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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 26/09

[Bielow, C. <Chr...@fu...>]

Dear all,

I wont make it for todays meeting (childcare).
Near future plans from my side until next TC: add PTX-QC metrics to the CV.

cheers
Chris

--
Dr. Chris Bielow

Bioinformatics Solution Center (BSC)
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


-----Original Message-----
From: Wout Bittremieux <wbi...@uc...> 
Sent: Tuesday, September 24, 2019 2:01 AM
To: psi...@li...
Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 26/09

Dear colleagues,

This is a reminder that our next teleconference is scheduled for Thursday,
September 26th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape
Town, 17h00 Turkey, 7h00 San Diego).

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

I'd like propose the following agenda items:

- Conception phase seems more or less finished: final action points.
- Documentation phase:
     - Website (including PR #82).
     - Documentation: specification document, implementation/validation
document.
- Please communicate any other agenda items that need to be addressed.

Thanks,
Wout


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

[Psidev-qc-dev] Upcoming teleconference Thursday 26/09

[Wout B. <wbi...@uc...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, September 26th, at 14h00 GMT (15h00 London, 16h00 Western 
Europe / Cape Town, 17h00 Turkey, 7h00 San Diego).

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

I'd like propose the following agenda items:

- Conception phase seems more or less finished: final action points.
- Documentation phase:
     - Website (including PR #82).
     - Documentation: specification document, implementation/validation 
document.
- Please communicate any other agenda items that need to be addressed.

Thanks,
Wout

[Psidev-qc-dev] NO teleconference 12/09

[Wout B. <wbi...@uc...>]

Dear colleagues,

As multiple people are preparing for the HUPO conference next week, we 
won't have a teleconference this week on Thursday 12/09. Our next 
teleconference is scheduled for Thursday 26/09, after which we'll revert 
to the monthly schedule again.

Best,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 29/08

[R S. <r7...@gm...>]

I’m away on holiday as well. Catch up next time.

Kind Regards,
Reza
On 28 Aug 2019, 01:12 +0200, Wout Bittremieux <wbi...@uc...>, wrote:
> Dear colleagues,
>
> This is a reminder that our next teleconference is scheduled for
> Thursday, August 29th, at 14h00 GMT (15h00 London, 16h00 Western Europe
> / Cape Town, 17h00 Turkey, 7h00 San Diego).
>
> You can connect to our teleconference on Google Hangouts through the
> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
>
> After having made nice progress on the CV and schema two weeks ago I
> propose the following agenda items:
>
> - Task distribution to finalize phase 1 (conception) on the action plan.
> - Base set of metrics in the CV
> - Schema definition
> - Reference implementation
> - Initiate phase 2 (documentation) on the action plan.
>
> I'm traveling from San Diego to Belgium tomorrow and on Thursday, so I'm
> not 100% sure yet I'll be able to attend the teleconference.
>
> Thanks,
> Wout
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Upcoming teleconference Thursday 29/08

[Wout B. <wbi...@uc...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, August 29th, at 14h00 GMT (15h00 London, 16h00 Western Europe 
/ Cape Town, 17h00 Turkey, 7h00 San Diego).

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

After having made nice progress on the CV and schema two weeks ago I 
propose the following agenda items:

- Task distribution to finalize phase 1 (conception) on the action plan.
     - Base set of metrics in the CV
     - Schema definition
     - Reference implementation
- Initiate phase 2 (documentation) on the action plan.

I'm traveling from San Diego to Belgium tomorrow and on Thursday, so I'm 
not 100% sure yet I'll be able to attend the teleconference.

