[Biopython] SciPy 2014 (July 6-12, Austin, Texas, USA)

Wed Jul 16 18:46:53 UTC 2014

Hi Bard,

Thanks so much for the email. A pleasure to virtually meet you. Great job
with Blue Collar Bio and thanks so much for helping organize the
bioinformatics track last year.

I was astonished to hear that almost no one had heard of biopython albeit
many in the BoF session were new comers. Greg did mention that the
scikit-bio has some pycogent DNA in it. :-)

I would welcome help if scipy works out for me next year.

Let's keep in touch.

Cheers,

Burke

-- 
R. Burke Squires
Computational Genomics Specialist
Contractor  Medical Sciences & Computing, Inc.
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
National Institutes of Allergy and Infectious Diseases (NIAID)
OCICB/OSMO/OD/NIAID/NIH

31 Center Drive, Room 3B62E.2
Bethesda, MD 20892
Office: 301-402-9408
Mobile: 240-454-4515
http://bioinformatics.niaid.nih.gov <http://bioinformatics.niaid.nih.gov/>
(Within NIH)
http://exon.niaid.nih.gov <http://exon.niaid.nih.gov/> (Public)
NIAID Bioinfo Twitter: @niaidbioit

Disclaimer: The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be used
by anyone who is not the original intended recipient. If you have received
this e-mail in error please inform the sender and delete it from your
mailbox or any other storage devices. National Institute of Allergy and
Infectious Diseases shall not accept liability for any statements made
that are sender's own and not expressly made on behalf of the NIAID by one
of its representatives.

On 7/16/14 2:28 PM, "Brad Chapman" <chapmanb at 50mail.com> wrote:

>
>Burke;
>Great to hear SciPy was good again this year. I helped organize the
>bioinformatics sessions last year and it was awesome to be able to
>connect with the SciPy community. Unfortunately this year it clashed
>with the Bioinformatics Open Source Conference so I couldn't make it.
>
>As a group we'd love to work more closely with the scikit folks. It
>looks like a useful toolkit, and we've tried in the past to do more
>tight integration with PyCogent, so definitely would like to overlap.
>
>Your suggestion of a set of training materials with Biopython,
>scikit-bio and other Python bioinformatics resources would be
>brilliant. Definitely let us know how we can help,
>Brad
>
>
>> Hi all,
>>
>> Just a quick note to mention that I attended SciPy 2014 last week and it
>> was a great conference. The bioinformatics talks and birds-of-a-feather
>> sessions were good BUT there seemed to be a general lack of knowledge of
>> the existence of biopython. There was a nice talk by Greg Caporaso,
>>author
>> of QIIME, about a scikit-bio package his group is authoring. During the
>>Q
>> & A I asked if there was any work going on to make it interactive with
>> biopython and he said there was not. The scikit-bio package seems to
>>have
>> a good deal of overlap with the biopython / EMBOSS system and I think it
>> would be nice to try to make the two interoperable.
>>
>> For those who are interested the scikit-bio presentation for SciPy 2014
>> can be viewed here:
>>
>> 	https://www.youtube.com/watch?v=hgBx_DBiPxA
>>
>> Additionally, I submitted a tutorial proposal for SciPy 2014 and was
>> turned down as the organizers thought that a tutorial on biopython was a
>> bit to specific for the conference. Perhaps next year we can organize a
>> more generic bioinformatics python resource tutorial with biopython,
>> scikit-bio and another resources of potential use to bioinfomratics
>>users.
>>
>> Cheers,
>>
>> Burke
>>  
>> -- 
>> R. Burke Squires
>> Computational Genomics Specialist
>> Contractor  Medical Sciences & Computing, Inc.
>> Computational Biology Section
>> Bioinformatics and Computational Biosciences Branch (BCBB)
>> National Institutes of Allergy and Infectious Diseases (NIAID)
>> OCICB/OSMO/OD/NIAID/NIH
>>
>> 31 Center Drive, Room 3B62E.2
>> Bethesda, MD 20892
>> Office: 301-402-9408
>> Mobile: 240-454-4515
>> http://bioinformatics.niaid.nih.gov
>><http://bioinformatics.niaid.nih.gov/>
>> (Within NIH)
>> http://exon.niaid.nih.gov <http://exon.niaid.nih.gov/> (Public)
>> NIAID Bioinfo Twitter: @niaidbioit
>>
>> Disclaimer: The information in this e-mail and any of its attachments is
>> confidential and may contain sensitive information. It should not be
>>used
>> by anyone who is not the original intended recipient. If you have
>>received
>> this e-mail in error please inform the sender and delete it from your
>> mailbox or any other storage devices. National Institute of Allergy and
>> Infectious Diseases shall not accept liability for any statements made
>> that are sender's own and not expressly made on behalf of the NIAID by
>>one
>> of its representatives.
>>
>>
>>
>>
>>
>>
>> On 4/1/14 11:44 AM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:
>>
>>>Dear Biopythoneers,
>>>
>>>It looks like there was an extension to the SciPy deadline, so
>>>*today* is your last chance to submit talk or poster abstracts!
>>>
>>>Thanks,
>>>
>>>Peter
>>>
>>>P.S. You have until this *Friday* to submit your BOSC abstracts.
>>>
>>>On Wed, Mar 12, 2014 at 3:48 PM, Peter Cock <p.j.a.cock at googlemail.com>
>>>wrote:
>>>> Hi all,
>>>>
>>>> It is a bit short notice, but some of you may be interested in
>>>>attending
>>>> SciPy 2014, which will again have a bioinformatics session. There
>>>> is still time to submit an abstract (deadline 14 March):
>>>>
>>>> https://conference.scipy.org/scipy2014/participate/presentations/
>>>>
>>>> "SciPy 2014, the thirteenth annual Scientific Computing with Python
>>>> conference, will be held this July 6th-12th in Austin, Texas. SciPy is
>>>> a community dedicated to the advancement of scientific computing
>>>> through open source Python software for mathematics, science, and
>>>> engineering. The annual SciPy Conference allows participants from
>>>> academic, commercial, and governmental organizations to showcase
>>>> their latest projects, learn from skilled users and developers, and
>>>> collaborate on code development."
>>>>
>>>> Unfortunately SciPy 2014 clashes with BOSC 2014 in Boston,
>>>> which you may prefer to attend, which is also currently accepting
>>>> abstracts:
>>>>
>>>> http://www.open-bio.org/wiki/BOSC_2014
>>>> http://www.open-bio.org/wiki/Codefest_2014
>>>>
>>>> *Disclaimer*: I am co-chairing BOSC this year.
>>>>
>>>> Regards,
>>>>
>>>> Peter
>>>_______________________________________________
>>>Biopython mailing list  -  Biopython at lists.open-bio.org
>>>http://lists.open-bio.org/mailman/listinfo/biopython
>>
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython