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From: Wout B. <wo...@uw...> - 2018-12-20 22:38:18
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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 |
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From: Wout B. <wo...@uw...> - 2018-12-20 18:00:27
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Dear colleages, You can find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/mzQC/blob/master/meeting_notes/20181220_telco.md Happy holidays and best wishes for a wonderful new year. Best, Wout On 12/17/18 8:31 PM, Wout Bittremieux wrote: > Dear colleagues, > > This is a reminder that the final teleconference of the year is > scheduled for Thursday, December 20th, 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: > > - Tasks to prepare for the PSI spring meeting. > - Conference season: ASMS/HUPO workshops, ... > - Updated group charter. > - Any additional items that need to be discussed... > > Thanks, > Wout > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Walzer <wa...@eb...> - 2018-12-20 09:36:10
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Hi there, On 18/12/2018 05:02, Tabb, David, Prof [dt...@su...] wrote: > Hi, all. > > > I will miss this call as I will be on my honeymoon in Spain. Mathias, are you available to chair? Sure thing. Have a great honeymoon! > > Happy Holidays, > > Dave Happy Holidays, mths > ________________________________ > From: Wout Bittremieux <wo...@uw...> > Sent: Tuesday, December 18, 2018 6:31:19 AM > To: psi...@li... > Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 20/12 > > Dear colleagues, > > This is a reminder that the final teleconference of the year is > scheduled for Thursday, December 20th, 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: > > - Tasks to prepare for the PSI spring meeting. > - Conference season: ASMS/HUPO workshops, ... > - Updated group charter. > - Any additional items that need to be discussed... > > 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 bere?l. 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... |
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From: Julian U. <jul...@ru...> - 2018-12-20 08:11:00
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Hi all, I have a lecture at the scheduled time this week, but might be able to join later. Best regards, Julian On 18.12.18 06:02, Tabb, David, Prof [dt...@su...] wrote: > > Hi, all. > > > I will miss this call as I will be on my honeymoon in Spain. Mathias, > are you available to chair? > > > Happy Holidays, > > Dave > > ------------------------------------------------------------------------ > *From:* Wout Bittremieux <wo...@uw...> > *Sent:* Tuesday, December 18, 2018 6:31:19 AM > *To:* psi...@li... > *Subject:* [Psidev-qc-dev] Upcoming teleconference Thursday 20/12 > Dear colleagues, > > This is a reminder that the final teleconference of the year is > scheduled for Thursday, December 20th, 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: > > - Tasks to prepare for the PSI spring meeting. > - Conference season: ASMS/HUPO workshops, ... > - Updated group charter. > - Any additional items that need to be discussed... > > Thanks, > Wout > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > <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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From: Tabb, D. P. [<dt...@su...> - 2018-12-18 06:38:33
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Hi, all. I will miss this call as I will be on my honeymoon in Spain. Mathias, are you available to chair? Happy Holidays, Dave ________________________________ From: Wout Bittremieux <wo...@uw...> Sent: Tuesday, December 18, 2018 6:31:19 AM To: psi...@li... Subject: [Psidev-qc-dev] Upcoming teleconference Thursday 20/12 Dear colleagues, This is a reminder that the final teleconference of the year is scheduled for Thursday, December 20th, 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: - Tasks to prepare for the PSI spring meeting. - Conference season: ASMS/HUPO workshops, ... - Updated group charter. - Any additional items that need to be discussed... 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 bere?l. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Wout B. <wo...@uw...> - 2018-12-18 04:31:51
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Dear colleagues, This is a reminder that the final teleconference of the year is scheduled for Thursday, December 20th, 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: - Tasks to prepare for the PSI spring meeting. - Conference season: ASMS/HUPO workshops, ... - Updated group charter. - Any additional items that need to be discussed... Thanks, Wout |
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From: Wout B. <wo...@uw...> - 2018-12-13 16:08:11
