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From: Wout B. <wou...@ua...> - 2025-11-27 17:40:32
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Dear colleagues, We have our next teleconference tomorrow, Friday November 28, at 11h00 CET (10h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * Biohackathon<https://github.com/MS-Quality-Hub/biohackathon2025>: recap * QC metrics categorization [#323<https://github.com/HUPO-PSI/mzQC/pull/323>] * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: finalization of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * GitHub<https://github.com/HUPO-PSI/mzQC/issues> * CV term requests: TDAuditor [#324<https://github.com/HUPO-PSI/mzQC/issues/324>] & DIAMetric [#318–#320] * QC tools overview [#326<https://github.com/HUPO-PSI/mzQC/pull/326>] * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * AOB Best, Wout |
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From: ricard-blum s. <syl...@un...> - 2025-11-10 13:30:41
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Dear colleagues, dear members of the HUPO-PSI community, The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of proteomics, glycomics and interaction data (see http://www.psidev.info for an overview of activities). The Mass Spectrometry and Proteomics Informatics Working Groups have submitted a new recommendation for a PSI standard, the ProForma (Proteoform and Peptidoform Notation) version 2.1 specification. This version is an update of ProForma version 2.0 which was ratified in February 2022. This update adds some options to describe more complex peptidoforms and is heavily rewritten te remove ambiguities and provide a better overview for implementors. After having passed a 14-day review by two members of the PSI steering committee, who suggested minor changes, the proposed specification now goes through the*30-day public and external review, which should end on December 10th, 2025.* The version 2.1, draft 02 of the specification is attached to this e-mail. This message is to encourage you to contribute to the standards development activity by commenting on the document. We invite both positive and negative comments on the relevance, correctness, clarity and appropriateness of the specification (e.g. is it presented in accordance with the templates and clearly written, is it sufficiently detailed and comprehensively described and are the examples in agreement with the specification?). Comments can be made on the specification as a whole or on specific parts. If you do not feel experienced enough to comment on this document, but know colleagues who are, please feel free to forward this message to them. There is no requirement that people commenting should have had any prior contact with the PSI. *Please send comments by e-mail directly to syl...@un... before December 10th, 2025.* I thank you very much in advance for your contribution and time. Kind regards. Professor Sylvie RICARD-BLUM, HUPO-PSI Editor Pericellular and Extracellular Supramolecular Assemblies UMR 5246 CNRS - University Lyon 1 Institute of Molecular and Supramolecular Chemistry and Biochemistry University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918 69622 Villeurbanne Cedex, France Phone: +33(0)6 82 02 44 22 E-mail: syl...@un... |
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From: Wout B. <wou...@ua...> - 2025-10-30 17:50:30
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Dear colleagues, We have our next teleconference tomorrow, Friday October 31, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * Biohackathon preparation: participant instructions<https://github.com/MS-Quality-Hub/biohackathon2025> [everyone: review in advance] * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: TDAuditor CV term requests * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-28 16:46:38
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Awesome, thanks Yasset. Yes, I don't expect that we will fully finish all tasks. The different options are more so that people can pick a project that most appeals to them. I agree that mzQC export is definitely a priority. Best, Wout ________________________________ From: Yasset Perez-Riverol <ypr...@gm...> Sent: Tuesday, October 28, 2025 17:03 To: Wout Bittremieux <wou...@ua...> Cc: psi...@li... <psi...@li...> Subject: Re: Please review ELIXIR BioHackathon instructions & tasks CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. I have given a quick view. My only question is that the amount of tasks looks heavy for a hackathon of five days, but I also have to say that I don’t know the specs of BioHackathon2025. If you have enough people, you can try to achieve this. >From my point of view, having support for mzQC in MultiQC and an IDFree scalable workflow and MultiQC+mzQC report that we can try to deploy in prod will be a dream that PRIDE has tried for years. Regards, Yasset Yasset Perez-Riverol Team Coordinator PRIDE resources Proteomics Services, EMBL-EBI ypr...@gm... On 28 Oct 2025, at 15:27, Wout Bittremieux <wou...@ua...> wrote: Hi all, I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 Could you please give everything a careful pass to ensure: 1. Completeness: all info participants need is present (setup, tasks, links, examples). 2. Clarity: instructions and task scopes make sense for newcomers. 3. Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. Thanks, Wout |
