Need community / collaboration on general tools / visualizations from GA4GH structured data

[jacmarjorie]

One natural thing that comes out of implementing the ga4gh api for deployed servers ("real-world", non-example instances) is the need to produce some general tooling / visualizations to allow users to actually interact with the data.*

I'd like to propose the start of a ga4gh api visualization / tooling group that would consisting of people who have / will be developing tools and visualizations for manipulating the ga4gh structured data. At start, this could be an informal group of people who would like to share tools which they have developed in order to allow other implementors to leverage/contribute to them. As the apis reach a more solid state and more tools start popping up, it would be of benefit to have these all in a central location / an online inventory of available tools. I realize that not all "toolers" will be interested in developing in the same language / using the same libraries, but as always it would be nice to prevent duplication of common ga4gh centered tools as more deployed ga4gh servers come on the scene.

Anyone interested in being involved? So far, OHSU and some folks at UCSC have shown interest. I'd love to hear from others who are interested. If you feel more comfortable contacting me via email, please do so at smijac@ohsu.edu.

Thanks! (feedback appreciated)

*Side note: other things that tend to creep up are the realization for a need for additional features in the API (like filtering on certain fields), identifying potential pitfalls of a schema, or just questioning why certain aspects of the schema were developed as they were.

[akiani]

+1 & Interested :)

On Thu, Jul 23, 2015 at 12:04 PM, Jaclyn Smith notifications@github.com
wrote:

One natural thing that comes out of implementing the ga4gh api for
deployed servers ("real-world", non-example instances) is the need to
produce some general tooling / visualizations to allow users to actually
interact with the data.*

I'd like to propose the start of a ga4gh api visualization / tooling group
that would consisting of people who have / will be developing tools and
visualizations for manipulating the ga4gh structured data. At start, this
could be an informal group of people who would like to share tools which
they have developed in order to allow other implementors to
leverage/contribute to them. As the apis reach a more solid state and more
tools start popping up, it would be of benefit to have these all in a
central location / an online inventory of available tools. I realize that
not all "toolers" will be interested in developing in the same language /
using the same libraries, but as always it would be nice to prevent
duplication of common ga4gh centered tools as more deployed ga4gh servers
come on the scene.

Anyone interested in being involved? So far, OHSU and some folks at UCSC
have shown interest. I'd love to hear from others who are interested. If
you feel more comfortable contacting me via email, please do so at
smijac@ohsu.edu.

Thanks! (feedback appreciated)

*Side note: other things that tend to creep up are the realization for a
need for additional features in the API (like filtering on certain fields),
identifying potential pitfalls of a schema, or just questioning why certain
aspects of the schema were developed as they were.

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#368.

[jeromekelleher]

This is a great idea @jacmarjorie; I agree and am interested.

[maximilianh]

+1 and interested.

On Wed, Jul 29, 2015 at 11:05 AM, Jerome Kelleher notifications@github.com
wrote:

This is a great idea @jacmarjorie https://github.com/jacmarjorie; I
agree and am interested.

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#368 (comment).

[mbaudis]

+1 / interested

[wanghaisheng]

+1 / interested

[david4096]

Currently the best resource we provide is bioapi-examples. It provides a number of python notebooks as a basis. I have done a few visualizations using D3.js and better community involvement will make those efforts easier to maintain!

I have also created an issue on the server to track related software ga4gh/ga4gh-server#1451