Fwd: [Gmod-ajax] JBrowse is hiring

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Fwd: [Gmod-ajax] JBrowse is hiring

Scott Cain

---------- Forwarded message ----------
From: Ian Holmes <[hidden email]>
Date: Wed, Sep 24, 2014 at 1:57 PM
Subject: [Gmod-ajax] JBrowse is hiring
To: [hidden email], [hidden email], "[hidden email]" <[hidden email]>, [hidden email]


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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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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