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From: Wout B. <wou...@ua...> - 2017-12-12 22:03:17
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Dear colleagues, I also opened a few issues just now concerning some of our recent discussion points. You can check them out on the Github repository: https://github.com/HUPO-PSI/qcML-development/issues I feel that at times we've been repeating some of our earlier discussions, so it might be useful to have a central record of the decisions we have made. The current issues seem the most important to me at this point. There are some further discussion points that have mentioned over the past few months as well and they should probably be revisited at some point. Clear examples of qcML files with the updated schema will be useful in resolving those points. These issues mainly deal with the XML schema. It might be beneficial to do the same for MIAPE and the CV in the future as well to have a clear record of our decisions. Best, Wout > On 11 Dec 2017, at 16:54, Wout Bittremieux <wou...@ua...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Thursday, December 14th, at 15h00 GMT (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, 23h00 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 for the teleconference: > > - Follow-up on the action points identified during last month's teleconference: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20171113_telco.md > > - Discussion of the QC hackathon session at the upcoming EuBIC developer's meeting. Mathias has already created an excellent schedule which you can find here: http://uahost.uantwerpen.be/eubic18/hackathon-dashboard.html > What datasets do we need to prepare in advance, is there further desired functionality not mentioned in the current plan (and that is feasible to implement), etc.? > > - CV status in moving towards a 1.0 version. We got a nice update on the status of the XML schema and MIAPE guidelines and the plan in moving forward during last month's teleconference. It would be useful to get a similar overview for the CV as well. > > - Although it's still early days we might discuss the working group's presence and visibility at conferences in 2018. The EuPA conference in Spain was mentioned, but similarly we might start making plans to advertise our efforts at ASMS (SIG organization?), HUPO, other big conferences, ... > > - Any additional items that need to be discussed... > > Thanks, > Wout > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wou...@ua...> - 2017-12-12 01:03:18
|
Dear colleagues, This is a reminder that our next teleconference is scheduled for Thursday, December 14th, at 15h00 GMT (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, 23h00 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 for the teleconference: - Follow-up on the action points identified during last month's teleconference: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20171113_telco.md - Discussion of the QC hackathon session at the upcoming EuBIC developer's meeting. Mathias has already created an excellent schedule which you can find here: http://uahost.uantwerpen.be/eubic18/hackathon-dashboard.html What datasets do we need to prepare in advance, is there further desired functionality not mentioned in the current plan (and that is feasible to implement), etc.? - CV status in moving towards a 1.0 version. We got a nice update on the status of the XML schema and MIAPE guidelines and the plan in moving forward during last month's teleconference. It would be useful to get a similar overview for the CV as well. - Although it's still early days we might discuss the working group's presence and visibility at conferences in 2018. The EuPA conference in Spain was mentioned, but similarly we might start making plans to advertise our efforts at ASMS (SIG organization?), HUPO, other big conferences, ... - Any additional items that need to be discussed... Thanks, Wout |
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From: Wout B. <wou...@ua...> - 2017-11-14 01:13:03
|
Dear colleagues, Please find the meeting notes of this morning's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20171113_telco.md We discussed the main issues that need to be solved to move towards a 1.0 version of the qcML format and our desired timeline to achieve this. Please note that we will change the timing of these monthly teleconferences in the future to Thursday's at 15h00 GMT. Our next teleconference will take place on Thursday December 14, 2017 at 15h00 GMT. A further notification will follow in the preceding week. Best, Wout > On 09 Nov 2017, at 19:21, Wout Bittremieux <wou...@ua...> wrote: > > Dear colleagues, > > To find the middle ground between me having to wake up early and the European time zones being able to leave work in time I propose to have our upcoming teleconference on Monday November 13, 2017 at 15h00 GMT (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, 23h00 Beijing). > > You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > Please see the previous email in this exchange for the proposed agenda items. > > I hope to speak to you on Monday. > > Best, > Wout > >> On 06 Nov 2017, at 19:57, Wout Bittremieux <wou...@ua...> wrote: >> >> Dear colleagues, >> >> It seems that next week Monday 13/11 between 14h00 and 17h00 GMT is best option. I've quickly created a second Doodle to settle on a specific time in that slot: https://doodle.com/poll/f6957ephrv3ba94k >> >> Best, >> Wout >> >>> On 19 Oct 2017, at 20:14, Wout Bittremieux <wou...@ua...> wrote: >>> >>> Indeed, it seems best to postpone this week's call. Dave is still away next week as well though, so you and other people that might participate should decide whether it'd be useful to have the call then. >>> >>> In any case, I would like to remind everyone to fill in the Doodle in the mean time: https://doodle.com/poll/a64wekmusekb3i2w >>> >>> Thanks, >>> Wout >>> >>>> On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: >>>> >>>> I'm afraid I will be busy/traveling at that time, too. I am at the Dagstuhl comp. prot. seminar right now. >>>> >>>> How about we postpone the call to next week? Or maybe already to a new slot? >>>> best, >>>> >>>> mths >>>> >>>> On 17/10/17 07:27, David Tabb wrote: >>>>> Hello, my friends! >>>>> >>>>> I will be unable to take part in Friday's teleconference. I am in Russia from October 19th to November 3rd. The conference will likely take place during my flight leg from Dubai to St. Petersburg. You will be happy to know that I am teaching a two-hour workshop on QC, using the CPTAC colon data set (1425 files) for the demonstration. >>>>> >>>>> Mathias, could you take the helm for Friday? >>>>> >>>>> Thanks, >>>>> Dave >>>>> >>>>> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >>>>> Dear colleagues, >>>>> >>>>> This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). >>>>> >>>>> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >>>>> >>>>> Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. >>>>> >>>>> I propose the following agenda items for the teleconference: >>>>> >>>>> - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. >>>>> >>>>> - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. >>>>> >>>>> - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. >>>>> As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. >>>>> >>>>> - Any additional items that need to be discussed... >>>>> >>>>> Thanks, >>>>> Wout >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Psidev-qc-dev mailing list >>>>> Psi...@li...<mailto:Psi...@li...> >>>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>>>> >>>>> >>>>> >>>>> The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! >>>>> http://sdm.link/slashdot >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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... >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Julian U. <jul...@ru...> - 2017-11-13 10:55:24
|