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-------- Forwarded Message -------- Subject: RE: PSI2019 Date: Thu, 13 Dec 2018 11:44:55 +0000 From: Jones, Andy <And...@li...> To: 'psi...@eb...' <psi...@eb...>, 'psi...@li...' <psi...@li...>, 'psi...@li...' <psi...@li...> Hi all, I am pleased to announce that registration is now open for the PSI 2019 meeting, which will take place in Cape Town, SA, March 18-20 : http://psidev.info/hupo-psi-meeting-2019. As a reminder, 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. We hope to see you there! Best wishes Andy |
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From: Tenzer, S. <te...@un...> - 2018-11-26 11:06:49
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Hi everyone, my apologies for being out of the discussion/webmeetings for a while - there has been a little too much on my desk the last months! I was following the updates and hope to be back in the meetings as soon as possible! Cheers, Stefan Univ.-Prof. Dr. rer. nat. Stefan Tenzer ______________________________________________ UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Immunologie Core Facility für Massenspektrometrie Gebäude 308A Langenbeckstr. 1, 55131 Mainz www.immunologie-mainz.de<http://www.immunologie-mainz.de> Telefon: +49 (0) 6131 17-6199 Telefax: +49 (0) 6131 17-6202 E-mail: te...@un... Am 26.11.2018 um 11:21 schrieb Walzer <wa...@eb...<mailto:wa...@eb...>>: Hi all, I definitively agree, Wout should be there (should have been in the first place, my apologies, I guess overlooked that because secretary wasn't included in the template). cheers, On 22/11/18 04:37, Tabb, David, Prof [dt...@su...<mailto:dt...@su...>] wrote: Hi, all. Working from an update by Mathias, I have edited our charter a fair bit (see attached). Could I get confirmation on these points? 1) Our charter did not name our secretary, but I have listed Wout in this role since he plays it so diligently! 2) Stefan Tenzer is listed as co-chair and as editor. Is he continuing in those roles? I haven't looked at our rosters from the telecons, but it seems like a while since we talked. 3) I have reshaped the text to reflect our work on mzQC rather than qcML (JSON rather than XML). Thanks, Dave [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents><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><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><http://www.sun.ac.za/emaildisclaimer> _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto: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...<mailto:wa...@eb...> _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Walzer <wa...@eb...> - 2018-11-26 10:21:32
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Hi all, I definitively agree, Wout should be there (should have been in the first place, my apologies, I guess overlooked that because secretary wasn't included in the template). cheers, On 22/11/18 04:37, Tabb, David, Prof [dt...@su...] wrote: > Hi, all. > > > Working from an update by Mathias, I have edited our charter a fair bit (see attached). Could I get confirmation on these points? > > > 1) Our charter did not name our secretary, but I have listed Wout in this role since he plays it so diligently! > > 2) Stefan Tenzer is listed as co-chair and as editor. Is he continuing in those roles? I haven't looked at our rosters from the telecons, but it seems like a while since we talked. > > 3) I have reshaped the text to reflect our work on mzQC rather than qcML (JSON rather than XML). > > > Thanks, > > 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 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... |
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From: Tabb, D. P. [<dt...@su...> - 2018-11-22 04:53:09
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Hi, all. Working from an update by Mathias, I have edited our charter a fair bit (see attached). Could I get confirmation on these points? 1) Our charter did not name our secretary, but I have listed Wout in this role since he plays it so diligently! 2) Stefan Tenzer is listed as co-chair and as editor. Is he continuing in those roles? I haven't looked at our rosters from the telecons, but it seems like a while since we talked. 3) I have reshaped the text to reflect our work on mzQC rather than qcML (JSON rather than XML). Thanks, 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 bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Bittremieux W. <wou...@ua...> - 2018-11-19 16:08:55