Thanks,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 15/08

[Wout B. <wbi...@uc...>]

Dear colleagues,

You can find the meeting notes of yesterday's call here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190815_telco.md

Best,
Wout

On 13/08/2019 19:57, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, August 15th, at 14h00 GMT (15h00 London, 16h00 Western Europe 
> / Cape Town, 17h00 Turkey, 7h00 San Diego).
> 
> You can connect to our teleconference on Google Hangouts through the 
> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2
> 
> I propose the following major agenda item now that Julian is available 
> again:
> 
> - CV: current state, open issues, moving forward.
> 
> Additional topics related to the JSON schema can be addressed if time 
> allows it.
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Upcoming teleconference Thursday 15/08

[Wout B. <wbi...@uc...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, August 15th, at 14h00 GMT (15h00 London, 16h00 Western Europe 
/ Cape Town, 17h00 Turkey, 7h00 San Diego).

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

I propose the following major agenda item now that Julian is available 
again:

- CV: current state, open issues, moving forward.

Additional topics related to the JSON schema can be addressed if time 
allows it.

Thanks,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 01/08

[Wout B. <wbi...@uc...>]

Dear colleagues,

You can find the meeting notes of yesterday's call here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190801_telco.md

I'm including our action points below:

- Request that missing terms are included in the CV. For example, all 
terms used in the example files that are not in the CV yet.
- Focus on the CV! We need a finalized CV to create proper mzQC example 
files.
- Several technical questions were identified in the follow-up mail to 
the meeting agenda. Resolve these in the next two weeks via issues on 
GitHub / the mailing list / Slack.

Please note that as we're currently crucial phase for mzQC v1 completion 
our next call will be in two weeks. The next call will be on Thursday 
August 15. A reminder will be circulated via the mailing list.

Best,
Wout

On 31/07/2019 11:42, Wout Bittremieux wrote:
> Additionally, if time allows we can discuss (and resolve) these items 
> from the issues on GitHub and from Slack:
> 
> CV:
> - #62: Convert the value type in the CV from XML nomenclature to JSON 
> nomenclature.
> - #72: Include units in the CV?
> - Fix and add CV terms: #26, #42, #52, #64, #72.
> - #65/#67 and #71: Several CV updates.
> - Slack question: Quantiles vs absolute values?
> 
> Schema:
> - #61: "accession" vs "term"?
> - #68: Move "unit" from "cvParameter" to "qualityMetric"?
> 
> 
> On 30/07/2019 16:40, Wout Bittremieux wrote:
>> Dear colleagues,
>>
>> This is a reminder that our next teleconference is scheduled for 
>> Thursday, August 1st, at 14h00 GMT (15h00 London, 16h00 Western Europe 
>> / Cape Town, 17h00 Turkey, 7h00 San Diego).
>>
>> 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:
>>
>> - Report progress on road map stage 1: CV metrics & reference 
>> implementation
>> - Follow up on the action points from last time:
>>      ❓ Everyone: Check whether all metrics in the implementations are 
>> already in the CV, otherwise request them.
>>      ❓ Everyone: Share the mzQC software implementations that are 
>> currently still in private development.
>>      ❓ Everyone: Compile good examples using your tools for various 
>> use cases.
>>      ❓ Dave: Contact Michael Bereman w.r.t. mzQC support in SProCoP.
>>      ✅ Chris: Share the report on QC for SWATH that was mentioned 
>> during the call.
>>
>>
>> Thanks,
>> 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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 01/08

[Wout B. <wbi...@uc...>]

Additionally, if time allows we can discuss (and resolve) these items 
from the issues on GitHub and from Slack:

CV:
- #62: Convert the value type in the CV from XML nomenclature to JSON 
nomenclature.
- #72: Include units in the CV?
- Fix and add CV terms: #26, #42, #52, #64, #72.
- #65/#67 and #71: Several CV updates.
- Slack question: Quantiles vs absolute values?

Schema:
- #61: "accession" vs "term"?
- #68: Move "unit" from "cvParameter" to "qualityMetric"?


