Ajax Programmer Job

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Wanted: JBrowse Developers

Interested applicants should do the following:

Wanted: Full-Time Developers for JBrowse, the JavaScript Genome Browser

We're bringing the power of social networking to genomics. Help make a contribution to the greatest scientific and medical endeavor of all time - interpreting the genomic code of human beings and the Earth's microbial ecology!


Project description

The JBrowse project was initiated in 2006 with the goal of bringing the "Web 2.0" experience to genomics. In a few years, JBrowse has become the JavaScript component of choice for genome-oriented bioinformatics websites, and is now used by many leading databases and websites for model organism, pathogen, and clinical/consumer-oriented genomics.

JBrowse has, in fact, fallen victim to its own success: our lead developer, Mitch Skinner, was recently recruited by a hot new medical genomics startup. (An occupational hazard of cutting-edge academic science!) Mitch still plans to contribute to the project from his new base, but we are looking for a programmer to replace him in-house.

In fact, since this job search comes at a time when we were expanding anyway, we plan to recruit up to two programmers. These will be temporary positions initially, but with the expectation that at least one, maybe both, of the positions will graduate to longer-term contracts after six months.

Google Maps for genomes

If you have not seen JBrowse before, go over to http://jbrowse.org/ and take a look. Our goal in starting the project was to offer the same improvement in navigational interfaces that the AJAX-heavy Google Maps offered over its CGI-based predecessors.

We feel we have succeeded in this: zooming and panning in JBrowse is a live, fluid experience, which helps avoid problems like getting "lost" in the map layout. (If you think it's easy to lose your place on a cartographic map, try navigating a genome... using laggy CGI.)

Furthermore, JBrowse scales better than most genome browsers, since a lot of the work is delegated to the JavaScript client. It also works on every major web platform, including the iPad!

Although we are proud of the progress so far, the really hard challenges are ahead: meeting the challenges of high-throughput sequencing, growing "market share", and developing a robust API for web-based genomics.

Essentially, we want to empower programmers -- from research lab to clinic -- to build the first-class websites that will comprise the bioinformatics infrastructure of the 21st century.


The JBrowse project assigns a great deal of responsibility and creative freedom to its programmers. Our past lead developers have been able to significantly influence the direction that the project has taken. We are looking for people with this kind of initiative who can turn a successful open-source project into a world-dominating one!

The job will also offer plenty of opportunities to participate in our lab's other research projects and collaborations -- such as probabilistic modeling of evolution and ecology, or genome annotation -- particularly web visualization of data from these projects, using JBrowse and other tools.

You will also have the chance to write & publish papers, if that is your inclination. Postdocs are welcome to apply, bearing in mind that these are developer positions first & foremost.

This is a chance to be involved in the early stages of a web application that will influence the direction of bioinformatics in a profound way. What if biologists could tag their own gene annotations.... see who else was interested in a particular gene... post questions and answers about genetic roles and functions... mark up a microbial genome with edits for a genetic engineering lab... or view the human and chimpanzee genomes side-by-side? What if clinical oncologists could browse transcriptomics profiles, view activated pathways and find case histories of similar tumors -- all from one integrated website? What if consumer genomics or genetic counseling felt like Facebook?

For bioinformatics, the emergence of the new web means faster tools, more interactivity and the rumblings of a "social network" approach to genomic science. Contribute to development in this prestigious open-source area and take advantage of this opportunity to build a revolutionary scientific web app with the potential for worldwide uptake and use.


Stanley Hall, University of California, Berkeley.


The ideal applicant will have experience in at least three of the following areas (and be primed to learn all of them):

  • Perl and/or Python, Ruby, other scripting language(s)
    • Catalyst, Rails, other MVC framework(s)
  • Javascript/AJAX programming
    • Dojo and/or other open-source Javascript libraries
    • Cross-browser portability
  • Databases (SQL and/or NoSQL)
  • RabbitMQ or other messaging architectures
  • Hadoop / MapReduce
  • Bioinformatics data formats and tools
  • UNIX programming


University of California, Berkeley, Grade: Programmer Analyst III.

Salary dependent on merit and relevant experience. $57,000 (minimum), $79,800 (midpoint), $102,600 (maximum). Most offers will not exceed the midpoint of the range.


Interested applicants should do the following:


Applications close April 30th, 2011.