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Begin forwarded message: From: "Jones, Andy" <And...@li...<mailto:And...@li...>> Subject: [Psi-announce] PSI2019 Date: 19 November 2018 at 07:59:37 GMT-8 To: "'psi...@eb...<mailto:psi...@eb...>'" <psi...@eb...<mailto:psi...@eb...>>, "'psi...@li...<mailto:psi...@li...>'" <psi...@li...<mailto:psi...@li...>>, "'psi...@li...<mailto:psi...@li...>'" <psi...@li...<mailto:psi...@li...>> Dear all, We have now finalised the location and date of the PSI2019 meeting, which will take place in Cape Town, South Africa on 18th-20th March, 2019. Please make a note in your diaries, if you are interested in joining the meeting. We will be updating the PSI website in the coming weeks with details of the talks, work group tracks and the venue/logistics. We look forward to seeing many of you there! Best wishes Andy From: Jones, Andy Sent: 24 October 2018 17:07 To: 'psi...@eb...<mailto:psi...@eb...>' <psi...@eb...<mailto:psi...@eb...>>; 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>>; 'psi...@li...<mailto:psi...@li...>' <psi...@li...<mailto:psi...@li...>> Subject: PSI2019 plans Hi all, Apologies for the cross-posting. The PSI steering committee will shortly be finalising the venue for the PSI2019 meeting. If you have been to a previous meeting or might be interested in participating in 2019, please can you complete this very short google form to indicate your preferred venue: https://goo.gl/forms/8t4CogZu3xVzRVJQ2, before end Oct i.e. within one week. We would like to take on board community considerations for overseas travel before selecting the final location in early November. We expect to announce the final, selected location by mid November. Best wishes Andy Jones _______________________________________________ Psi-announce mailing list Psi...@eb...<mailto:Psi...@eb...> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
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From: Jinmeng J. <jia...@16...> - 2018-11-15 13:40:43
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Hi everyone, I am still in a group meeting that I might not be able to join today’s discussion. I have wrote the minimum checklist for both targeted and untargeted metabolomics, and I will upload it to Github as soon as I finished the ‘meeting MIAPE’ paragraph. My apologies. Best, Jinmeng At 2018-11-14 11:32:18, "Wout Bittremieux" <wo...@uw...> wrote: Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, November 15th, at 14h00 GMT (14h00 London, 15h00 Western Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing). Please note that the timing of our teleconference might have shifted by one hour depending on your local daylight savings time settings! You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Based on our discussion from last month I propose the following agenda items (based on who can attend): - MIAPE metabolomics discussion (Jinmeng & Reza). - CV update (Julian). - Review multivariate example files (Mathias' example reworked to validate against the JSON schema here). - Any additional items that need to be discussed... Thanks, Wout -- 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 |
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From: Wout B. <wo...@uw...> - 2018-11-14 03:36:22
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, November 15th, at 14h00 GMT (14h00 London, 15h00 Western Europe, 16h00 Cape Town, 6h00 Seattle, 22h00 Beijing). Please note that the timing of our teleconference might have shifted by one hour depending on your local daylight savings time settings! You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Based on our discussion from last month I propose the following agenda items (based on who can attend): - MIAPE metabolomics discussion (Jinmeng & Reza). - CV update (Julian). - Review multivariate example files (Mathias' example reworked to validate against the JSON schema here <https://github.com/HUPO-PSI/mzQC/blob/json-schema/schema/v0_0_11/examples/iPRG2015_sample1.qc.json>). - Any additional items that need to be discussed... Thanks, Wout |
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From: Wout B. <wo...@uw...> - 2018-10-25 18:10:11
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Dear colleagues, You can find the meeting notes of today's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20181025_telco.md Best, Wout > On 25 Oct 2018, at 05:37, Walzer <wa...@eb...> wrote: > > Dear colleagues, > > I'd like to add some points or details to the agenda regarding the multi file metrics and the schema: > > I added an example for a multivariate metric in PR #48: > https://github.com/HUPO-PSI/qcML-development/blob/c82eb68fa574ee596c90cf4fdfe64d3cd61ba5e6/schema/v0_0_10/examples/iPRG2015_sample1.qc.json > Maybe we find 5-10 minutes to discuss the old metrics C-6A and C-6B, as they are a special case of single file metrics, that however need multiple files. But I am a bit unsure about them and would like to discuss that with you. > > Also, we need to discuss the points Wout raised about the schema in #47, see: > https://github.com/HUPO-PSI/qcML-development/pull/47 > and we need to discuss how/if we keep the XML schema updated. > > And because it fell