Hi all, I hope to join the talk again in the future, but this time slot coincides with an (irregular) seminar at our lab. So, today I cannot join and at all another slot would be better (sorry, did not take part in the Doodle a complain now... not to nice probably.) Regards, Julian On 10.11.2017 06:47, David Tabb wrote: > Hi, all. > > Thanks for organizing our next call, Wout. I will make every effort > to make it to this time, though this time will be problematic when I > am once again in choir rehearsals in January. > > Talk to you all soon! > Dave > > On 11/10/2017 5:21 AM, Wout Bittremieux wrote: >> Dear colleagues, >> >> To find the middle ground between me having to wake up early and the >> European time zones being able to leave work in time I propose to >> have our upcoming teleconference on *Monday November 13, 2017 at >> 15h00 GMT* (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, >> 23h00 Beijing). >> >> You can connect to our teleconference on Google Hangouts through the >> following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >> <http://hangouts.google.com/group/taNzRy6ELMDK9wbk2> >> >> Please see the previous email in this exchange for the proposed >> agenda items. >> >> I hope to speak to you on Monday. >> >> Best, >> Wout >> >>> On 06 Nov 2017, at 19:57, Wout Bittremieux >>> <wou...@ua... >>> <mailto:wou...@ua...>> wrote: >>> >>> Dear colleagues, >>> >>> It seems that next week Monday 13/11 between 14h00 and 17h00 GMT is >>> best option. I've quickly created a second Doodle to settle on a >>> specific time in that slot: https://doodle.com/poll/f6957ephrv3ba94k >>> >>> Best, >>> Wout >>> >>>> On 19 Oct 2017, at 20:14, Wout Bittremieux >>>> <wou...@ua...> wrote: >>>> >>>> Indeed, it seems best to postpone this week's call. Dave is still >>>> away next week as well though, so you and other people that might >>>> participate should decide whether it'd be useful to have the call then. >>>> >>>> In any case, I would like to remind everyone to fill in the Doodle >>>> in the mean time: https://doodle.com/poll/a64wekmusekb3i2w >>>> >>>> Thanks, >>>> Wout >>>> >>>>> On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: >>>>> >>>>> I'm afraid I will be busy/traveling at that time, too. I am at the >>>>> Dagstuhl comp. prot. seminar right now. >>>>> >>>>> How about we postpone the call to next week? Or maybe already to a >>>>> new slot? >>>>> best, >>>>> >>>>> mths >>>>> >>>>> On 17/10/17 07:27, David Tabb wrote: >>>>>> Hello, my friends! >>>>>> >>>>>> I will be unable to take part in Friday's teleconference. I am >>>>>> in Russia from October 19th to November 3rd. The conference will >>>>>> likely take place during my flight leg from Dubai to St. >>>>>> Petersburg. You will be happy to know that I am teaching a >>>>>> two-hour workshop on QC, using the CPTAC colon data set (1425 >>>>>> files) for the demonstration. >>>>>> >>>>>> Mathias, could you take the helm for Friday? >>>>>> >>>>>> Thanks, >>>>>> Dave >>>>>> >>>>>> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >>>>>> Dear colleagues, >>>>>> >>>>>> This is a reminder that our next teleconference is scheduled for >>>>>> Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, >>>>>> 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific >>>>>> Time). >>>>>> >>>>>> You can connect to our teleconference on Google Hangouts through >>>>>> the following link: >>>>>> https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >>>>>> >>>>>> Unfortunately so far I haven't been able yet to start up the >>>>>> discussion with Mathias regarding some points I raised concerning >>>>>> the XML schema. That's my bad, and I hope to be able to set aside >>>>>> some time soon to pick this up. >>>>>> >>>>>> I propose the following agenda items for the teleconference: >>>>>> >>>>>> - Overview of the status of the XML schema and MIAPE guidelines. >>>>>> Evaluation and allocation of the tasks that need to be done to >>>>>> move to a 1.0 version. >>>>>> >>>>>> - Mathias did a great job submitting a project proposal for the >>>>>> EuBIC developer's meeting in Ghent in January, which has been >>>>>> accepted for the >>>>>> meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. >>>>>> The proposal already contains some information based on the >>>>>> things we discussed the previous time, but if you have additional >>>>>> ideas etc. it would be good to discuss those. Furthermore, >>>>>> preparing some datasets, a work plan, etc. in advance during this >>>>>> and next month's teleconference will enable us to have >>>>>> everything ready in advance to ensure that a valuable result >>>>>> comes out of the meeting, while hopefully engaging new >>>>>> enthusiastic collaborators. >>>>>> >>>>>> - As I live in Seattle now due to its timing I won't be able to >>>>>> attend the teleconference. As we discussed last >>>>>> month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle >>>>>> to evaluate whether other time slots would be an option. I've >>>>>> used some broad time slots to try (and fail) to keep the number >>>>>> of options somewhat reasonable. Normally you should see the time >>>>>> blocks in your local time zone, but please verify this. I've >>>>>> used the third week of November now as that's our current >>>>>> schedule, but that can be up for discussion as well of course. >>>>>> As there probably won't be a single ideal time to have people on >>>>>> three continents participate in the teleconference an option is >>>>>> to have alternating teleconferences at two different times. >>>>>> Please fill in the Doodle so the possible options can be >>>>>> evaluated during the upcoming telco. >>>>>> >>>>>> - Any additional items that need to be discussed... >>>>>> >>>>>> Thanks, >>>>>> Wout >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Psidev-qc-dev mailing list >>>>>> Psi...@li...<mailto:Psi...@li...> >>>>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>>>>> >>>>>> >>>>>> >>>>>> The integrity and confidentiality of this email is governed by >>>>>> these terms / Hierdie terme bepaal die integriteit en >>>>>> vertroulikheid van hierdie >>>>>> epos. http://www.sun.ac.za/emaildisclaimer >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! >>>>>> http://sdm.link/slashdot >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> 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... >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! >>>>> http://sdm.link/slashdot_______________________________________________ >>>>> Psidev-qc-dev mailing list >>>>> Psi...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> _______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! >>> http://sdm.link/slashdot_______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: David T. <dt...@su...> - 2017-11-10 06:02:40
|
Hi, all. Thanks for organizing our next call, Wout. I will make every effort to make it to this time, though this time will be problematic when I am once again in choir rehearsals in January. Talk to you all soon! Dave On 11/10/2017 5:21 AM, Wout Bittremieux wrote: > Dear colleagues, > > To find the middle ground between me having to wake up early and the > European time zones being able to leave work in time I propose to have > our upcoming teleconference on *Monday November 13, 2017 at 15h00 > GMT* (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, 23h00 Beijing). > > You can connect to our teleconference on Google Hangouts through the > following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > <http://hangouts.google.com/group/taNzRy6ELMDK9wbk2> > > Please see the previous email in this exchange for the proposed agenda > items. > > I hope to speak to you on Monday. > > Best, > Wout > >> On 06 Nov 2017, at 19:57, Wout Bittremieux >> <wou...@ua... >> <mailto:wou...@ua...>> wrote: >> >> Dear colleagues, >> >> It seems that next week Monday 13/11 between 14h00 and 17h00 GMT is >> best option. I've quickly created a second Doodle to settle on a >> specific time in that slot: https://doodle.com/poll/f6957ephrv3ba94k >> >> Best, >> Wout >> >>> On 19 Oct 2017, at 20:14, Wout Bittremieux >>> <wou...@ua...