On 30/07/2019 16:40, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, August 1st, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
> Cape Town, 17h00 Turkey, 7h00 San Diego).
> 
> 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:
> 
> - Report progress on road map stage 1: CV metrics & reference 
> implementation
> - Follow up on the action points from last time:
>      ❓ Everyone: Check whether all metrics in the implementations are 
> already in the CV, otherwise request them.
>      ❓ Everyone: Share the mzQC software implementations that are 
> currently still in private development.
>      ❓ Everyone: Compile good examples using your tools for various use 
> cases.
>      ❓ Dave: Contact Michael Bereman w.r.t. mzQC support in SProCoP.
>      ✅ Chris: Share the report on QC for SWATH that was mentioned during 
> the call.
> 
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Upcoming teleconference Thursday 01/08

[Wout B. <wbi...@uc...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, August 1st, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
Cape Town, 17h00 Turkey, 7h00 San Diego).

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:

- Report progress on road map stage 1: CV metrics & reference implementation
- Follow up on the action points from last time:
     ❓ Everyone: Check whether all metrics in the implementations are 
already in the CV, otherwise request them.
     ❓ Everyone: Share the mzQC software implementations that are 
currently still in private development.
     ❓ Everyone: Compile good examples using your tools for various use 
cases.
     ❓ Dave: Contact Michael Bereman w.r.t. mzQC support in SProCoP.
     ✅ Chris: Share the report on QC for SWATH that was mentioned during 
the call.


Thanks,
Wout

Re: [Psidev-qc-dev] Automatic generation of SWATH metrics in mzQC format

[Pauw, M, M. [<pau...@su...>]

Wow! Thank you so much, Wout!

I really appreciate the feedback, will get right on it.

Kind regards,
Marina Pauw

-----Original Message-----
From: Wout Bittremieux <wbi...@uc...>
Sent: Friday, 19 July 2019 02:19
To: Tabb, David, Prof [dt...@su...] <dt...@su...>; Pauw, M, Mej [pau...@su...] <pau...@su...>; psi...@li...
Subject: Re: [Psidev-qc-dev] Automatic generation of SWATH metrics in mzQC format

Great work! 👏

I briefly went through the file and I have a few small comments:

- You forgot the outer curly brackets around the mzQC element, which should also be a string.
- Make sure you use the correct capitalization of the JSON keys. For example, "URI" in analysisSoftware and the CVs -> "uri".
- runQuality/inputFiles/analysisSoftware should be lists.
- The "location" of input files should be a URI; i.e. prefixed by "file://" for local files. Also, the location and name should match.
- It is mandatory to specify the type of the input file (i.e. raw, mzML, ...).
- Make sure the name of the quality parameters exactly matches the terms in the CV, otherwise the semantic validation will fail.
- You should request that the missing terms are added to the CV in an issue on the repository.
- Are the units for metrics swDensity50/PeakCapacity/PeakSymmetry
correct? It's specified as a count, but the values are floats. Similarly for metric swDensityIQR/MS2TICTotal/MS1TICTotal, although there at least all the floats are xxx.0.
- CV term MS:1000040 can be used to specify an m/z unit.
- Make sure the CV keys in the CV list are the same as used for the quality parameters, i.e. capitalization is different here. If these are not the same the correct CV can't be found (and the validator will throw an error).
- The CV URIs should be the raw obo files rather than the Github web pages containing the obo files, otherwise the ontology parser won't be able to load it correctly. This is wrong in the current examples files that are online as well. Probably ideally we should also use URIs that include a specific commit rather than master, as the content of the files can change in that case.

It's great to see some tools automatically exporting to mzQC.

On 2019-07-18 06:44, Tabb, David, Prof [dt...@su...] wrote:
> Hi, all.
>
> I am really proud of Marina Pauw’s progress with her “SwaMe” quality
> control metric generator for SWATH data sets (with some very helpful
> input from Paul Brack).  Her prototype now exports its quality metrics
> in JSON!  I am attaching an example of the output at this early stage.
> We are still finalizing the list of metrics that will be included in
> the manuscript introducing the software, but this is what we believe
> represents the current thinking for our data structures.
>
> Talk to you shortly,
> Dave
>
> <http://www.sun.ac.za/english/about-us/strategic-documents>
>
> The integrity and confidentiality of this email are governed by these
> terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer > Die
> integriteit en vertroulikheid van hierdie e-pos word deur die volgende
> bepalings bereël. Vrywaringsklousule
> <http://www.sun.ac.za/emaildisclaimer >
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
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The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/07