short last time, we might want to begin the call with MIAPE topics? > > cheers, > mths > > On 15/10/18 21:21, Wout Bittremieux wrote: >> Dear colleagues, >> >> This month we'll slightly deviate from our normal schedule and postpone the teleconference for a week until Thursday, October 25th, 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 >> >> >> Based on our action items from last month I propose the following agenda items: >> >> - MIAPE update & discussion. >> - Review new example files: Dave's example file >> <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20181005-1091_Pool_start_v0.2.qc.json> >> ; more files by Mathias & Wout forthcoming... >> - Roadmap towards version 1.0: What do we need? What is our timeline? >> >> Thanks, >> Wout >> >> >> >> >> >> >> >> _______________________________________________ >> 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 |
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From: Walzer <wa...@eb...> - 2018-10-25 15:11:10
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Dear colleagues, as discussed in the call, our github repository will be renamed to mzQC. Please be advised that the renaming will change the git protocol endpoints and might interfere with your forks and local checkouts. The renaming will commence on Friday night, unless I receive any objections. cheers, On 25/10/18 13:37, Walzer wrote: > Dear colleagues, > > I'd like to add some points or details to the agenda regarding the > multi file metrics and the schema: > > I added an example for a multivariate metric in PR #48: > https://github.com/HUPO-PSI/qcML-development/blob/c82eb68fa574ee596c90cf4fdfe64d3cd61ba5e6/schema/v0_0_10/examples/iPRG2015_sample1.qc.json > > Maybe we find 5-10 minutes to discuss the old metrics C-6A and C-6B, > as they are a special case of single file metrics, that however need > multiple files. But I am a bit unsure about them and would like to > discuss that with you. > > Also, we need to discuss the points Wout raised about the schema in > #47, see: > https://github.com/HUPO-PSI/qcML-development/pull/47 > and we need to discuss how/if we keep the XML schema updated. > > And because it fell short last time, we might want to begin the call > with MIAPE topics? > > cheers, > mths > > On 15/10/18 21:21, Wout Bittremieux wrote: >> Dear colleagues, >> >> This month we'll slightly deviate from our normal schedule and >> postpone the teleconference for a week until Thursday, October 25th, >> 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 >> >> Based on our action items from last month I propose the following >> agenda items: >> >> - MIAPE update & discussion. >> - Review new example files: Dave's example file >> <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20181005-1091_Pool_start_v0.2.qc.json>; >> more files by Mathias & Wout forthcoming... >> - Roadmap towards version 1.0: What do we need? What is our timeline? >> >> 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 -- Mathias Walzer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Office: +44 (0)1223 494 2610 E-mail: wa...@eb... |
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From: Walzer <wa...@eb...> - 2018-10-25 12:37:38
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Dear colleagues, I'd like to add some points or details to the agenda regarding the multi file metrics and the schema: I added an example for a multivariate metric in PR #48: https://github.com/HUPO-PSI/qcML-development/blob/c82eb68fa574ee596c90cf4fdfe64d3cd61ba5e6/schema/v0_0_10/examples/iPRG2015_sample1.qc.json Maybe we find 5-10 minutes to discuss the old metrics C-6A and C-6B, as they are a special case of single file metrics, that however need multiple files. But I am a bit unsure about them and would like to discuss that with you. Also, we need to discuss the points Wout raised about the schema in #47, see: https://github.com/HUPO-PSI/qcML-development/pull/47 and we need to discuss how/if we keep the XML schema updated. And because it fell short last time, we might want to begin the call with MIAPE topics? cheers, mths On 15/10/18 21:21, Wout Bittremieux wrote: > Dear colleagues, > > This month we'll slightly deviate from our normal schedule and postpone the teleconference for a week until Thursday, October 25th, 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 > > Based on our action items from last month I propose the following agenda items: > > - MIAPE update & discussion. > - Review new example files: Dave's example file <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20181005-1091_Pool_start_v0.2.qc.json>; more files by Mathias & Wout forthcoming... > - Roadmap towards version 1.0: What do we need? What is our timeline? > > Thanks, > Wout > > > > > > > _______________________________________________ > 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... |