> wrote: >>> >>> Indeed, it seems best to postpone this week's call. Dave is still >>> away next week as well though, so you and other people that might >>> participate should decide whether it'd be useful to have the call then. >>> >>> In any case, I would like to remind everyone to fill in the Doodle >>> in the mean time: https://doodle.com/poll/a64wekmusekb3i2w >>> >>> Thanks, >>> Wout >>> >>>> On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: >>>> >>>> I'm afraid I will be busy/traveling at that time, too. I am at the >>>> Dagstuhl comp. prot. seminar right now. >>>> >>>> How about we postpone the call to next week? Or maybe already to a >>>> new slot? >>>> best, >>>> >>>> mths >>>> >>>> On 17/10/17 07:27, David Tabb wrote: >>>>> Hello, my friends! >>>>> >>>>> I will be unable to take part in Friday's teleconference. I am in >>>>> Russia from October 19th to November 3rd. The conference will >>>>> likely take place during my flight leg from Dubai to St. >>>>> Petersburg. You will be happy to know that I am teaching a >>>>> two-hour workshop on QC, using the CPTAC colon data set (1425 >>>>> files) for the demonstration. >>>>> >>>>> Mathias, could you take the helm for Friday? >>>>> >>>>> Thanks, >>>>> Dave >>>>> >>>>> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >>>>> Dear colleagues, >>>>> >>>>> This is a reminder that our next teleconference is scheduled for >>>>> Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, >>>>> 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). >>>>> >>>>> You can connect to our teleconference on Google Hangouts through >>>>> the following link: >>>>> https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >>>>> >>>>> Unfortunately so far I haven't been able yet to start up the >>>>> discussion with Mathias regarding some points I raised concerning >>>>> the XML schema. That's my bad, and I hope to be able to set aside >>>>> some time soon to pick this up. >>>>> >>>>> I propose the following agenda items for the teleconference: >>>>> >>>>> - Overview of the status of the XML schema and MIAPE guidelines. >>>>> Evaluation and allocation of the tasks that need to be done to >>>>> move to a 1.0 version. >>>>> >>>>> - Mathias did a great job submitting a project proposal for the >>>>> EuBIC developer's meeting in Ghent in January, which has been >>>>> accepted for the >>>>> meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. >>>>> The proposal already contains some information based on the things >>>>> we discussed the previous time, but if you have additional ideas >>>>> etc. it would be good to discuss those. Furthermore, preparing >>>>> some datasets, a work plan, etc. in advance during this and next >>>>> month's teleconference will enable us to have everything ready >>>>> in advance to ensure that a valuable result comes out of the >>>>> meeting, while hopefully engaging new enthusiastic collaborators. >>>>> >>>>> - As I live in Seattle now due to its timing I won't be able to >>>>> attend the teleconference. As we discussed last >>>>> month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle >>>>> to evaluate whether other time slots would be an option. I've used >>>>> some broad time slots to try (and fail) to keep the number of >>>>> options somewhat reasonable. Normally you should see the time >>>>> blocks in your local time zone, but please verify this. I've >>>>> used the third week of November now as that's our current >>>>> schedule, but that can be up for discussion as well of course. >>>>> As there probably won't be a single ideal time to have people on >>>>> three continents participate in the teleconference an option is to >>>>> have alternating teleconferences at two different times. Please >>>>> fill in the Doodle so the possible options can be evaluated during >>>>> the upcoming telco. >>>>> >>>>> - Any additional items that need to be discussed... >>>>> >>>>> Thanks, >>>>> Wout >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Psidev-qc-dev mailing list >>>>> Psi...@li...<mailto:Psi...@li...> >>>>> >>>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>>>> >>>>> >>>>> >>>>> The integrity and confidentiality of this email is governed by >>>>> these terms / Hierdie terme bepaal die integriteit en >>>>> vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! >>>>> http://sdm.link/slashdot >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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... >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! >>>> http://sdm.link/slashdot_______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot_______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wou...@ua...> - 2017-11-10 03:23:02
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Dear colleagues, To find the middle ground between me having to wake up early and the European time zones being able to leave work in time I propose to have our upcoming teleconference on Monday November 13, 2017 at 15h00 GMT (16h00 Western Europe, 17h00 Cape Town, 7h00 Seattle, 23h00 Beijing). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Please see the previous email in this exchange for the proposed agenda items. I hope to speak to you on Monday. Best, Wout > On 06 Nov 2017, at 19:57, Wout Bittremieux <wou...@ua...> wrote: > > Dear colleagues, > > It seems that next week Monday 13/11 between 14h00 and 17h00 GMT is best option. I've quickly created a second Doodle to settle on a specific time in that slot: https://doodle.com/poll/f6957ephrv3ba94k > > Best, > Wout > >> On 19 Oct 2017, at 20:14, Wout Bittremieux <wou...@ua...> wrote: >> >> Indeed, it seems best to postpone this week's call. Dave is still away next week as well though, so you and other people that might participate should decide whether it'd be useful to have the call then. >> >> In any case, I would like to remind everyone to fill in the Doodle in the mean time: https://doodle.com/poll/a64wekmusekb3i2w >> >> Thanks, >> Wout >> >>> On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: >>> >>> I'm afraid I will be busy/traveling at that time, too. I am at the Dagstuhl comp. prot. seminar right now. >>> >>> How about we postpone the call to next week? Or maybe already to a new slot? >>> best, >>> >>> mths >>> >>> On 17/10/17 07:27, David Tabb wrote: >>>> Hello, my friends! >>>> >>>> I will be unable to take part in Friday's teleconference. I am in Russia from October 19th to November 3rd. The conference will likely take place during my flight leg from Dubai to St. Petersburg. You will be happy to know that I am teaching a two-hour workshop on QC, using the CPTAC colon data set (1425 files) for the demonstration. >>>> >>>> Mathias, could you take the helm for Friday? >>>> >>>> Thanks, >>>> Dave >>>> >>>> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >>>> Dear colleagues, >>>> >>>> This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). >>>> >>>> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >>>> >>>> Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. >>>> >>>> I propose the following agenda items for the teleconference: >>>> >>>> - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. >>>> >>>> - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. >>>> >>>> - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. >>>> As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. >>>> >>>> - Any additional items that need to be discussed... >>>> >>>> Thanks, >>>> Wout >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>> >>>> >>>> >>>> _______________________________________________ >>>> Psidev-qc-dev mailing list >>>> Psi...@li...<mailto:Psi...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>>> >>>> >>>> >>>> The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! >>>> http://sdm.link/slashdot >>>> >>>> >>>> _______________________________________________ >>>> 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... >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wou...@ua...> - 2017-11-07 04:02:38
