[Biopython] Biopython 2018 Project Update talk at BOSC; was Call for Abstracts: GCCBOSC 2018

Thu Mar 15 14:34:00 UTC 2018

That is looking good - thanks Ben!

I think we could mention hoping to move from epydoc to
Sphinx for the API documentation (long term this opens
the door to moving the main tutorial from LaTeX to RST
and Sphinx to unify everything, and trying Read The Docs
or similar).

Technically we switched to wheels last year, so we
can't really talk about that as a headline item. However,
if this does significantly smooth the release process it
could be worth a slide in the talk itself?

Everyone else - please keep your feedback coming even
after submission, as we'll have a chance to tweak the
abstract later in reply to any reviewer's comments/

Regards,

Peter

On Thu, Mar 15, 2018 at 2:16 PM, Fulton, Ben <befulton at iu.edu> wrote:
> Here is what I have. There's definitely room for another paragraph if we have some ideas for features upcoming after the next release. Please let me know if there are more updates, and I will submit sometime before the deadline tomorrow night.
>
> --
> Ben Fulton
> Research Technologies
> Scientific Applications and Performance Tuning
> Indiana University
> E-Mail: befulton at iu.edu
>
> -----Original Message-----
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Sent: Thursday, March 15, 2018 5:29 AM
> To: Fulton, Ben <befulton at iu.edu>
> Cc: Biopython Mailing List <biopython at mailman.open-bio.org>
> Subject: Re: [Biopython] Biopython 2018 Project Update talk at BOSC; was Call for Abstracts: GCCBOSC 2018
>
> Good work Ben.
>
> I was going to try to squeeze in time this week for the overdue Biopython 1.71 release, but there looks to be a PDB regression we ought to fix first. In any case, we should at least have that out before GCC BOSC 2018 this summer.
>
> It wouldn't be unreasonable to aim to have Biopython 1.72 released a few months later just before BOSC, especially if the new wheel building system continues to work without issue.
>
> We could perhaps put planned dates in the abstract,
> - March/April 2018 - Biopython 1.71
> - June/July - Biopython 172
>
> Also we are getting closer to having the API docs working in Sphinx, and I think we could do this and epydoc for Biopython
> 1.71 using my branch of sphinx with a modified api-doc.
> Getting the new functionality into Sphinx may take a while longer, there seems to be disagreement on where to put the proposed new settings.
>
> https://github.com/biopython/biopython/pull/1388
> https://github.com/sphinx-doc/sphinx/pull/4076
>
> Peter
>
> On Wed, Mar 14, 2018 at 11:41 PM, Fulton, Ben <befulton at iu.edu> wrote:
>> My fork is here:
>> https://github.com/benfulton/talks/tree/master/2018_BOSC
>>
>> It appears that the 1.70 release actually took place before BOSC of
>> last year, so there isn't a new release to discuss. I think we'll be
>> doing "Coming real soon now!" type features :)
>>
>>
>> -----Original Message-----
>> From: Fulton, Ben
>> Sent: Wednesday, March 14, 2018 1:45 PM
>> To: 'Peter Cock' <p.j.a.cock at googlemail.com>
>> Cc: Biopython Mailing List <biopython at mailman.open-bio.org>
>> Subject: RE: [Biopython] Biopython 2018 Project Update talk at BOSC;
>> was Call for Abstracts: GCCBOSC 2018
>>
>> LaTex is fine. Is there a list of new features for 2017 somewhere?
>>
>>
>> -----Original Message-----
>> From: Peter Cock [mailto:p.j.a.cock at googlemail.com]
>> Sent: Wednesday, March 14, 2018 11:53 AM
>> To: Fulton, Ben <befulton at iu.edu>
>> Cc: Biopython Mailing List <biopython at mailman.open-bio.org>
>> Subject: Re: [Biopython] Biopython 2018 Project Update talk at BOSC;
>> was Call for Abstracts: GCCBOSC 2018
>>
>> Thanks Ben, that'd be perfect. Are you able to spare time over the next couple of days to help draft the abstract?
>> And, are you happy using LaTex for this?
>>
>> If so, I suggest you fork this repo and work there:
>>
>> https://github.com/cbrueffer/talks
>>
>> Otherwise, in place of LaTeX, we could use something else - there are a few suggested template here:
>>
>> https://www.open-bio.org/wiki/BOSC_Abstract_Submission
>>
>> Peter
>>
>> On Wed, Mar 14, 2018 at 3:47 PM, Fulton, Ben <befulton at iu.edu> wrote:
>>> That's an awful lot of slides for 15 minutes! I haven't contributed much, but I am planning on being in Portland (if my abstract is accepted so no pressure there). I could probably give the talk.
>>>
>>> --
>>> Ben Fulton
>>> Research Technologies
>>> Scientific Applications and Performance Tuning Indiana University
>>> E-Mail: befulton at iu.edu
>>>
>>> -----Original Message-----
>>> From: Biopython
>>> <biopython-bounces+befulton=iu.edu at mailman.open-bio.org> On Behalf Of
>>> Peter Cock
>>> Sent: Wednesday, March 14, 2018 7:07 AM
>>> To: Biopython Mailing List <biopython at mailman.open-bio.org>
>>> Subject: [Biopython] Biopython 2018 Project Update talk at BOSC; was
>>> Call for Abstracts: GCCBOSC 2018
>>>
>>> Dear Biopythoneers,
>>>
>>> As usual, the deadline has crept up on me (THIS FRIDAY), but I would like us to submit a Biopython Project Update talk for BOSC 2018.
>>>
>>> This year BOSC is colocating with the Galaxy Community Conference for a combined Bioinformatics Community Conference, which will hopefully be of broad appeal.
>>>
>>> https://www.open-bio.org/wiki/BOSC_2018