[Wout B. <wbi...@uc...>]

Dear colleagues,

You can find the meeting notes of today's call here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190718_telco.md

I'm including our action points below:

- Everyone: Check whether all metrics in the implementations are already 
in the CV, otherwise request them.
- Everyone: Share the mzQC software implementations that are currently 
still in private development.
- Everyone: Compile good examples using your tools for various use cases.
- Chris: Share the report on QC for SWATH that was mentioned during the 
call.
- Dave: Contact Michael Bereman w.r.t. mzQC support in SProCoP.

Please note that as we're currently crucial phase for mzQC v1 completion 
our next call will be in two weeks. The next call will be on Thursday 
August 1. A reminder will be circulated via the mailing list.

Best,
Wout

On 2019-07-16 17:09, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
> Cape Town, 17h00 Turkey, 7h00 Seattle).
> 
> 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:
> 
> - Revisit road map to mzQC v1.0: 
> https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1 
> 
> - Timeline and task distribution to finalize mzQC v1.0.
> - Please communicate any other agenda items that need to be addressed.
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Automatic generation of SWATH metrics in mzQC format

[Wout B. <wbi...@uc...>]

Great work! 👏

I briefly went through the file and I have a few small comments:

- You forgot the outer curly brackets around the mzQC element, which 
should also be a string.
- Make sure you use the correct capitalization of the JSON keys. For 
example, "URI" in analysisSoftware and the CVs -> "uri".
- runQuality/inputFiles/analysisSoftware should be lists.
- The "location" of input files should be a URI; i.e. prefixed by 
"file://" for local files. Also, the location and name should match.
- It is mandatory to specify the type of the input file (i.e. raw, mzML, 
...).
- Make sure the name of the quality parameters exactly matches the terms 
in the CV, otherwise the semantic validation will fail.
- You should request that the missing terms are added to the CV in an 
issue on the repository.
- Are the units for metrics swDensity50/PeakCapacity/PeakSymmetry 
correct? It's specified as a count, but the values are floats. Similarly 
for metric swDensityIQR/MS2TICTotal/MS1TICTotal, although there at least 
all the floats are xxx.0.
- CV term MS:1000040 can be used to specify an m/z unit.
- Make sure the CV keys in the CV list are the same as used for the 
quality parameters, i.e. capitalization is different here. If these are 
not the same the correct CV can't be found (and the validator will throw 
an error).
- The CV URIs should be the raw obo files rather than the Github web 
pages containing the obo files, otherwise the ontology parser won't be 
able to load it correctly. This is wrong in the current examples files 
that are online as well. Probably ideally we should also use URIs that 
include a specific commit rather than master, as the content of the 
files can change in that case.

It's great to see some tools automatically exporting to mzQC.

On 2019-07-18 06:44, Tabb, David, Prof [dt...@su...] wrote:
> Hi, all.
> 
> I am really proud of Marina Pauw’s progress with her “SwaMe” quality 
> control metric generator for SWATH data sets (with some very helpful 
> input from Paul Brack).  Her prototype now exports its quality metrics 
> in JSON!  I am attaching an example of the output at this early stage.  
> We are still finalizing the list of metrics that will be included in the 
> manuscript introducing the software, but this is what we believe 
> represents the current thinking for our data structures.
> 
> Talk to you shortly,
> Dave
> 
> <http://www.sun.ac.za/english/about-us/strategic-documents>
> 
> The integrity and confidentiality of this email are governed by these 
> terms. Disclaimer <http://www.sun.ac.za/emaildisclaimer >
> Die integriteit en vertroulikheid van hierdie e-pos word deur die 
> volgende bepalings bereël. Vrywaringsklousule 
> <http://www.sun.ac.za/emaildisclaimer >
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
> 

[Psidev-qc-dev] Automatic generation of SWATH metrics in mzQC format

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

Hi, all.