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Dear colleagues, It seems that next week Monday 13/11 between 14h00 and 17h00 GMT is best option. I've quickly created a second Doodle to settle on a specific time in that slot: https://doodle.com/poll/f6957ephrv3ba94k Best, Wout > On 19 Oct 2017, at 20:14, Wout Bittremieux <wou...@ua...> wrote: > > Indeed, it seems best to postpone this week's call. Dave is still away next week as well though, so you and other people that might participate should decide whether it'd be useful to have the call then. > > In any case, I would like to remind everyone to fill in the Doodle in the mean time: https://doodle.com/poll/a64wekmusekb3i2w > > Thanks, > Wout > >> On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: >> >> I'm afraid I will be busy/traveling at that time, too. I am at the Dagstuhl comp. prot. seminar right now. >> >> How about we postpone the call to next week? Or maybe already to a new slot? >> best, >> >> mths >> >> On 17/10/17 07:27, David Tabb wrote: >>> Hello, my friends! >>> >>> I will be unable to take part in Friday's teleconference. I am in Russia from October 19th to November 3rd. The conference will likely take place during my flight leg from Dubai to St. Petersburg. You will be happy to know that I am teaching a two-hour workshop on QC, using the CPTAC colon data set (1425 files) for the demonstration. >>> >>> Mathias, could you take the helm for Friday? >>> >>> Thanks, >>> Dave >>> >>> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >>> Dear colleagues, >>> >>> This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). >>> >>> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >>> >>> Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. >>> >>> I propose the following agenda items for the teleconference: >>> >>> - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. >>> >>> - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. >>> >>> - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. >>> As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. >>> >>> - Any additional items that need to be discussed... >>> >>> Thanks, >>> Wout >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> >>> >>> >>> _______________________________________________ >>> Psidev-qc-dev mailing list >>> Psi...@li...<mailto:Psi...@li...> >>> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >>> >>> >>> >>> The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! >>> http://sdm.link/slashdot >>> >>> >>> _______________________________________________ >>> 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... >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Martin E. <mar...@ru...> - 2017-10-25 13:14:20
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Dear colleague, dear member of the Proteomics community, meanwhile the authors of the proBAM specification have submitted a revised version, also reacting on the reviewers comments. Attached are the revised specification document and a file with responses to all reviewers comments. Also, all necessary information can be found on http://www.psidev.info/proBAM, including links to the documents and example files (accommodating all the implemented changes suggested by the reviewers). If you want to comment on the revised version, leave a comment on the web page http://www.psidev.info/proBAM-in-docproc or e-mail me until November 15th. Many thanks for your work Martin -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Ruhr-University Bochum Building ZKF 0.056 | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554 E-mail <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de Von: Martin Eisenacher [mailto:mar...@ru...] Gesendet: Donnerstag, 30. März 2017 09:50 An: 'psi...@li...' <psi...@li...>; 'psi...@li...' <psi...@li...>; 'psi...@li...' <psi...@li...>; 'ps...@eb...' <ps...@eb...>; 'psi...@eb...' <psi...@eb...> Betreff: HUPO PSI recommendation document (file format proBAM), 60-days public review Dear colleague, dear member of the Proteomics community, please forward this message to potentially interested colleagues! The HUPO Proteomics Standards Initiative (PSI) develops standards for documentation and storage of Proteomics data (see http://www.psidev.info for an overview of activities). A recommendation document specifying the proBAM file format has been submitted to the PSI document process. The submission can be found here: http://www.psidev.info/proBAM-in-docproc After having passed a 30-day review of the PSI steering group with minor changes, the proposed document version 1.0.0 DRAFT now goes through 60-days public comments and external review phase (end: 31st May 2017). The format represents output from proteogenomic studies, mapping the MS-based proteomics PSM information to the genome. Background: The proBAM format builds upon the structure of the original SAM/BAM format (http://samtools.github.io/hts-specs/SAMv1.pdf) by extending it with other mandatory fields to accommodate unique features on MS-based proteomics peptide-spectrum matches (PSMs) information. PLEASE ADD COMMENTS to the submission page (http://www.psidev.info/proBAM-in-docproc) or send them directly to martin.eisenacher: at : rub.de for example regarding the following criteria: - That it is well formed that is, it is presented in accordance with the templates and is clearly written. - That it is sufficiently detailed and clearly contains and comprehensively describes the necessary and sufficient explanation of the format. - That the examples are in accordance with the specification.> > This message is to encourage you to contribute to the standards development activity by commenting on the material that is available online. We invite both positive and negative comments. If negative comments are being made, these could be on the relevance, clarity, correctness, appropriateness, etc, of the proposal as a whole or of specific parts of the proposal. If you do not feel well placed to comment on this document, but know someone who may be, please consider forwarding this request. There is no requirement that people commenting should have had any prior contact with the PSI. Many thanks for your valuable time and participation Martin Eisenacher (PSI Editor) -- PD DR. MARTIN EISENACHER Department Leader DEPARTMENT Medical Bioinformatics Medizinisches Proteom-Center Ruhr-University Bochum Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554 E-mail <mailto:mar...@ru...> mar...@ru... <http://www.medizinisches-proteom-center.de/> www.medizinisches-proteom-center.de |
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From: Slebos, R. J. <Rob...@mo...> - 2017-10-20 15:31:21
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Hi Dave, Nice code, ran perfectly! I second Dan's consideration, especially where you link the quality metrics to outcome (peptide counts etc.). There are biological differences between the 95 samples and it is impossible to know how much those affect your findings. It would be interesting to see how the CompRef samples behave, the Sci Data paper has the assembly for all 32 CompRef runs we did during tumor and normal analyses. In my mind, the question is still about how variability of the QC metrics matter for the final product (good PSMs). Have you looked at what parameters determine PC1, 2 etc? Rob On 10/18/2017 6:04 AM, David Tabb wrote: > Hi, all! > > I am presenting a quality control workshop in Moscow on November 1st. I > am using the QuaMeter analysis of our 1425 CPTAC colon files from the > attached paper by Rob Slebos (DOI 10.1038/sdata.2015.22) as a basis for > this two-hour tutorial. I have made some small edits to Xia Wang's R > script for this purpose, and I have reconstructed the data files from > which it was produced. Today I have finished writing a Word document to > guide people through the script to understand its operation. > > I hope you will have a chance to look through the attached files to see > whether or not my Word document 1) reflects the technical principles > correctly and 2) avoids casting aspersions in the data (I don't think > the variation we saw across months of instrument operation was unusual > or unexpected). The presentation isn't until November 1st, so there's > still time to make some corrections. > > I will have intermittent contact with the network during October > 19th-October 29th. > > Thanks, > Dave > The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer > > Please consider the environment before printing this email. -- ------------------------- Robbert Slebos, PhD Senior Staff Scientist Clinical Science Lab, MRC-2067B Moffitt Cancer Center 13131 Magnolia Drive Tampa, FL 33612 Tel: 813-745-3685 email: rob...@mo... ------------------------- Denken Sie an die Umwelt - Drucken Sie nur wenn nötig. Denk aan het milieu voordat u dit bericht print! This transmission may be confidential or protected from disclosure and is only for review and use by the intended recipient. Access by anyone else is unauthorized. Any unauthorized reader is hereby notified that any review, use, dissemination, disclosure or copying of this information, or any act or omission taken in reliance on it, is prohibited and may be unlawful. If you received this transmission in error, please notify the sender immediately. Thank you. |
