Fwd: JBrowse is hiring

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Fwd: JBrowse is hiring

Chris Mungall
Apologies for the cross-posting. The JBrowse project is looking to
recruit a new developer, details below.

Forwarded message:

> From: Ian Holmes <[hidden email]>
> To: [hidden email], [hidden email],
> [hidden email] <[hidden email]>,
> [hidden email]
> Subject: JBrowse is hiring
> Date: Wed, 24 Sep 2014 10:57:18 -0700
>
> Description
>
> The JBrowse project is recruiting a new lead developer. If you are
> excited
> by the maturation of bioinformatics into a web-based, broad-utility
> discipline, this is the job for you. Since 2007 JBrowse has been
> bringing a
> modern dynamic HTML aesthetic to the “traditional” genome browser,
> being
> the first mainstream web-based genome browser with live panning,
> zooming,
> interactive track rearrangement and dynamic filtering of track lists.
> Since
> 2010, JBrowse has been the platform for Web Apollo, the first
> web-based
> tool for truly collaborative genome annotation, offering live visual
> feedback on gene model edits from non-local collaborators. In a sense,
> the
> JBrowse project represents both the “Google Maps” and the
> “Google Docs” of
> the genome browser space.
>
> We have more exciting offshoots planned, from synthetic biology design
> aids
> to genome-based social networking tools. These will demand the
> visualization of more bioinformatic data types (e.g. gene ontology
> annotations, phylogenetic trees, sequence alignments, synteny
> relationships, gene pathways and networks) and integration of
> associated
> computational analysis tools. The job requirements go far beyond that
> of a
> “maintenance programmer” position, demanding a high level of
> knowledge of
> bioinformatics practise, involvement in all aspects of the software
> life
> cycle (initial R&D, prototyping, test development, devops deployment,
> maintenance) as well as clear and effective communication with users
> and
> stakeholders.
>
> Your desk will be in the Holmes Lab on the UC Berkeley campus,
> co-located
> with the Web Apollo team in Stanley Hall, right at the nexus of genome
> engineering and applied bioinformatics in the SF Bay Area. This
> project has
> a high-visibility, high-impact position at the leading edge of
> web-based
> bioinformatics tool development. Previous incumbents of this position
> have
> “graduated” to high-responsibility equity-holding positions at key
> companies in the emerging computational genomics market, such as
> Foundation
> Medicine (cancer therapeutics) and Counsyl (prenatal genetic
> counseling).
>
> Responsibilities
>
> The primary role will be JBrowse development. JBrowse primarily
> consists of
> a JavaScript frontend supported by server-side Perl scripts. A
> one-year
> goal is the release of JBrowse version 2, a refactoring-in-progress to
> facilitate integration with other web services and data backends. In
> the
> shorter term the role will also support of Web Apollo and various
> other
> collaborating projects. The job will also involve a small and limited
> amount of user support. Along the way there will be numerous
> opportunities
> to prototype and develop new web-based technologies for the
> collaborative
> analysis of genomic data.
>
>
> Qualifications
>
> Essential:
>
> -
>
> B.S. in Computer Engineering, Bioinformatics or a related field with a
> minimum of five years related experience, or an equivalent combination
> of
> education and experience. Advanced degree is preferred.
> -
>
> Experience in development with JavaScript in client contexts:
> -
>
>    Experience in understanding and using a variety of libraries and
>    resources in an application
>    -
>
>    Experience with class prototyping frameworks
>    -
>
>    Experience with graphics frameworks such as d3
>    -
>
>    Experience with client testing frameworks such as Selenium
>    -
>
>    Experience with user interface frameworks such as Dojo and jQuery
> UI
>    -
>
>    Experience with CSS and CSS3 (e.g. responsive layout, media
> queries)
>    -
>
> Experience in development in UNIX server contexts:
> -
>
>    JavaScript (NodeJS), Perl, and/or Ruby
>    -
>
>    Experience with server unit testing frameworks
>    -
>
> Demonstrated experience in developing robust web-based user-facing
> software projects.
> -
>
> Familiarity with current issues in web development and design (e.g.
> HTML5, WebSockets, Web Workers, message queue frameworks).
> -
>
> Experience with a range of database technologies (e.g. relational,
> NoSQL, triplestores).
> -
>
> Excellent verbal and written communication skills.
> -
>
> Ability to perform research and make independent decisions about
> approaches and tools to reach specific goals.
> -
>
> Ability to apply analytical skills and creativity to solve complex
> software and data management problems.
>
> Desirable:
>
> -
>
> Familiarity with genomic sequence data (next-gen sequencing, reads,
> assemblies)
> -
>
> Experience with ontologies for annotation of genomic data
> -
>
> Experience with collaborative coding and build tools and workflows
> (notably github)
>
>
> Applications
>
>
> Apply at jobs.berkeley.edu, job id# 18514.

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