I am really proud of Marina Pauw's progress with her "SwaMe" quality control metric generator for SWATH data sets (with some very helpful input from Paul Brack).  Her prototype now exports its quality metrics in JSON!  I am attaching an example of the output at this early stage.  We are still finalizing the list of metrics that will be included in the manuscript introducing the software, but this is what we believe represents the current thinking for our data structures.

Talk to you shortly,
Dave
[http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents>

The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bere?l. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/07

[eralp d. <era...@gm...>]

Dear all,

Due to a conflicting meeting, I won’t be able to join this month.

Best,
Eralp

> On Jul 17, 2019, at 09:24, Julian Uszkoreit via Psidev-qc-dev <psi...@li...> wrote:
> 
> Hej all,
> 
> 
> I won't be there as well, the holiday season is beginning to start.
> 
> But as our lab-move is now finally done (also for the IT), I will have time for mzQC again from mid-August onwards.
> 
> 
> Best,
> 
> Julian
> 
> 
> 
> On 17.07.19 07:52, Tenzer, Stefan wrote:
>> Hi everyone,
>> 
>> I unfortunately will not be able to participate tomorrow.
>> 
>> Best wishes,
>> 
>> Stefan
>> 
>> 
>> Am 17.07.2019 um 02:16 schrieb Wout Bittremieux <wbi...@uc...>:
>> 
>>> Sorry, I forgot the update the date in the main text. That should be July 18th.
>>> 
>>> Best,
>>> Wout
>>> 
>>> On 2019-07-16 17:09, Wout Bittremieux wrote:
>>>> Dear colleagues,
>>>> This is a reminder that our next teleconference is scheduled for Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape Town, 17h00 Turkey, 7h00 Seattle).
>>>> 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:
>>>> - Revisit road map to mzQC v1.0: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1 - Timeline and task distribution to finalize mzQC v1.0.
>>>> - Please communicate any other agenda items that need to be addressed.
>>>> Thanks,
>>>> 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
>> 
>> 
>> _______________________________________________
>> 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

Eralp Dogu
Associate Professor
Mugla University
Department of Statistics
Mugla TURKEY
email: era...@mu...
https://sites.google.com/site/eralpdogu/

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/07

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

Hej all,


I won't be there as well, the holiday season is beginning to start.

But as our lab-move is now finally done (also for the IT), I will have 
time for mzQC again from mid-August onwards.


Best,

Julian



On 17.07.19 07:52, Tenzer, Stefan wrote:
> Hi everyone,
>
> I unfortunately will not be able to participate tomorrow.
>
> Best wishes,
>
> Stefan
>
>
> Am 17.07.2019 um 02:16 schrieb Wout Bittremieux <wbi...@uc...>:
>
>> Sorry, I forgot the update the date in the main text. That should be July 18th.
>>
>> Best,
>> Wout
>>
>> On 2019-07-16 17:09, Wout Bittremieux wrote:
>>> Dear colleagues,
>>> This is a reminder that our next teleconference is scheduled for Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape Town, 17h00 Turkey, 7h00 Seattle).
>>> 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:
>>> - Revisit road map to mzQC v1.0: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1 - Timeline and task distribution to finalize mzQC v1.0.
>>> - Please communicate any other agenda items that need to be addressed.
>>> Thanks,
>>> 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
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/07

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

Hi everyone,

I unfortunately will not be able to participate tomorrow.