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From: Wout B. <wou...@ua...> - 2017-10-20 03:22:16
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Indeed, it seems best to postpone this week's call. Dave is still away next week as well though, so you and other people that might participate should decide whether it'd be useful to have the call then. In any case, I would like to remind everyone to fill in the Doodle in the mean time: https://doodle.com/poll/a64wekmusekb3i2w Thanks, Wout > On 17 Oct 2017, at 01:09, Walzer <wa...@eb...> wrote: > > I'm afraid I will be busy/traveling at that time, too. I am at the Dagstuhl comp. prot. seminar right now. > > How about we postpone the call to next week? Or maybe already to a new slot? > best, > > mths > > On 17/10/17 07:27, David Tabb wrote: >> Hello, my friends! >> >> I will be unable to take part in Friday's teleconference. I am in Russia from October 19th to November 3rd. The conference will likely take place during my flight leg from Dubai to St. Petersburg. You will be happy to know that I am teaching a two-hour workshop on QC, using the CPTAC colon data set (1425 files) for the demonstration. >> >> Mathias, could you take the helm for Friday? >> >> Thanks, >> Dave >> >> On 10/17/2017 1:59 AM, Wout Bittremieux wrote: >> Dear colleagues, >> >> This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). >> >> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >> >> Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. >> >> I propose the following agenda items for the teleconference: >> >> - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. >> >> - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. >> >> - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. >> As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. >> >> - Any additional items that need to be discussed... >> >> Thanks, >> Wout >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> >> _______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li...<mailto:Psi...@li...> >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev >> >> >> >> The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot >> >> >> _______________________________________________ >> 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... > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Daniel L. <dan...@pr...> - 2017-10-18 22:22:19
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Dave, I’ll let the others respond on their own. I have no real concerns. You do suggest that an instrument becoming increasingly erratic with time could explain one of your observations. I am confident that the data for the CompRef samples supports our assertion that the system was sufficiently stable to make reliable comparisons across runs and time. This was a major element of the data analysis by Bing’s group. However, nobody has looked at the data with a tool like this (although I’d bet Steve Stein has by now). Although you explained your reasoning for not analyzing the CompRef data, that was nevertheless the main dataset through which we evaluated system stability over time. It might be interesting to reconsider. Dan ---------- Daniel C. Liebler, Ph.D. | President | Protypia, LLC 9720 Turner Lane | Brentwood, TN 37027 | (615) 715-4312 http://protypia.com On 10/18/17, 5:03 AM, "David Tabb" <dt...@su...> wrote: Hi, all! I am presenting a quality control workshop in Moscow on November 1st. I am using the QuaMeter analysis of our 1425 CPTAC colon files from the attached paper by Rob Slebos (DOI 10.1038/sdata.2015.22) as a basis for this two-hour tutorial. I have made some small edits to Xia Wang's R script for this purpose, and I have reconstructed the data files from which it was produced. Today I have finished writing a Word document to guide people through the script to understand its operation. I hope you will have a chance to look through the attached files to see whether or not my Word document 1) reflects the technical principles correctly and 2) avoids casting aspersions in the data (I don't think the variation we saw across months of instrument operation was unusual or unexpected). The presentation isn't until November 1st, so there's still time to make some corrections. I will have intermittent contact with the network during October 19th-October 29th. Thanks, Dave The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer |
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From: David T. <dt...@su...> - 2017-10-18 10:20:28
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Hi, all! I am presenting a quality control workshop in Moscow on November 1st. I am using the QuaMeter analysis of our 1425 CPTAC colon files from the attached paper by Rob Slebos (DOI 10.1038/sdata.2015.22) as a basis for this two-hour tutorial. I have made some small edits to Xia Wang's R script for this purpose, and I have reconstructed the data files from which it was produced. Today I have finished writing a Word document to guide people through the script to understand its operation. I hope you will have a chance to look through the attached files to see whether or not my Word document 1) reflects the technical principles correctly and 2) avoids casting aspersions in the data (I don't think the variation we saw across months of instrument operation was unusual or unexpected). The presentation isn't until November 1st, so there's still time to make some corrections. I will have intermittent contact with the network during October 19th-October 29th. Thanks, Dave The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer |
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From: Walzer <wa...@eb...> - 2017-10-17 08:09:39
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I'm afraid I will be busy/traveling at that time, too. I am at the Dagstuhl comp. prot. seminar right now. How about we postpone the call to next week? Or maybe already to a new slot? best, mths On 17/10/17 07:27, David Tabb wrote: > Hello, my friends! > > I will be unable to take part in Friday's teleconference. I am in > Russia from October 19th to November 3rd. The conference will likely > take place during my flight leg from Dubai to St. Petersburg. You > will be happy to know that I am teaching a two-hour workshop on QC, > using the CPTAC colon data set (1425 files) for the demonstration. > > Mathias, could you take the helm for Friday? > > Thanks, > Dave > > On 10/17/2017 1:59 AM, Wout Bittremieux wrote: > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for > Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 > Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). > > You can connect to our teleconference on Google Hangouts through the > following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > Unfortunately so far I haven't been able yet to start up the > discussion with Mathias regarding some points I raised concerning the > XML schema. That's my bad, and I hope to be able to set aside some > time soon to pick this up. > > I propose the following agenda items for the teleconference: > > - Overview of the status of the XML schema and MIAPE guidelines. > Evaluation and allocation of the tasks that need to be done to move to > a 1.0 version. > > - Mathias did a great job submitting a project proposal for the EuBIC > developer's meeting in Ghent in January, which has been accepted for > the meeting's > hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The > proposal already contains some information based on the things we > discussed the previous time, but if you have additional ideas etc. it > would be good to discuss those. Furthermore, preparing some datasets, > a work plan, etc. in advance during this and next month's > teleconference will enable us to have everything ready in advance to > ensure that a valuable result comes out of the meeting, while > hopefully engaging new enthusiastic collaborators. > > - As I live in Seattle now due to its timing I won't be able to attend > the teleconference. As we discussed last month > here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate > whether other time slots would be an option. I've used some broad time > slots to try (and fail) to keep the number of options somewhat > reasonable. Normally you should see the time blocks in your local time > zone, but please verify this. I've used the third week of November now > as that's our current schedule, but that can be up for discussion as > well of course. > As there probably won't be a single ideal time to have people on three > continents participate in the teleconference an option is to have > alternating teleconferences at two different times. Please fill in the > Doodle so the possible options can be evaluated during the upcoming > telco. > > - Any additional items that need to be discussed... > > Thanks, > Wout > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > _______________________________________________ > Psidev-qc-dev mailing list > Psi...