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

[Psidev-qc-dev] HUPO-PSI, April 18-20, 2018, Heidelberg, Germany

[David T. <dt...@su...>]

Hi, all.

I wanted to update you that our working group will be meeting for its own track for two of the three days in our meeting at Heidelberg.  I hope almost all of us can make it!

At the moment, our track's topics include:

  *   qcML / minimal requirements
  *   Metrics integration and CV crafting
  *   Software support
  *   Implementation in repositories
  *   Minimal reporting requirements

Would you like to see any of these removed, updated, or replaced?

Martin Eisenacher wrote to me last week.  His schedule has become sufficiently busy that he can no longer reliably attend our monthly meetings.  I believe a member of his group may be able to continue our team's integration of the CV, though!

Thanks,
Dave

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

Re: [Psidev-qc-dev] interested in qcML

[David T. <dt...@su...>]

You are very welcome, Paul!  It will be great to work with you again.

Happy Holidays,
Dave

On 12/20/2017 1:26 AM, Paul Rudnick wrote:
Hi,
I'd be interested in participating in your meetings and working on qcML.
Many thanks
Paul

--
Paul A. Rudnick, Ph.D.
President & Co-Founder
Spectragen Informatics LLC
business: (206) 842-4980
email: pau...@sp...<mailto:pau...@sp...>
web: http://www.spectragen-informatics.com



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Re: [Psidev-qc-dev] interested in qcML

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

Hi Paul,

Great to hear that, your experience will be very valuable for our efforts!

We have a monthly teleconference on the third Thursday of the month at 15:00 GMT. That's a bit early for us on the West Coast, but I hope you'll still be able to participate some time. Our next teleconference will be January 18.
A reminder is typically posted to this mailing list in the week leading up to every teleconference.

It's also useful to point you to our GitHub repository: https://github.com/HUPO-PSI/qcML-development
Our activities are documented there, with an ongoing discussion on the development of the new qcML schema. You can also find meeting notes and other information on there.

Finally of course I recommend you to subscribe to this mailing list if that's not the case yet, as this is our main mode of communication for announcements, etc.

Best regards,
Wout

> On 19 Dec 2017, at 15:26, Paul Rudnick <pau...@sp...> wrote:
> 
> Hi,
> I'd be interested in participating in your meetings and working on qcML.
> Many thanks
> Paul
> 
> -- 
> Paul A. Rudnick, Ph.D.
> President & Co-Founder
> Spectragen Informatics LLC
> business: (206) 842-4980
> email: pau...@sp...
> web: http://www.spectragen-informatics.com
> ------------------------------------------------------------------------------
> 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

[Psidev-qc-dev] interested in qcML

[Paul R. <pau...@sp...>]

Hi,
I'd be interested in participating in your meetings and working on qcML.
Many thanks
Paul

-- 
Paul A. Rudnick, Ph.D.
President & Co-Founder
Spectragen Informatics LLC
business: (206) 842-4980
email: pau...@sp...
web: http://www.spectragen-informatics.com

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 14/12

[Wout B. <wou...@ua...>]

Dear colleagues,

Thank you for participating in our teleconference. It's always nice to see some new people joining the call.

Please find the meeting notes of yesterday's teleconference here: https://github.com/HUPO-PSI/qcML-development/blob/master/meeting_notes/20171214_telco.md

As Mathias remarked, it would be useful if you could have a look at the recent issues on GitHub. We can continue our discussions there and then summarize everything during next month's call.

Best,
Wout

> On 14 Dec 2017, at 08:24, Walzer <wa...@eb...> wrote:
> 
> Hey everyone,
> 
> good talking to you! One issue we did not touch is issue [#35] . Have a look at that, esp. if you are compiling a list of metrics for addition into the (pre)release of our CV. 
> The issue is (amongst others) about how cv value representation in the schema/file will reflect upon how we do the definition of the metric cv terms.
> When we can decide on a way(s) to do, I will complete and port the cv additions of PR #31 and the old metrics.
> 
> until then, happy holidays
>   mths
> 
> #35: [https://github.com/HUPO-PSI/qcML-development/issues/35]
> 
> On 12/12/17 00:54, Wout Bittremieux 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
> 
> -- 
> 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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 14/12

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

Hey everyone,

good talking to you! One issue we did not touch is issue [#35] . Have a 
look at that, esp. if you are compiling a list of metrics for addition 
into the (pre)release of our CV.

The issue is (amongst others) about how cv value representation in the 
schema/file will reflect upon how we do the definition of the metric cv 
terms.

When we can decide on a way(s) to do, I will complete and port the cv 
additions of PR #31 and the old metrics.


until then, happy holidays

   mths

#35: [https://github.com/HUPO-PSI/qcML-development/issues/35]

On 12/12/17 00:54, Wout Bittremieux 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

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

Re: [Psidev-qc-dev] Upcoming teleconference Thursday 14/12

[Wout B. <wou...@ua...>]

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

[Psidev-qc-dev] Upcoming teleconference Thursday 14/12

[Wout B. <wou...@ua...>]

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

Re: [Psidev-qc-dev] Upcoming teleconference Friday 13/11

[Wout B. <wou...@ua...>]

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

Re: [Psidev-qc-dev] Upcoming teleconference Friday 13/11

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

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

Re: [Psidev-qc-dev] Upcoming teleconference Friday 13/11

[David T. <dt...@su...>]

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

[Psidev-qc-dev] Upcoming teleconference Friday 13/11

[Wout B. <wou...@ua...>]

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

Re: [Psidev-qc-dev] Upcoming teleconference Friday 20/10

[Wout B. <wou...@ua...>]

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

[Psidev-qc-dev] revised version R1 of HUPO PSI recommendation document (file format proBAM), 3-weeks public review

[Martin E. <mar...@ru...>]

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

 



 

Re: [Psidev-qc-dev] Quality Control workshop for ClinProt 2017

[Slebos, R. J. <Rob...@mo...>]

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.

Re: [Psidev-qc-dev] Upcoming teleconference Friday 20/10

[Wout B. <wou...@ua...>]

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

Re: [Psidev-qc-dev] Quality Control workshop for ClinProt 2017

[Daniel L. <dan...@pr...>]

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
    

[Psidev-qc-dev] Quality Control workshop for ClinProt 2017

[David T. <dt...@su...>]

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

Re: [Psidev-qc-dev] Upcoming teleconference Friday 20/10

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

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...

Re: [Psidev-qc-dev] Upcoming teleconference Friday 20/10

[David T. <dt...@su...>]

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



------------------------------------------------------------------------------
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engaging tech sites, Slashdot.org! http://sdm.link/slashdot



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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

[Psidev-qc-dev] Upcoming teleconference Friday 20/10

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

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

[Psidev-qc-dev] EuBIC 2018 developer’s meeting - Meeting registration & program

[EuBIC developer's m. <eu...@gm...>]

*— 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'.

Re: [Psidev-qc-dev] Upcoming teleconference Friday 15/09

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

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

[Psidev-qc-dev] EuBIC2018

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

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...

Re: [Psidev-qc-dev] Upcoming teleconference Friday 15/09

[Wout B. <wou...@ua...>]

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
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