Best wishes,

Stefan


Am 17.07.2019 um 02:16 schrieb Wout Bittremieux <wbi...@uc...>:

> Sorry, I forgot the update the date in the main text. That should be July 18th.
> 
> Best,
> Wout
> 
> On 2019-07-16 17:09, Wout Bittremieux wrote:
>> Dear colleagues,
>> This is a reminder that our next teleconference is scheduled for Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / Cape Town, 17h00 Turkey, 7h00 Seattle).
>> 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:
>> - Revisit road map to mzQC v1.0: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1 - Timeline and task distribution to finalize mzQC v1.0.
>> - Please communicate any other agenda items that need to be addressed.
>> Thanks,
>> 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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 18/07

[Wout B. <wbi...@uc...>]

Sorry, I forgot the update the date in the main text. That should be 
July 18th.

Best,
Wout

On 2019-07-16 17:09, Wout Bittremieux wrote:
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for 
> Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
> Cape Town, 17h00 Turkey, 7h00 Seattle).
> 
> 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:
> 
> - Revisit road map to mzQC v1.0: 
> https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1 
> 
> - Timeline and task distribution to finalize mzQC v1.0.
> - Please communicate any other agenda items that need to be addressed.
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

[Psidev-qc-dev] Upcoming teleconference Thursday 18/07

[Wout B. <wbi...@uc...>]

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, June 20th, at 14h00 GMT (15h00 London, 16h00 Western Europe / 
Cape Town, 17h00 Turkey, 7h00 Seattle).

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:

- Revisit road map to mzQC v1.0: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md#roadmap-to-mzqc-v1
- Timeline and task distribution to finalize mzQC v1.0.
- Please communicate any other agenda items that need to be addressed.

Thanks,
Wout

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06

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

Dear colleagues,

You can find the meeting notes of today's call here: 
https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20190620_telco.md

Best,
Wout

On 2019-06-20 03:08, Walzer wrote:
> Good morning all,
> I'd like to add few points to the agenda.
> 
> - after the last call I talked to Chris a bit longer and he gave me 
> valuable feedback which I think we should include in our release planning.
> 
> - I implemented a python library (which I hope can serve as reference 
> implementation). Most is done (data structures, I/O, syntactic 
> validation), though it needs some more days of work (for semantic 
> validation, R adapter and unit tests). Whilst implementing, I stumbled 
> upon some schema details that I'd like to discuss (amongst others #68).
> 
> - Working on adapter and semantic validation bits, I realized we do not 
> have a document that specifies the semantics. It does not have to be a 
> separate document in the end, but can be in the documentation. For now 
> however, it would serve the purpose of focus to collect the points we 
> figure in the call first, then build it in the doc.
> 
> - Increase frequency of calls during the hot phase?
> 
> best,
> 
>    mths
> 
> On 19/06/2019 21:05, Tabb, David, Prof [dt...@su...] wrote:
> 
> Hi, all. I am on vacation this week. For my part, I was very glad to 
> meet Eralp Dogu at ASMS. He develops the MSstats quality module, which 
> can import quality metrics from SProCoP from Skyline! I believe he's 
> part of this group now. Welcome, sir! I will return to a more normal 
> schedule on June 30th. Thanks, Dave -----Original Message----- From: 
> Wout Bittremieux <wo...@uw...> Sent: Wednesday, June 19, 2019 10:32 AM 
> To: psi...@li... Subject: [Psidev-qc-dev] 
> Upcoming teleconference Thursday 20/06 Dear colleagues, This is a 
> reminder that our next teleconference is scheduled for Thursday, June 
> 20th, 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 propose the 
> following agenda items: - QC overview at ASMS. - Resolve outstanding 
> issues identified during the spring meeting in Cape Town: 
> https://github.com/HUPO-PSI/mzQC/pull/67 - Timeline and task 
> distribution to finalize mzQC 1.0 in the summer. - Please communicate 
> any other agenda items that need to be addressed. Thanks, Wout 
> _______________________________________________ Psidev-qc-dev mailing 
> list Psi...@li... 
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev 
> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> 
> The integrity and confidentiality of this email are governed by these 
> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit 
> en vertroulikheid van hierdie e-pos word deur die volgende bepalings 
> bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> 
> _______________________________________________ Psidev-qc-dev mailing 
> list Psi...@li... 
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
> -- 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 mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06