@li...<mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > > The integrity and confidentiality of this email is governed by these > terms / Hierdie terme bepaal die integriteit en vertroulikheid van > hierdie epos. http://www.sun.ac.za/emaildisclaimer > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > 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: David T. <dt...@su...> - 2017-10-17 07:01:21
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Hello, my friends! I will be unable to take part in Friday's teleconference. I am in Russia from October 19th to November 3rd. The conference will likely take place during my flight leg from Dubai to St. Petersburg. You will be happy to know that I am teaching a two-hour workshop on QC, using the CPTAC colon data set (1425 files) for the demonstration. Mathias, could you take the helm for Friday? Thanks, Dave On 10/17/2017 1:59 AM, Wout Bittremieux wrote: Dear colleagues, This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. I propose the following agenda items for the teleconference: - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon<http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here<https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. - Any additional items that need to be discussed... Thanks, Wout ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-qc-dev mailing list Psi...@li...<mailto:Psi...@li...> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer |
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From: Wout B. <wo...@uw...> - 2017-10-17 00:00:22
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Dear colleagues, This is a reminder that our next teleconference is scheduled for Friday, October 20th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China, 2:00 Pacific Time). You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 Unfortunately so far I haven't been able yet to start up the discussion with Mathias regarding some points I raised concerning the XML schema. That's my bad, and I hope to be able to set aside some time soon to pick this up. I propose the following agenda items for the teleconference: - Overview of the status of the XML schema and MIAPE guidelines. Evaluation and allocation of the tasks that need to be done to move to a 1.0 version. - Mathias did a great job submitting a project proposal for the EuBIC developer's meeting in Ghent in January, which has been accepted for the meeting's hackathon <http://uahost.uantwerpen.be/eubic18/hackathon.html>. The proposal already contains some information based on the things we discussed the previous time, but if you have additional ideas etc. it would be good to discuss those. Furthermore, preparing some datasets, a work plan, etc. in advance during this and next month's teleconference will enable us to have everything ready in advance to ensure that a valuable result comes out of the meeting, while hopefully engaging new enthusiastic collaborators. - As I live in Seattle now due to its timing I won't be able to attend the teleconference. As we discussed last month here <https://doodle.com/poll/a64wekmusekb3i2w> is a Doodle to evaluate whether other time slots would be an option. I've used some broad time slots to try (and fail) to keep the number of options somewhat reasonable. Normally you should see the time blocks in your local time zone, but please verify this. I've used the third week of November now as that's our current schedule, but that can be up for discussion as well of course. As there probably won't be a single ideal time to have people on three continents participate in the teleconference an option is to have alternating teleconferences at two different times. Please fill in the Doodle so the possible options can be evaluated during the upcoming telco. - Any additional items that need to be discussed... Thanks, Wout |
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From: EuBIC developer's m. <eu...@gm...> - 2017-10-10 17:20:11
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*— EuBIC 2018 developer’s meeting —* Dear colleague, We are happy to announce that the registration for the EuBIC 2018 developer’s meeting has now been opened. We encourage everyone to register in a timely manner as the number of participants is limited and to be able to enjoy the reduced early bird rate. The meeting’s program has also been finalized, with various interesting hackathon projects and keynote speakers. Please find more information below and on the meeting website. We look forward to meeting you in Ghent! *Meeting registration* More information: http://uahost.uantwerpen.be/eubic18/registration.html Early registration fees: - General registration: €100 - PhD student at Ghent University: €50 The registration fees cover the following activities and items: - Meeting attendance - On-site catering including coffee breaks and lunches - Opening reception - Closing lunch Additionally you can join the social event on Wednesday 10th January for €10. *Hackathon projects* More information: http://uahost.uantwerpen.be/eubic18/hackathon.html Topics for the hackathon sessions are divided into the (i) quality control, (ii) workflows, protocols, and guidelines, and (iii) quantification tracks. You can find more information on the specific topics included in these three tracks on the meeting’s website. You can indicate the project to which you want to contribute during the registration. *Keynote speakers* More information: http://uahost.uantwerpen.be/eubic18/keynote.html The meeting is honored to welcome the following keynote speakers: - dr. Laurent Gatto, Cambridge University, United Kingdom - prof. dr. Lukas Käll, KTH Royal Institute of Technology, Sweden - dr. Frédérique Lisacek, SIB Swiss Institute of Bioinformatics, Switzerland - prof. dr. Lennart Martens, Ghent University, Belgium *Other useful information* Date: January 9-12, 2018 Location: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium Venue: http://uahost.uantwerpen.be/eubic18/venue.html Transport: http://uahost.uantwerpen.be/eubic18/transport.html Accommodation: http://uahost.uantwerpen.be/eubic18/accommodation.html *Key dates* November 10, 2017: Early bird meeting registration deadline December 22, 2017: Late meeting registration deadline January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *More information* - website: http://uahost.uantwerpen.be/eubic18/ - social media hashtag: #EuBIC18 - conference email: eu...@gm... *Sponsorship *inquiries are still welcome at eu...@gm.... Supported by FWO Scientific Research Network ‘Novel Knowledge from Public Life Sciences Data'. |
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From: Walzer <wa...@eb...> - 2017-09-27 10:23:41
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Thanks Wout, aggreed. https://github.com/HUPO-PSI/qcML-development/issues/33 Let's add the points there one at a time and discuss there. cheers, On 25/09/17 17:52, Wout Bittremieux wrote: > Dear colleagues, > > Please find the meeting notes of the recent teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20170915_telco.md > > @Mathias: As to the discussion related to the XML format, do you think it would be useful to make a separate issue on GitHub per discussion point and do it like that? > > Best, > Wout > >> On 12 Sep 2017, at 06:54, Wout Bittremieux <wou...@ua...> wrote: >> >> Dear colleagues, >> >> This is a reminder that our next teleconference is scheduled for Friday, September 15th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China). >> >> You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 >> >> Based on Mathias' notes from last month the agenda items are: >> - Discussion of XML implementation issues and encoding. More information in last month's meeting notes and my previous list of remarks. >> - Topic proposal for the EuBIC developer's meeting hackathon. >> - Working group representation at the upcoming HUPO conference in Dublin. >> - Any additional items that need to be discussed... >> >> I hope to talk to all of you on Friday. >> >> Best, >> Wout >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ >> Psidev-qc-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > _______________________________________________ > 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...> - 2017-09-27 09:58:38
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Dear all, I recently submitted a workshop topic suggestion for EuBIC2018 on their organising github page: https://github.com/eubic/eubic18/issues/5 (on short order to meet the deadline ;) I designed the work plan and details in a way I saw fit to lead this meeting project if it is selected. We briefly touched upon that during last telco, but I am to get helping input or discussion points here. (You can of course just leave your likes with the issue ;) The project aim is, in short, to outfit our metrics and qcML documents with some supporting (and nice) visualisations and to give folks a chance to get more familiar with the way we propose to handle QC data. I am confident that we will have a robust beta of the CV and shared understanding of qcML usage to form a spec-doc precursor by then. best, -- Mathias Walzer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Office: +44 (0)1223 494 2610 E-mail: wa...@eb... |
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From: Wout B. <wou...@ua...> - 2017-09-25 17:01:53
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Dear colleagues, Please find the meeting notes of the recent teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20170915_telco.md @Mathias: As to the discussion related to the XML format, do you think it would be useful to make a separate issue on GitHub per discussion point and do it like that? Best, Wout > On 12 Sep 2017, at 06:54, Wout Bittremieux <wou...@ua...> wrote: > > Dear colleagues, > > This is a reminder that our next teleconference is scheduled for Friday, September 15th, at 9:00 GMT (10:00 British Summer Time, 11:00 Western Europe & South Africa, 17:00 China). > > You can connect to our teleconference on Google Hangouts through the following link: https://hangouts.google.com/group/taNzRy6ELMDK9wbk2 > > Based on Mathias' notes from last month the agenda items are: > - Discussion of XML implementation issues and encoding. More information in last month's meeting notes and my previous list of remarks. > - Topic proposal for the EuBIC developer's meeting hackathon. > - Working group representation at the upcoming HUPO conference in Dublin. > - Any additional items that need to be discussed... > > I hope to talk to all of you on Friday. > > Best, > Wout > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________ > Psidev-qc-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-qc-dev |
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From: Wout B. <wo...@bi...> - 2017-09-20 14:58:22
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Hi Mathias, Nice. It seems this largely corresponds to our MIAPE-QC guidelines, so we should aim to sync both efforts. Best, Wout > On 20 Sep 2017, at 03:19, Walzer <wa...@eb...> wrote: > > Hi everyone, > I just sat together with the EuBiC guys present at HUPO bioinformatics hub, discussing an interesting effort that is quite complementary with our goals for qcML. > > It is a list of information available when publishing a proteomics project - 'Submission Review'. For starts, this will be quite informal, and be refined step by step. We are aware there are more intricate PSI documents regarding minimum requirements, and it is my impression this will still not run in concurrence with them. This checklist can be very helpful e.g. for creating qcML from already acquired, analysed and published projects, and some of the items we already discussed for being important when creating a qcML. Ideas and comments are collected in the document you can find in the included link. > link for reference: http://wiki.proteomics-academy.org/Project:SubmissionReview > best, > -- > Mathias Walzer > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus, Hinxton, Cambridge, UK > Office: +44 (0)1223 494 2610 > E-mail: > wa...@eb... > > -- > You received this message because you are subscribed to the Google Groups "Eupa-Bioinfo" group. > To unsubscribe from this group and stop receiving emails from it, send an email to eup...@go.... > To post to this group, send email to eup...@go.... > Visit this group at https://groups.google.com/group/eupa-bioinfo. > To view this discussion on the web, visit https://groups.google.com/d/msgid/eupa-bioinfo/30076079-2c12-1fc8-6c7d-4bf23ac04120%40ebi.ac.uk. > For more options, visit https://groups.google.com/d/optout. |
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From: Walzer <wa...@eb...> - 2017-09-20 10:19:18
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Hi everyone, I just sat together with the EuBiC guys present at HUPO bioinformatics hub, discussing an interesting effort that is quite complementary with our goals for qcML. It is a list of information available when publishing a proteomics project - '*Submission Review <http://wiki.proteomics-academy.org/Project:SubmissionReview>*'. For starts, this will be quite informal, and be refined step by step. We are aware there are more intricate PSI documents regarding minimum requirements, and it is my impression this will still not run in concurrence with them. This checklist can be very helpful e.g. for creating qcML from already acquired, analysed and published projects, and some of the items we already discussed for being important when creating a qcML. Ideas and comments are collected in the document you can find in the included link. link for reference: http://wiki.proteomics-academy.org/Project:SubmissionReview best, -- Mathias Walzer European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge, UK Office: +44 (0)1223 494 2610 E-mail: wa...@eb... |
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From: Martin E. <mar...@ru...> - 2017-09-20 08:00:23
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Dear colleague,
The 60-days public comments and external
review phase for PSI-MI XML 3.0.0 ends soon! (29th September 2017).
Best regards
Martin Eisenacher (PSI Editor)
Von: Martin Eisenacher [mailto:mar...@ru...]
Gesendet: Freitag, 28. Juli 2017 17:10
An: 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'psi...@li...'
<psi...@li...>; 'ps...@eb...'
<ps...@eb...>; 'psi...@eb...' <psi...@eb...>
Betreff: HUPO PSI recommendation document (file format PSI-MI XML 3.0.0),
60-days public review
Dear colleague,
dear member of the Proteomics community,
please forward this message to potentially interested colleagues!
The HUPO Proteomics Standards Initiative (PSI) develops standards
for documentation and storage of Proteomics data (see
http://www.psidev.info for an overview of activities).
There has been a submission to the PSI Document Process
by the Molecular Interactions workgroup updating the
PSI-MI format to version 3.0.0
(from long-time stable XML 2.5, released 2005).
The submission (incl. current version of the specification document) can
be found here:
http://www.psidev.info/PSI-MI-in-docproc
After having passed a review of the PSI steering group
with minor changes, the proposed document version 3.0.0 DRAFT
now goes through 60-days public comments and external
review phase (end: 29th September 2017).
Purpose of the format (excerpt from the spec. doc.):
The existing XML standard (PSI-MI XML2.5) has proven to be,
and will continue to be, capable of capturing the vast majority
of molecular interaction data, which are generated by
techniques such as protein complementation assays,
affinity capture, biophysical measurements and enzyme assays.