>>> https://gccbosc2018.sched.com/
>>>
>>> Please everyone consider submitting an abstract for your own open source bioinformatics work (speaking as a conference committee member).
>>>
>>> Also, as usual I would like to ask for volunteers from our contributors to present the annual Biopython Project Update talk?
>>>
>>> Who is planning to be in Portland Oregon for GCC BOSC 2018 (and hopefully the preceding CodeFest)?
>>>
>>> Would you like to volunteer? The talk slot is usually under 15 minutes, so its not too scary.
>>>
>>> Christian Brueffer did this for BOSC 2016, the slides and video are online:
>>>
>>> https://youtu.be/JxOm1Bjyt9M
>>> http://f1000research.com/slides/5-1712
>>>
>>> Sourav Singh was going to present at BOSC 2017 (and was awarded an OBF Travel Fellowship to attend), but was unable to due to visa problems. Again, Christian kindly did the presentation:
>>>
>>> https://youtu.be/tYD9P0aE8tA
>>> https://f1000research.com/slides/6-1238
>>>
>>> Note we have a simple LaTeX template for generating a nicely formatted PDF abstract on GitHub:
>>>
>>> https://github.com/cbrueffer/talks
>>>
>>> I hope to be there myself, and if no one else volunteers am willing to do the talk (again).
>>>
>>> Thanks,
>>>
>>> Peter
>>>
>>> Disclaimer: I am on the BOSC 2018 organising committee, and was previously co-chair. I will not be involved in reviewing the Biopython abstract.
>>>
>>> ---------- Forwarded message ----------
>>> From: Nomi Harris <nlharris at gmail.com>
>>> Date: Tue, Feb 20, 2018 at 9:42 PM
>>> Subject: [Bosc] Call for Abstracts: GCCBOSC 2018
>>> To: bosc-announce at open-bio.org
>>> Cc: bosc at open-bio.org, Nomi Harris <nlharris at gmail.com>
>>>
>>>
>>> GCCBOSC 2018: A Bioinformatics Community Conference Call for
>>> Abstracts
>>>
>>>
>>>
>>>  Dates: June 25-30, 2018
>>>  Location: Reed College, Portland, OR  GCCBOSC website:
>>> https://gccbosc2018.sched.com/  BOSC website:
>>> https://www.open-bio.org/wiki/BOSC_2018
>>>  Email BOSC organizers: bosc at open-bio.org  BOSC announcements mailing list:
>>> http://lists.open-bio.org/mailman/listinfo/bosc-announce
>>>  Twitter: @OBF_BOSC, #GCCBOSC
>>>
>>>
>>> Important Dates
>>>
>>> Abstract submission deadline: March 16, 2018 Authors notified: April
>>> 10, 2018 Travel fellowship application deadline: April 15, 2017
>>> GCCBOSC 2018 Training: June 25-26, 2018 GCCBOSC 2018 Talks: June
>>> 27-28 GCCBOSC CollaborationFest: June 29-30
>>>
>>> About BOSC
>>> Since 2000, the yearly Bioinformatics Open Source Conference (BOSC) has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.
>>>
>>> Why is BOSC partnering with GCC in 2018?
>>> In past years, BOSC has been part of the ISMB conference. Because of our continuing focus on broadening and deepening the BOSC community, we've been exploring ways to reach those in the bioinformatics community who aren’t already part of the audience attracted by ISMB.
>>> As part of that exploration, we have looked at other organizations and conferences that have been successful at establishing a strong and growing community of participants, such as the Galaxy Community Conference (GCC).
>>>
>>> After much discussion and planning, we decided to hold BOSC in conjunction with GCC in 2018. We hope that this will be an enjoyable and productive experience for all participants, and we welcome your feedback before, during and after the event.
>>>
>>> As always, BOSC 2018 will include two days of talks and posters, two keynote speakers, a panel discussion, Birds of a Feather, and more.
>>> BOSC sessions will run in parallel with GCC 2018 sessions, with some sessions shared. The two days of talks will be preceded by two days of training on topics nominated by the community, and will be followed by a two-day CollaborationFest that merges BOSC's Codefest and Galaxy's Developer and User Hackathon Days.
>>>
>>> Abstract submission
>>> We encourage you to submit one-page abstracts (due March 16) on any
>>> topic relevant to open source bioinformatics or open science. After
>>> review, some abstracts will be selected for lightning talks, longer
>>> talks, demos and/or posters. Abstract submission instructions and a
>>> link to the EasyChair submission portal can be found on
>>> https://www.open-bio.org/wiki/BOSC_Abstract_Submission
>>>
>>> BOSC session topics include (but are not limited to):
>>>
>>> Open Science and Reproducible Research Open Biomedical Data
>>> Citizen/Participatory Science Standards and Interoperability Data
>>> Science Workflows Visualization Medical and Translational
>>> Bioinformatics Developer Tools and Libraries Bioinformatics Open
>>> Source Project Progress Reports
>>>
>>> We look forward to receiving your abstract and meeting you at GCCBOSC 2018!
>>>
>>> Sincerely,
>>>       BOSC 2018 Organizing Committee: Nomi Harris (chair), Heather
>>> Wiencko (co-chair), Brad Chapman (co-chair), Peter Cock, Christopher
>>> Fields, Bastian Greshake, Karsten Hokamp, Hilmar Lapp, Monica
>>> Munoz-Torres
>>>
>>>
>>> P.S. Don't forget to submit your BOSC abstract by March 16 at https://www.open-bio.org/wiki/BOSC_Abstract_Submission! Please share this announcement with your colleagues!
>>>
>>> _______________________________________________
>>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>>> http://mailman.open-bio.org/mailman/listinfo/biopython