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From: Wout B. <wo...@uw...> - 2018-10-24 23:32:11
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Dear colleagues, I've created a JSON schema specification to validate mzQC JSON files, which you can find in pull request #47 <https://github.com/HUPO-PSI/qcML-development/pull/47>. Please check it out and let me know your comments. The mzQC JSON schema is based on draft 7 of the JSON Schema <https://json-schema.org/>. You can use the online JSON Schema Validator <https://www.jsonschemavalidator.net/> to easily validate mzQC files against the schema (later on this will be built into our APIs of course, including additional external validation based on the CV). You can find the schema file here: https://github.com/HUPO-PSI/qcML-development/blob/json-schema/schema/v0_0_10/mzqc_0_0_10.schema.json I have also adapted Dave's most recent example file so it's valid against this schema: https://github.com/HUPO-PSI/qcML-development/blob/json-schema/schema/v0_0_10/examples/20181005-1091_Pool_start_v0.2.qc.json Best, Wout |
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From: Bittremieux W. <wou...@ua...> - 2018-10-24 16:33:56
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Begin forwarded message: From: "Jones, Andy" <And...@li...<mailto:And...@li...>> Subject: [Psi-announce] PSI2019 plans Date: 24 October 2018 at 09:06:58 GMT-7 To: "'psi...@eb...<mailto:psi...@eb...>'" <psi...@eb...<mailto:psi...@eb...>>, "'psi...@li...<mailto:psi...@li...>'" <psi...@li...<mailto:psi...@li...>>, "'psi...@li...<mailto:psi...@li...>'" <psi...@li...<mailto:psi...@li...>> Hi all, Apologies for the cross-posting. The PSI steering committee will shortly be finalising the venue for the PSI2019 meeting. If you have been to a previous meeting or might be interested in participating in 2019, please can you complete this very short google form to indicate your preferred venue: https://goo.gl/forms/8t4CogZu3xVzRVJQ2, before end Oct i.e. within one week. We would like to take on board community considerations for overseas travel before selecting the final location in early November. We expect to announce the final, selected location by mid November. Best wishes Andy Jones _______________________________________________ Psi-announce mailing list Psi...@eb...<mailto:Psi...@eb...> https://listserver.ebi.ac.uk/mailman/listinfo/psi-announce |
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From: Wout B. <wo...@uw...> - 2018-10-15 20:22:06
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Dear colleagues, This month we'll slightly deviate from our normal schedule and postpone the teleconference for a week until Thursday, October 25th, 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 Based on our action items from last month I propose the following agenda items: - MIAPE update & discussion. - Review new example files: Dave's example file <https://github.com/HUPO-PSI/qcML-development/blob/master/schema/v0_0_10/examples/20181005-1091_Pool_start_v0.2.qc.json>; more files by Mathias & Wout forthcoming... - Roadmap towards version 1.0: What do we need? What is our timeline? Thanks, Wout |
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From: Wout B. <wo...@uw...> - 2018-10-09 17:07:21
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Dear colleagues, I would like to point again to the Doodle I sent around previously: https://doodle.com/poll/gwppg93ywdsnh83c Originally our upcoming teleconference is planned for next week Thursday, October 18. There was a proposal however to postpone the teleconference for a week because not everyone could make it then. Please fill in the Doodle so we can hopefully find a date where we'll be able to maximize attendance. We have several important action points, including: - MIAPE update - Road map to version 1.0 - New example files The agenda will be adapted based on who can be present at the teleconference. So please fill out the Doodle and I will send around the most suitable date and agenda early next week. Thanks, Wout |
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From: Tabb, D. P. [<dt...@su...> - 2018-10-05 11:24:27
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Hi, all. I reworked my example of JSON output from QuaMeter IDFree today (see attached and in GitHub examples for schema 0.0.10). In essence, the modifications involved updating the QC CV accessions. The redo for CV accessions is missing two of my metrics, though: MS1-Freq-Max, MS1-Density seem to be absent. It seems we haven't changed the schema version number in quite a while; I entered "0.1.0" as the schema version number at the head of the JSON, even though this schema does not exist yet! I am in Ghana for two weeks, returning Oct. 21. Thanks, 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 bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer> |