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From: Yasset Perez-R. <ypr...@gm...> - 2025-10-28 16:04:11
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I have given a quick view. My only question is that the amount of tasks looks heavy for a hackathon of five days, but I also have to say that I don’t know the specs of BioHackathon2025. If you have enough people, you can try to achieve this. From my point of view, having support for mzQC in MultiQC and an IDFree scalable workflow and MultiQC+mzQC report that we can try to deploy in prod will be a dream that PRIDE has tried for years. Regards, Yasset Yasset Perez-Riverol Team Coordinator PRIDE resources Proteomics Services, EMBL-EBI ypr...@gm... > On 28 Oct 2025, at 15:27, Wout Bittremieux <wou...@ua...> wrote: > > Hi all, > > I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 > > Could you please give everything a careful pass to ensure: > Completeness: all info participants need is present (setup, tasks, links, examples). > Clarity: instructions and task scopes make sense for newcomers. > Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. > > Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. > > Thanks, > Wout |
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From: Wout B. <wou...@ua...> - 2025-10-28 16:00:27
|
Hi all, I've prepared the hackathon materials here: https://github.com/MS-Quality-Hub/biohackathon2025 Could you please give everything a careful pass to ensure: 1. Completeness: all info participants need is present (setup, tasks, links, examples). 2. Clarity: instructions and task scopes make sense for newcomers. 3. Technical accuracy: commands, repositories/branches, CV terms, and validation steps are correct. Feel free to edit directly, open a PR with proposed changes, or send comments to me if that's easier. Thanks, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-23 09:40:40
|
Dear colleagues, We have our next teleconference tomorrow, Friday October 24, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * Biohackathon preparation: internal TODO list<https://docs.google.com/document/d/1PEsWowuvagZSw7m4ohimwtOGr-_qXiO2hF0KPV4LojU/edit>, organization document<https://docs.google.com/document/d/1x9aDGEUVWcThQZV9Lp9viBmC9ASw0GGCeZK-02lQBgM/edit?usp=sharing> * pymzQC<https://github.com/MS-Quality-hub/pymzqc> v1.0.1 updates [Matthias]: semantic validation * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: TDAuditor CV term requests * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-10-09 19:34:37
|
Dear colleagues, We have our next teleconference tomorrow, Friday October 10, at 15h00 CET (12h00 BST, 11h00 GMT). ⚠️ Please note the deviation from our usual time slot. You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s We have one key agenda item: * Biohackathon preparation: internal TODO list<https://docs.google.com/document/d/1PEsWowuvagZSw7m4ohimwtOGr-_qXiO2hF0KPV4LojU/edit> If time and desires permit, we might tackle some of our regular topics afterwards. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-09-18 15:18:13
|
Dear colleagues, We have our next teleconference tomorrow, Friday September 19, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub: broken links [Mathias to integrate fix in validator PR<https://github.com/HUPO-PSI/mzQC/pull/314>] * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout has reviewed wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/pull/400> and TDAuditor * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-09-11 15:43:36
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Dear colleagues, We have our next teleconference tomorrow, Friday September 12, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * Introduction to pMultiQC<https://docs.quantms.org/latest/pmultiqc.html> [Yasset] * GitHub: broken links [Mathias to integrate fix in validator PR<https://github.com/HUPO-PSI/mzQC/pull/314>] * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout has reviewed wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380> and TDAuditor * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-08-21 14:32:50
|
Dear colleagues, We have our next teleconference tomorrow, Friday August 22, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub: broken links [Mathias to integrate fix in validator PR<https://github.com/HUPO-PSI/mzQC/pull/314>] * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout to review wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-08-07 14:15:53
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Dear colleagues, We have our next teleconference tomorrow, Friday August 8, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub: broken links [Mathias to integrate fix in validator PR<https://github.com/HUPO-PSI/mzQC/pull/314>] * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout to review wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-07-31 19:14:55
