Implement an evaluation framework for software that manipulates HGVS-formatted variants

[skeenan]

IMPORTANT: This hackathon will now be held at the Marriott, near the Vancouver Convention Center. See http://www.ga4gh.org/#/hackathon2016 for details.

Background

HGVS is a syntax and set of recommendations used to represent sequence variants. The guidelines are broad and complex, and packages that implement these guidelines may not implement all features or may miss critical cases. This leads to uncertainty among users about which packages to use for particular purposes. The goal of the hgvs-eval project is to provide an objective framework by which HGVS tools may be assessed. It is envisioned that the primary user-visible product will be a web page that facilitates comparing packages (and package versions) on evaluation suite results.

Major tasks

Specific tasks for this project are:

• Define REST interface for manipulating HGVS variants.
• Define and implement an initial set of tests by which packages will be assessed.
• Implement tests. Implementation will enable both language-agnostic unit tests as well as REST-based evaluation.
• Implement REST interface for one package (https://bitbucket.org/biocommons/hgvs/).
• Implement a test database and rudimentary web interface that summarizes results.
• Document REST interface using swagger or RAML, sufficient to enable package owners to implement a REST interface using their tools.

Note: A REST interface, tests, and design considerations are provided in this draft proposal, which will be refined prior to the HackSeq event.

Ideal candidates

First, you're all ideal. 😄

The implementation will be in Python, so all contributors should have good Python skills. In addition, applicants should have experience with at least a few of the following: Python unit testing, REST interface design, HGVS variant nomenclature, simple web interfaces.

Participants: @cchng @dandanxu @jpdna @davecap @nicoleruiz (remote) @reece

Project Lead: Reece Hart / @reece / Industry Professional / Invitae

[gaberudy]

I wish I could be there for this one, but I won't be arriving until Tuesday evening.

Still if there is any support or armchair contributing I can do remotely, I'd be happy to stay in the loop.

Gabe

[jpdna]

I plan to attend

Justin Paschall

[reece]

Crosslink: hackseq/hackseq_projects_2016#10

[reece]

There will be many kinds of tasks for this project. Here are a few I can think of (and we may not have all represented, which is okay):

• test (feature evaluation) design: What features are we testing and how?
• db: design and implement schema (sqlite likely)
• REST interface: design interface urls, responses, and status
• Web UI: tabular layout and selection
• start implementation of at least 1 interface: mutalyzer (via soap interface), hgvs, or pyhgvs

I have some ideas (and some docs) on all of these, and some early docker images that I will try to have available by Thu (earlier, I hope).

If you anticipate coding, you may want to install docker (https://docs.docker.com/engine/installation/) in the meantime and then try to install hgvs as a python package with pip install hgvs (detailed instructions) or install using docker.

Finally, I will be giving an HGVS Workshop on Saturday at 11am at UBC. Details and laptop prep instructions are at https://github.com/hackseq/October_2016/blob/master/workshop_details.md#saturday.

[reece]

The following is a compilation of participation replies from several sources. Please reply to this issue if any of these are incorrect.

I moved the respondents to the issue description.

[cchng]

Hi Reece, yes, I will be able to attend at the Marriott.

[davecap]

I'd like to help out with this as well!

[Madelinehazel]

Sorry, I will be working on project 6 at UBC!

[reece]

Thanks @Madelinehazel. Have a good time!

[dfornika]

Thanks for mentioning me but I'll be participating in the hackseq hackathon. I'm hoping to attend the GA4GH plenary on Tuesday. I'm looking forward to seeing the results of all this hacking!

[reece]

@cchng @dandanxu @jpdna @davecap @nicoleruiz:

I look forward to our hackathon tomorrow!
Mercifully, the hackathon starts at 9am and not 8am like today's sessions.
Thanks in advance for your participation!
If you have time, here's a quick sketch of what I think we'll be doing tomorrow:

Nicole -- I'll send you a zoom video link separately.

https://docs.google.com/document/d/1x5SS_uaKFVwg3e4YYFqB1YK_P2dcg61Ubd3FvwB2AgI/edit?usp=sharing

[reece]

If anyone's following along at home, code is here:
https://github.com/biocommons/hgvs-eval