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From: Tabb, D. P. [<dt...@su...> - 2018-09-30 19:32:10
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Hi, Eric. My apologies, but I won't have slides for you in time. The short version is that we've been working up a "clean" CV rather than including our wanderings there. We're going to target JSON output directly, without the XML formatting. We'll call it mzQC rather than QCML to keep the name in tune with past formats. Thank you for understanding! Dave ________________________________ From: Eric Deutsch <ede...@sy...> Sent: Wednesday, September 26, 2018 9:11:27 PM To: Tabb, David, Prof [dt...@su...] Cc: Eric Deutsch Subject: Few summary slides of PSI QC? Hi Dave, would you send me a few slides summarizing the state of the PSI QC working group? I’ll be presenting the state of the PSI next Tuesday. Thanks! Eric ------------------------------ Eric W. Deutsch Senior Research Scientist Institute for Systems Biology 401 Terry Ave North Seattle WA 98109 Email: ede...@sy...<mailto:ede...@sy...> ORCiD: 0000-0001-8732-0928 Office: +1-206-732-1397 Fax: +1-206-732-1260 WWW: https://www.systemsbiology.org/eric-deutsch [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> |
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From: Wout B. <wo...@uw...> - 2018-09-27 00:08:47
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Dear colleagues, Thank you for the productive teleconference last week. Now you can find the meeting notes here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20180920_telco.md Next month's teleconference is currently scheduled for October 18. Some people are unable to attend the teleconference at that time though, so a proposal to postpone the meeting for a week was made. Unfortunately this doesn't work for everyone either. To see if we can find another date I have created a doodle for all days in those two weeks mid-October here: https://doodle.com/poll/gwppg93ywdsnh83c To maximize attendance and continue our good discussion from last week we can see which date works best for everyone involved. I propose to stick to the 14h00 GMT timing on all days as this seems to be a sweet spot between early-yet-not-too-early for people in the US, and late-yet-not-too-late for people in China. Thanks, Wout > On 18 Sep 2018, at 08:33, Wout Bittremieux <wo...@uw...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Thursday, September 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: > > - New CV organisation. Please check out Julian's work on the new CV in pull request #44 and provide any feedback. > - Discussion of QC metrics spanning multiple files. @Mathias: Can you share that example for MaxQuant MBR metrics you mentioned the previous time? > - Overview of the use of QC in metabolomics (if Reza can attend the call). > > Thanks, > Wout > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Tenzer, S. <te...@un...> - 2018-09-19 07:20:41
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Hi everyone, I have to apologize, I will be unable to participate due to a local symposium, which I have to attend. Best wishes, Stefan Univ.-Prof. Dr. rer. nat. Stefan Tenzer ______________________________________________ UNIVERSITÄTSMEDIZIN der Johannes Gutenberg-Universität Institut für Immunologie Core Facility für Massenspektrometrie Gebäude 308A Langenbeckstr. 1, 55131 Mainz www.immunologie-mainz.de<http://www.immunologie-mainz.de> Telefon: +49 (0) 6131 17-6199 Telefax: +49 (0) 6131 17-6202 E-mail: te...@un... Am 18.09.2018 um 17:33 schrieb Wout Bittremieux <wo...@uw...<mailto:wo...@uw...>>: Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, September 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: - New CV organisation. Please check out Julian's work on the new CV in pull request #44<https://github.com/HUPO-PSI/qcML-development/pull/44> and provide any feedback. - Discussion of QC metrics spanning multiple files. @Mathias: Can you share that example for MaxQuant MBR metrics you mentioned the previous time? - Overview of the use of QC in metabolomics (if Reza can attend the call). Thanks, Wout _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wo...@uw...> - 2018-09-18 15:36:12
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, September 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: - New CV organisation. Please check out Julian's work on the new CV in pull request #44 <https://github.com/HUPO-PSI/qcML-development/pull/44> and provide any feedback. - Discussion of QC metrics spanning multiple files. @Mathias: Can you share that example for MaxQuant MBR metrics you mentioned the previous time? - Overview of the use of QC in metabolomics (if Reza can attend the call). Thanks, Wout |
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