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Dear colleagues, We have our next teleconference tomorrow, Friday August 1, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub: broken links [Mathias to integrate fix in validator PR] * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout to review wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-07-17 09:56:02
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Dear colleagues, We have our next teleconference tomorrow, Friday July 18, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub: broken links [Mathias to integrate fix in validator PR] * pymzqc & rmzqc updates * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> [Wout to review wording of messages] * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Sylvie R. <syl...@un...> - 2025-07-16 16:37:09
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Dear colleagues, dear members of the HUPO-PSI community, The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of proteomics, glycomics and interaction data (see http://www.psidev.info for an overview of activities). Members of the Molecular Interactions Working Group have submitted a new recommendation for a PSI standard, *PSI-MI FeatureTab*, *an exchange format for molecular interaction features*. The PSI-MI FeatureTab format is part of the PSI-MI 2.5 standard. It is related to the tabular format provided by PSI MITAB 2.5 and subsequent updates. However, while the PSI MITAB 2.5 describes binary interactions, one pair of interactors per row, in the PSI-MI FeatureTab each row is feature centric and describes in detail a specific feature at the participant level and the effect of a feature, if any, on the second participant. After having passed a 14-day review by two members of the PSI steering committee, who suggested minor changes, the proposed specification now goes through the 30-day public and external review, which should end on August 16th, 2025 but is *extended to August 31st, 2025 *due to summer holidays. The draft of the specification (version 1.0, draft 02) is attached to this e-mail. This message is to encourage you to contribute to the standards development activity by commenting on the document. We invite both positive and negative comments on the relevance, correctness, clarity and appropriateness of the specification (e.g. is it presented in accordance with the templates and clearly written, is it sufficiently detailed and comprehensively described and are the examples in agreement with the specification?). Comments can be made on the specification as a whole or on specific parts. If you do not feel experienced enough to comment on this document, but know colleagues who are, please feel free to forward this message to them. There is no requirement that people commenting should have had any prior contact with the PSI. *Please send comments by e-mail directly to syl...@un... before August 31st, 2025.* I thank you very much in advance for your contribution and time. Kind regards. Professor Sylvie RICARD-BLUM, HUPO-PSI Editor Pericellular and Extracellular Supramolecular Assemblies UMR 5246 CNRS - University Lyon 1 Institute of Molecular and Supramolecular Chemistry and Biochemistry University Claude Bernard Lyon 1, 43 Boulevard du 11 novembre 1918 69622 Villeurbanne Cedex, France Phone: +33(0)6 82 02 44 22 E-mail: syl...@un... |
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From: Wout B. <wou...@ua...> - 2025-07-03 13:08:56
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Dear colleagues, We have our next teleconference tomorrow, Friday July 4 (🇺🇸🦅🎆), at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * mzQC specification: JSON schema out of data (label in metadata<https://github.com/HUPO-PSI/mzQC/pull/312>, URI for analysisSoftware<https://github.com/HUPO-PSI/mzQC/pull/316>) * pymzqc: various updates and bugfixes * Semantic validation: see discussion on Slack<https://hupo-psi.slack.com/archives/CJJHF8EBX/p1750946912901659?thread_ts=1750229425.643959&cid=CJJHF8EBX>, semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC<https://github.com/HUPO-PSI/psi-ms-CV/issues/380>, TDAuditor, and DIAMetric<https://github.com/HUPO-PSI/psi-ms-CV/pull/391> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon<https://biohackathon-europe.org/>: project description<https://github.com/elixir-europe/biohackathon-projects-2025/blob/main/29.md>, planning * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-06-12 18:42:31
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Dear colleagues, We have our next teleconference tomorrow, Friday June 13, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * mzQC specification: JSON schema out of data (label in metadata) * pymzqc: cvParameters in metadata * rmzqc: table export * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAMetric * Repository-scale QC (metabolomics) * Other use cases * BioHackathon * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-05-22 13:32:10
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Dear colleagues, We have our next teleconference on Friday May 23, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-05-15 10:21:07
