Psidev-qc-dev] Upcoming teleconference 8/9

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210908_telco.md

Our next meeting will be on Sept. 29, by which time we should have prepared a full draft program for our ASMS workshop.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, September 7, 2021 17:27
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 8/9

Dear colleagues,

We have our next teleconference tomorrow, Wednesday September 8, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Merging the QC CV and MS CV: https://github.com/HUPO-PSI/psi-ms-CV/issues/80
  *   ASMS workshop: status and updates

Best,
Wout

[Psidev-qc-dev] Upcoming teleconference 8/9

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday September 8, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   Merging the QC CV and MS CV: https://github.com/HUPO-PSI/psi-ms-CV/issues/80
  *   ASMS workshop: status and updates

Best,
Wout

Re: [Psidev-qc-dev] [Psidev-ms-vocab] QC-CV -> MS-CV

[Eric D. <ede...@sy...>]

Hi everyone, this conversation is now here:

https://github.com/HUPO-PSI/psi-ms-CV/issues/80



Please participate there if you are interested in this.



Thanks,

Eric





*From:* Mathias Walzer <wa...@eb...>
*Sent:* Tuesday, August 17, 2021 9:49 AM
*To:* psi...@li...
*Cc:* psi...@li...
*Subject:* [Psidev-ms-vocab] QC-CV -> MS-CV



Dear PSI-MS CV community,

I am writing on behalf of the PSI-QC working group, as we want to get our
QC-CV 'into the fold'. Before that however, we thought it'd be best to
start a
conversation on how.
We have been developing a separate CV initially to have some freedoms on
what/how things work out best for the mzQC format, which relies heavily on
CV control.
Our CV holds the metric definitions, relations and few additional
'organisational' terms, so far <300 entries, for which we chose the QC
prefix (naturally). We ditched the `xref: value-type` declarations in
favour of defining term values with full CV terms and relations, which
works nicely with the format.
The mzQC format is, unlike most PSI formats, JSON based. One of the goals
in the design was to bring the format closer to the last miles of analysis
(R/pandas/web) but also as something that works between any steps of a MS
based study workflow (lightweight with high automation potential). If you
want to know more, check out our specification document draft (
https://hupo-psi.github.io/mzQC/). For mzQC, we
have to cover a vast range of QC/MS related topics in the CV. For that,
we've devised a set of templates and rules for adding new term/metrics via
GitHub issues. To keep better track of the entries, Nils created a GitHub
workflow for obo-to-markup conversion to enhance browsability. QC-CV is not
standalone, we base as much as possible on existing definitions, so we
imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course.
So, overall I think QC-CV would fit in nicely, either as big PR or
piece-wise. As for the merge, maybe we can follow the same playbook as the
PEFF integration did?
What do you think?

TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a
gargantuan PR, we should talk.

Best,

-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

Re: [Psidev-qc-dev] Upcoming teleconference 18/8

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of yesterday's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210818_telco.md

Additionally, we are collecting ideas for our QC workshop at the ASMS 2021 conference in this document<https://docs.google.com/document/d/1frOR9Z1BZE5ELzl0XznQsPqZWE0IzEEnK9hvsZ87Lds/edit?usp=sharing>.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, August 17, 2021 9:48
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 18/8

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 18, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   ASMS workshop! Our proposal has been accepted as a workshop at the upcoming ASMS conference. We will start discussing the format and content of the workshop. See the submitted workshop abstract<https://docs.google.com/document/d/10-ZY-hiIZqlcKjsgyarlRUF2MN7GuTWJJlaV3MQjcMY/edit> and the notes from our previous discussion on the same topic<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210630_telco.md#asms-workshop>.

Best,
Wout

[Psidev-qc-dev] Instrument dashboard video for ASMS workshop

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

Hi, Paul.

We would like to incorporate some very short (~5 minute) videos demonstrating quality control software into the evening workshop we will produce for the ASMS conference in the first week of November.

Could you produce such a video illustrating the instrument monitoring software you created for the Manchester facility?  I think your software would be a very compelling vision for PIs who manage fleets of instruments-many of them probably assume we are years from producing that kind of functionality.  If you can show historical data in which an instrument flipped from "in control" to "out of control," that would be particularly compelling.  Some of it could be screen recording, but we would also like some clips where you speak on camera.  If you need help editing together clips, I could probably manage some of that for you.  I would like an MP4 to play live at the conference, but we would also likely share the video via YouTube, if that would be okay with you.

Let us know if this is feasible!

Thanks,
Dave

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The integrity and confidentiality of this email are governed by these terms. Disclaimer<https://www.sun.ac.za/emaildisclaimer/default.aspx>
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[Psidev-qc-dev] PTXQC demo video for ASMS workshop

[David T. <dav...@pa...>]

Hi, Chris.

We would like to incorporate some very short (~5 minute) videos demonstrating quality control software into the evening workshop we will produce for the ASMS conference in the first week of November.

Could you produce such a video demonstrating the basic use of PTXQC with a MaxQuant experiment?  Some of it could be screen recording, but we would also like some clips where you speak on camera.  If you need help editing together clips, I could probably manage some of that for you.  I am sure there are _many_ users of MaxQuant who don't realize your very cool toolkit is available, so this would be a way we can improve user takeup of PTXQC.  I would like an MP4 to play live at the conference, but we would also likely share the video via YouTube, if that would be okay with you.

Let us know if this is feasible!

Thanks,
Dave

[Psidev-qc-dev] QC-CV -> MS-CV

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

Dear PSI-MS CV community,

I am writing on behalf of the PSI-QC working group, as we want to get our 
QC-CV 'into the fold'. Before that however, we thought it'd be best to start a 
conversation on how.
We have been developing a separate CV initially to have some freedoms on 
what/how things work out best for the mzQC format, which relies heavily on 
CV control.
Our CV holds the metric definitions, relations and few additional 
'organisational' terms, so far <300 entries, for which we chose the QC 
prefix (naturally). We ditched the `xref: value-type` declarations in 
favour of defining term values with full CV terms and relations, which 
works nicely with the format. 
The mzQC format is, unlike most PSI formats, JSON based. One of the goals 
in the design was to bring the format closer to the last miles of analysis 
(R/pandas/web) but also as something that works between any steps of a MS 
based study workflow (lightweight with high automation potential). If you 
want to know more, check out our specification document draft (https://hupo-psi.github.io/mzQC/). For mzQC, we 
have to cover a vast range of QC/MS related topics in the CV. For that, 
we've devised a set of templates and rules for adding new term/metrics via 
GitHub issues. To keep better track of the entries, Nils created a GitHub 
workflow for obo-to-markup conversion to enhance browsability. QC-CV is not 
standalone, we base as much as possible on existing definitions, so we 
imported few other CVs: UO, OBI, STATO (,NCIT) and PSI-MS of course. 
So, overall I think QC-CV would fit in nicely, either as big PR or 
piece-wise. As for the merge, maybe we can follow the same playbook as the 
PEFF integration did?
What do you think?

TL;DR: mzQC wants to merge their CV into PSI-MS. But before opening a 
gargantuan PR, we should talk.

Best,
-- 
Mathias Walzer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Office: +44 (0)1223 494 2610
E-mail: wa...@eb...

[Psidev-qc-dev] Upcoming teleconference 18/8

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 18, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   ASMS workshop! Our proposal has been accepted as a workshop at the upcoming ASMS conference. We will start discussing the format and content of the workshop. See the submitted workshop abstract<https://docs.google.com/document/d/10-ZY-hiIZqlcKjsgyarlRUF2MN7GuTWJJlaV3MQjcMY/edit> and the notes from our previous discussion on the same topic<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210630_telco.md#asms-workshop>.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference 11/8

[Bittremieux, W. <wbi...@he...>]

Dear colleagues,

You can find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2021/20210811_telco.md

We discussed the important topic of integrating our CV with the PSI-MS CV. We have outlined a few items that should be addressed. As a first step, we'd like to discuss these items on our Slack, so please join us there. Next, we will reach out to the PSI-MS working group to facilitate this integration.

Best,
Wout
________________________________
From: Bittremieux, Wout
Sent: Tuesday, August 10, 2021 17:24
To: psi...@li... <psi...@li...>
Subject: Upcoming teleconference 11/8

Dear colleagues,

We have our next teleconference tomorrow, Wednesday August 11, at 14h00 GMT (15h00 London, 16h00 Western Europe, 7h00 San Diego).

You can connect to our teleconference on Zoom through the following link: https://uchealth.zoom.us/j/92419363577?pwd=WVp5Q3FXNU9vaVdJT0ZNRllXWlN3Zz09
(Password: 012575)

Agenda items:

  *   One major item! Integration of the QC CV with the MS CV. Feedback from the PSI steering committee on the specification document is that we should try to harmonize and/or integrate both CVs. What are potential issues hindering this and how can we solve them?

Best,
Wout