However, use cases have arisen which cannot be adequately
described within this XML schema, for example allosteric
interactions, abstracted interactions and dynamic interactions.
In order to meet these specialist use cases, a new version of
the XML format has been developed, PSI-MI XML3.0.
Specification document: attached and at
http://www.psidev.info/PSI-MI-in-docproc
Schema MIF300.xsd:
https://github.com/HUPO-PSI/miXML/blob/master/3.0/src/MIF300.xsd
Schema documentation (Schema browser):
<https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html>
https://rawgit.com/HUPO-PSI/miXML/master/3.0/doc/MIF300.html
Schema documentation and use case examples (as Word docs.):
See appendix documents
at https://github.com/HUPO-PSI/miXML/tree/master/3.0/pub
or
<https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0>
https://www.dropbox.com/sh/0oclv5c3xxluc1z/AACorWMii2v_MpwukezXi34Ca?dl=0
(details of appendices in the spec. doc. and below).
PLEASE ADD COMMENTS to the submission page
(http://www.psidev.info/PSI-MI-in-docproc)
or send them directly to martin.eisenacher: at : rub.de for
example regarding the following criteria:
- That it is well formed that is, it is presented in accordance with the
templates and is clearly written.
- That it is sufficiently detailed and clearly contains and comprehensively
describes the necessary and sufficient explanation of the format.
- That the examples are in accordance with the specification.> >
This message is to encourage you to contribute to the standards
development activity by commenting on the material that is
available online. We invite both positive and negative comments.
If negative comments are being made, these could be on the relevance,
clarity, correctness, appropriateness, etc, of the proposal as
a whole or of specific parts of the proposal.
If you do not feel well placed to comment on this document, but
know someone who may be, please consider forwarding this request.
There is no requirement that people commenting should have had any
prior contact with the PSI.
Many thanks for your valuable time and participation
Martin Eisenacher (PSI Editor)
1. Appendices
Example files showing how the schema meets each of the use cases listed in
section 1.3. Note, all examples available in the IntAct database (
<http://www.ebi.ac.uk/intact> www.ebi.ac.uk/intact) unless otherwise stated
1.1 Appendix 1 Schema documentation for MIF300.xsd
1.2 Appendix 2 Example file showing the representation of all
molecular interaction data from a single publication (PMID: 26919541) in
PSI-MI XML3.0 note, includes use case 1.3k, rewrite of bibliography
section
1.3 Appendix 3 Representation of a negative feature range (use case
1.3a)
1.4 Appendix 4 Representation of the sequence change caused by
introduction of a mutation (use case 1.3b)
1.5 Appendix 5 Representation of multiple feature detection methods
and feature roles (use cases 1.3c, 1.3d)
1.6 Appendix 6 Representation of kinetic parameters added at feature
level (use case 1.3e)
1.7 Appendix 7 Representation of variable conditions (dynamic
interactions) in an experiment (use case 1.3f)
1.8 Appendix 8 Representation of an abstracted interaction, a
manually curated protein complex, in PSI-MI XML3.0 (use case 1.3g)
1.9 Appendix 9 Representation of a cooperative interaction in PSI-MI
XML3.0 (Use case 1.3h)
1.10 Appendix 10 Representation of molecule sets i.e. cases where a
participant may be one of a list of molecules (use case 1.3i)
1.11 Appendix 11 Representation of the systematic capture of the
stoichiometry of molecules within an interaction (use case 1.3j)
--
PD DR. MARTIN EISENACHER
Department Leader
DEPARTMENT Medical Bioinformatics
Medizinisches Proteom-Center
Ruhr-University Bochum
Building ZKF E.141 | Universitätsstraße 150 | D-44801 Bochum
Fon +49 (0)234 32-29288 | Fax +49 (0)234 32-14554
E-mail <mailto:mar...@ru...> mar...@ru...
<http://www.medizinisches-proteom-center.de/>
www.medizinisches-proteom-center.de
|
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From: Eric D. <ede...@sy...> - 2017-09-17 21:52:52
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Great, thanks, Dave! -----Original Message----- From: David Tabb [mailto:dt...@su...] Sent: Friday, September 15, 2017 11:16 PM To: Martin Eisenacher via Psidev-qc-dev <psi...@li...>; Eric Deutsch <ede...@sy...> Subject: HUPO qcML slides Hi, Eric. I produced two simple slides for potential inclusion in your HUPO-PSI presentation for HUPO. I hope that these will be useful! The group reminded me yesterday that the conference started Sunday. Thanks, Dave The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer |
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From: EuBIC developer's m. <eu...@gm...> - 2017-09-16 08:30:17
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*— EuBIC 2018 developer’s meeting —* *Project proposal submission deadline extended!* Project submission proposal is now open until *September 24, 2017*. EuBIC members will be present at the HUPO conference in Dublin this week. Find us there at the bioinformatics hub to get more information about the developer’s meeting and discuss your project proposal. To submit a project proposal please follow the instructions provided here: http://uahost.uantwerpen.be/eubic18/submission.html *EuBIC 2018 developer’s meeting* Date: January 9-12, 2018 Venue: Hotel Monasterium PoortAckere, Oude Houtlei 56, 9000 Gent, Belgium For more details on the program, please check the website: http://uahost.uantwerpen.be/eubic18/ *Key dates* *September 24, 2017: Extended project proposal submission deadline* October 2, 2017: Announcement of selected projects October 2, 2017: Conference registration opens January 9-12, 2018: EuBIC 2018 developer's meeting in Ghent *Topics* Hackathon projects can cover all topics in proteomics bioinformatics, including, but not limited to: - Tools - Extension of existing bioinformatics tools under the guidance of their original authors - Development of novel bioinformatics tools to solve open problems - Benchmarking - Compilation of gold-truth datasets - Collection of reference algorithmic implementations - Specification of benchmarking criteria - Workflows - Definition of formal protocols - Development of tutorials for bioinformatics software usage - Data analysis - (Re)analysis of publicly available proteomics datasets *More information* - website: http://uahost.uantwerpen.be/eubic18/ - social media hashtag: #EuBIC18 - conference email: eu...@gm... *Sponsorship *inquiries are welcome at eu...@gm... We look forward to welcoming you in Ghent! On behalf of the organizing committee, Wout Bittremieux |
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From: David T. <dt...@su...> - 2017-09-16 06:32:29
|
Hi, Eric. I produced two simple slides for potential inclusion in your HUPO-PSI presentation for HUPO. I hope that these will be useful! The group reminded me yesterday that the conference started Sunday. Thanks, Dave The integrity and confidentiality of this email is governed by these terms / Hierdie terme bepaal die integriteit en vertroulikheid van hierdie epos. http://www.sun.ac.za/emaildisclaimer |
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