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Dear colleagues, We have our next teleconference on Friday May 16, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC, TDAuditor, and DIAMetric * pymzqc validator: semantic checks severity logging level<https://github.com/MS-Quality-Hub/pymzqc/issues/60> * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * Outlier detection * Lipidomics * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-04-16 14:56:42
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Dear colleagues, We have our next teleconference on Friday April 18, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * Spring Meeting: recap<https://github.com/HUPO-PSI/mzQC/blob/main/meeting_notes/2025/20250402_psi2025.md> * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * @Mathias: Validation fails with message "No mzQC structure detectable." * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests for McQuaC and TDAuditor * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * DIAmetric: QC for DIA * Repository-scale QC (metabolomics) * Other use cases * AOB Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-04-03 11:07:37
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Dear colleagues, Thank you for the fruitful discussion on the mzQC manuscript and related use cases. You can find the draft manuscript here<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit?usp=sharing>. Feel free to add comments and text. Best, Wout ________________________________ From: Wout Bittremieux <wou...@ua...> Sent: Wednesday, April 2, 2025 14:09 To: d.l...@ru... <d.l...@ru...>; jul...@ru... <jul...@ru...>; pa...@eb... <pa...@eb...>; yel...@uc... <yel...@uc...>; sw...@ko... <sw...@ko...>; n.h...@fz... <n.h...@fz...>; bo....@nu... <bo....@nu...>; ser...@br... <ser...@br...> Subject: HUPO-PSI QC working group links Dear colleagues, Thank you for your participation in the PSI QC Working Group. Here are some relevant links: * Meeting notes: https://docs.google.com/document/d/1zFye2rlhoHs7zVIorftIizPeqAuGT0w-vHYRlF6S5E8/edit?usp=sharing * Feel free to take notes liberally and add any other thoughts. * mzQC GitHub repository: https://github.com/HUPO-PSI/mzQC * mzQC documentation website: https://hupo-psi.github.io/mzQC/ Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-03-06 14:38:24
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Dear colleagues, We have our next teleconference on Friday March 7, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * TDAuditor<https://docs.google.com/document/d/10idAq_WiL8rhWNSYdLnnxV03u7amh28qMW-nd3FeXJ8/edit>: CV terms for top-down proteomics * DIAmetric: QC for DIA * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-02-26 12:40:21
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Dear colleagues, We have our next teleconference on Friday February 28, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * TDAuditor<https://docs.google.com/document/d/10idAq_WiL8rhWNSYdLnnxV03u7amh28qMW-nd3FeXJ8/edit>: CV terms for top-down proteomics * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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From: Martin E. <mar...@ru...> - 2025-02-03 13:17:46
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UNSUBSCRIBE -----Ursprüngliche Nachricht----- Von: Wout Bittremieux <wou...@ua...> Gesendet: Mittwoch, 29. Januar 2025 09:03 An: psi...@li... Betreff: [Psidev-qc-dev] Upcoming teleconference January 31 Dear colleagues, We have our next teleconference on Friday January 31, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00M TAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb -2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217 e647f61b0%22%7d <https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00 MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08f b-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-21 7e647f61b0%22%7d> * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub <https://github.com/HUPO-PSI/mzQC/issues> : CV term requests * mzQC website <https://hupo-psi.github.io/mzQC/> : metabo-batches example (#233 <https://github.com/HUPO-PSI/mzQC/pull/233> ) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript <https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfq cjqs/edit> : continuation of use cases * AOB. Best, Wout |
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From: Wout B. <wou...@ua...> - 2025-01-29 08:37:35
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Dear colleagues, We have our next teleconference on Friday January 31, at 13h00 CET (12h00 BST, 11h00 GMT). You can connect to our teleconference on Microsoft Teams through the following link: https://teams.microsoft.com/l/meetup-join/19%3ameeting_MzNhNGFmODEtY2QxZi00MTAyLTlkODMtMDBiNTgxMzNkMWQx%40thread.v2/0?context=%7b%22Tid%22%3a%22792e08fb-2d54-4a8e-af72-202548136ef6%22%2c%22Oid%22%3a%2242f2bf26-cfd5-4653-8e93-217e647f61b0%22%7d * Meeting ID: 311 403 481 845 * Passcode: Jm4d4s Agenda items: * GitHub<https://github.com/HUPO-PSI/mzQC/issues>: CV term requests * mzQC website<https://hupo-psi.github.io/mzQC/>: metabo-batches example (#233<https://github.com/HUPO-PSI/mzQC/pull/233>) * pymzqc validator: semantic checks severity logging level * mzQC specification manuscript<https://docs.google.com/document/d/1fYPqDBqFamcjXlzX0RMStPOKQD4aHlQd9JHJAfqcjqs/edit>: continuation of use cases * AOB. Best, Wout |
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