Discussion group for interoperability of biological tools

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Brad Chapman

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May 17, 2013, 11:44:42 AM5/17/13
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Hi all;
Hope everyone has been keeping well since the Boston Hackathon. I wanted
to give another big thanks to everyone for all the hard work.
This mailing list as a place to keep in touch and more generally discuss
topics relating to interoperability of biological tools.

Since the hackathon I've been in touch with Gil Alterovitz, who has been
working on a similar interoperability initiative called SMART genomics
centered around defining APIs for exchanging genomic information:

http://smartgenomics.wikispaces.com/SMART+Genomics+API

The long term goal is hopefully to integrate our approaches where it
makes sense, so we can provide stable open source tools to help making
building biological software easier.

Looking forward to lots of great discussion and work,
Brad

Michael Heuer

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May 17, 2013, 12:18:10 PM5/17/13
to Brad Chapman, bioin...@googlegroups.com
Thanks for the getting this started, Brad.

I have a technical follow-up to the genome connector APIs we were
working on at the hackathon. I can't build some of my dependencies

Unit test failures in
com.github.jmchilton.blend4j.galaxy.IntegrationTest, LibrariesTest
https://github.com/jmchilton/blend4j/issues/4

Maven build fails with test failure in usageLogger
https://bitbucket.org/GenomeSpace/combined/issue/271

and corporate IT is not too keen on adding snapshot repositories and
clojars repositories to our Nexus.

michael

Alex Frieden

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May 17, 2013, 12:59:49 PM5/17/13
to Michael Heuer, Brad Chapman, bioin...@googlegroups.com
Would the idea be to take what we learned from the initial project and work within this API.  At least that is what I was thinking.  



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Alexander Frieden

Gil Alterovitz

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May 17, 2013, 1:05:32 PM5/17/13
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Yes, exactly!

Michael Heuer

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May 17, 2013, 2:02:55 PM5/17/13
to Gil Alterovitz, Alex Frieden, Brad Chapman, bioin...@googlegroups.com
Hello Gil,

I don't see a license for the SMART APIs, and from what I understand
of HL7 and FHIR there may be some other licensing concerns there.

Can you clarify?

michael

Michael Heuer

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May 17, 2013, 3:45:43 PM5/17/13
to Gil Alterovitz, Alex Frieden, Brad Chapman, bioin...@googlegroups.com, Jenny Cheng
Very cool. Thank you, Gil.

michael


On Fri, May 17, 2013 at 2:08 PM, Gil Alterovitz
<gil_alt...@hms.harvard.edu> wrote:
> Hi Michael,
>
> SMART uses Apache 2 license. We can add this to the wiki.
>
> Here is an article on SMART (mentions license and details too):
> http://jamia.bmj.com/content/early/2012/03/16/amiajnl-2011-000622.full
>
> -Gil

Gil Alterovitz

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May 17, 2013, 3:08:33 PM5/17/13
to Michael Heuer, Alex Frieden, Brad Chapman, bioin...@googlegroups.com, Jenny Cheng
Hi Michael,

SMART uses Apache 2 license. We can add this to the wiki.

Here is an article on SMART (mentions license and details too):
http://jamia.bmj.com/content/early/2012/03/16/amiajnl-2011-000622.full

-Gil


Gil Alterovitz

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May 17, 2013, 3:36:09 PM5/17/13
to Michael Heuer, Alex Frieden, Brad Chapman, bioin...@googlegroups.com, Jenny Cheng
Hi all,
If anyone would like to edit the wiki, please send me your email and I
will add you to the wiki list (anyone can view now, but editing is
limited currently) so you can make any changes you would like.
-Gil



On Fri, May 17, 2013 at 3:08 PM, Gil Alterovitz
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