[Chris B. <chr...@fu...>]

Dear all,

I could not make it, since currently on holidays. Talk to you next time :)

cheers

Chris

Am 2019-06-20 um 3:11 PM schrieb eralp dogu:
> Many thanks for the introduction Dave! Great to be on board.
>
> Eralp
>
>> On Jun 19, 2019, at 23:05, Tabb, David, Prof [dt...@su... 
>> <mailto:dt...@su...>] <dt...@su... <mailto:dt...@su...>> 
>> wrote:
>>
>> Hi, all.
>>
>> I am on vacation this week.
>>
>> For my part, I was very glad to meet Eralp Dogu at ASMS.  He develops 
>> the MSstats quality module, which can import quality metrics from 
>> SProCoP from Skyline!  I believe he's part of this group now. 
>>  Welcome, sir!
>>
>> I will return to a more normal schedule on June 30th.
>>
>> Thanks,
>> Dave
>>
>> -----Original Message-----
>> From: Wout Bittremieux <wo...@uw... <mailto:wo...@uw...>>
>> Sent: Wednesday, June 19, 2019 10:32 AM
>> To: psi...@li... 
>> <mailto:psi...@li...>
>> Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06
>>
>> Dear colleagues,
>>
>> This is a reminder that our next teleconference is scheduled for 
>> Thursday, June 20th, 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 propose the following agenda items:
>>
>> - QC overview at ASMS.
>> - Resolve outstanding issues identified during the spring meeting in 
>> Cape Town: https://github.com/HUPO-PSI/mzQC/pull/67
>> - Timeline and task distribution to finalize mzQC 1.0 in the summer.
>> - Please communicate any other agenda items that need to be addressed.
>>
>> Thanks,
>> Wout
>>
>>
>> _______________________________________________
>> Psidev-qc-dev mailing list
>> Psi...@li... 
>> <mailto:Psi...@li...>
>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents>
>>
>> The integrity and confidentiality of this email are governed by these 
>> terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
>> Die integriteit en vertroulikheid van hierdie e-pos word deur die 
>> volgende bepalings bereël. 
>> Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
>>
>> _______________________________________________
>> Psidev-qc-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
>
> Eralp Dogu
> Associate Professor
> Mugla University
> Department of Statistics
> Mugla TURKEY
> email: era...@mu... <mailto:era...@mu...>
> https://sites.google.com/site/eralpdogu/
>
>
>
>
>
>
>
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06

[eralp d. <era...@gm...>]

Many thanks for the introduction Dave! Great to be on board. 

Eralp

> On Jun 19, 2019, at 23:05, Tabb, David, Prof [dt...@su...] <dt...@su...> wrote:
> 
> Hi, all.
> 
> I am on vacation this week.
> 
> For my part, I was very glad to meet Eralp Dogu at ASMS.  He develops the MSstats quality module, which can import quality metrics from SProCoP from Skyline!  I believe he's part of this group now.  Welcome, sir!
> 
> I will return to a more normal schedule on June 30th.
> 
> Thanks,
> Dave
> 
> -----Original Message-----
> From: Wout Bittremieux <wo...@uw...>
> Sent: Wednesday, June 19, 2019 10:32 AM
> To: psi...@li...
> Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06
> 
> Dear colleagues,
> 
> This is a reminder that our next teleconference is scheduled for Thursday, June 20th, 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 propose the following agenda items:
> 
> - QC overview at ASMS.
> - Resolve outstanding issues identified during the spring meeting in Cape Town: https://github.com/HUPO-PSI/mzQC/pull/67
> - Timeline and task distribution to finalize mzQC 1.0 in the summer.
> - Please communicate any other agenda items that need to be addressed.
> 
> Thanks,
> Wout
> 
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
> [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents>
> 
> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>
> 
> _______________________________________________
> Psidev-qc-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev

Eralp Dogu
Associate Professor
Mugla University
Department of Statistics
Mugla TURKEY
email: era...@mu...
https://sites.google.com/site/eralpdogu/

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06

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

Good morning all,
I'd like to add few points to the agenda.

- after the last call I talked to Chris a bit longer and he gave me 
valuable feedback which I think we should include in our release planning.

- I implemented a python library (which I hope can serve as reference 
implementation). Most is done (data structures, I/O, syntactic 
validation), though it needs some more days of work (for semantic 
validation, R adapter and unit tests). Whilst implementing, I stumbled 
upon some schema details that I'd like to discuss (amongst others #68).

- Working on adapter and semantic validation bits, I realized we do not 
have a document that specifies the semantics. It does not have to be a 
separate document in the end, but can be in the documentation. For now 
however, it would serve the purpose of focus to collect the points we 
figure in the call first, then build it in the doc.

- Increase frequency of calls during the hot phase?

best,

   mths

On 19/06/2019 21:05, Tabb, David, Prof [dt...@su...] wrote:

Hi, all. I am on vacation this week. For my part, I was very glad to 
meet Eralp Dogu at ASMS. He develops the MSstats quality module, which 
can import quality metrics from SProCoP from Skyline! I believe he's 
part of this group now. Welcome, sir! I will return to a more normal 
schedule on June 30th. Thanks, Dave -----Original Message----- From: 
Wout Bittremieux <wo...@uw...> Sent: Wednesday, June 19, 2019 10:32 AM 
To: psi...@li... Subject: [Psidev-qc-dev] 
Upcoming teleconference Thursday 20/06 Dear colleagues, This is a 
reminder that our next teleconference is scheduled for Thursday, June 
20th, 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 propose the 
following agenda items: - QC overview at ASMS. - Resolve outstanding 
issues identified during the spring meeting in Cape Town: 
https://github.com/HUPO-PSI/mzQC/pull/67 - Timeline and task 
distribution to finalize mzQC 1.0 in the summer. - Please communicate 
any other agenda items that need to be addressed. Thanks, Wout 
_______________________________________________ Psidev-qc-dev mailing 
list Psi...@li... 
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev 
[http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> 
The integrity and confidentiality of this email are governed by these 
terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit 
en vertroulikheid van hierdie e-pos word deur die volgende bepalings 
bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> 
_______________________________________________ Psidev-qc-dev mailing 
list Psi...@li... 
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
-- 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 Thursday 20/06

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

Hi, all.

I am on vacation this week.

For my part, I was very glad to meet Eralp Dogu at ASMS.  He develops the MSstats quality module, which can import quality metrics from SProCoP from Skyline!  I believe he's part of this group now.  Welcome, sir!

I will return to a more normal schedule on June 30th.

Thanks,
Dave

-----Original Message-----
From: Wout Bittremieux <wo...@uw...>
Sent: Wednesday, June 19, 2019 10:32 AM
To: psi...@li...
Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 20/06

Dear colleagues,

This is a reminder that our next teleconference is scheduled for Thursday, June 20th, 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 propose the following agenda items:

- QC overview at ASMS.
- Resolve outstanding issues identified during the spring meeting in Cape Town: https://github.com/HUPO-PSI/mzQC/pull/67
- Timeline and task distribution to finalize mzQC 1.0 in the summer.
- Please communicate any other agenda items that need to be addressed.

Thanks,
Wout


_______________________________________________
Psidev-qc-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev
[http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents>

The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer>
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

[Psidev-qc-dev] Upcoming teleconference Thursday 20/06

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

Dear colleagues,

This is a reminder that our next teleconference is scheduled for 
Thursday, June 20th, 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 propose the following agenda items:

- QC overview at ASMS.
- Resolve outstanding issues identified during the spring meeting in 
Cape Town: https://github.com/HUPO-PSI/mzQC/pull/67
- Timeline and task distribution to finalize mzQC 1.0 in the summer.
- Please communicate any other agenda items that need to be addressed.

Thanks,
Wout