Senior Bioinformatician / Lead Software Developer position at Xenbase

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Senior Bioinformatician / Lead Software Developer position at Xenbase

Jeff Bowes
Xenbase, at the University of Calgary, is seeking a Senior
Bioinformatician / Lead Software Developer.

Xenbase ( is the model organism database for Xenopus
tropicalis and Xenopus laevis. These two frog species are powerful
systems for understanding how genes function in embryo development.
Xenbase integrates genomic sequences, literature, experimental images
and other data generated in research using Xenopus and makes it
available to scientists around the world on a 24/7 basis.

Xenbase offers numerous interesting software development challenges
including representing complex biological objects; working with large
datasets; information visualization; integration of multiple
bioinformatics software packages, data and text mining; and developing
compelling, intuitive web interfaces for scientists. Xenbase is entering
an exciting new phase of development that will involve the incorporation
of new genomes, genome annotation, phenotypes, and deep sequencing data.
We are looking for an experienced bioinformatician / software developer
ready to play a key part in these developments.

This position has an important role in the areas of bioinformatics and
web development. As Senior Bioinformatician, you will be responsible for
overseeing and designing data pipelines that process and move data in
and out of Xenbase. You will be responsible for various forms of
biological data analysis and providing customized data exports to users.
As Lead Software Developer, you will play a key role in designing,
testing and maintaining Xenbase web modules.


You are a versatile software developer. You have a keen interest in
science and technology and keep abreast of advances in these areas. You
are driven to learn new skills and methodologies. You are knowledgeable
and zealous about following good software engineering practices. This is
demonstrated by your documentation, code and tests. You are passionate
about creating positive user experiences.

You have experience providing technical leadership on projects and enjoy
sharing your knowledge and mentoring others. You are always looking for
ways to improve methodologies and processes. You are comfortable working
in a small team and are willing to lend a hand wherever it is needed.
You are able to clearly communicate concepts to people from outside your

You will meet the general requirements described below and have all the
mandatory skills and a number of additional requirements in either the
area of bioinformatics or web development.


   * 5 or more years of experience in software development
   * BSc in computer science, bioinformatics, or biological sciences with
     additional training in software development. An MSc is preferred.
   * Solid understanding or relational databases, especially MySQL & DB2
   * Linux
   * Knowledge of the Chado database schema is an asset


   * Fluent Perl (mandatory) with BioPerl
   * Bioinformatics Applications: Blast, Blat, GBrowse, Textpresso,
     Apollo, Biomart, etc.
   * Web Services (especially NCBI E-utilities)
   * Shell scripting

Web Development

   * Enterprise Java (mandatory)
   * Object Oriented Design (mandatory)
   * MVC frameworks (especially Struts)
   * ORM frameworks (especially MyBatis)
   * HTML, Javascript, AJAX (mandatory)
   * XML and XSLT
   * WebSphere, Apache
   * Rational Application Developer, Eclipse
   * Test Driven Development, Watir

If your skills are primarily in bioinformatics or web development you
should expect to develop them in the other area as well.

You must be currently legally eligible to work in Canada or the United

Application Deadline: March 15, 2012

This full time Fixed Term position is for approximately two years, with
the likelihood of extension, contingent upon continued funding. Xenbase
is principally funded by the U.S. NIH and is in the second year of a
five year renewal to its initial primary 5 year grant. As a well-used
on-line community resource, we fully expect Xenbase to receive continued
funding on an ongoing basis.

This position reports to the database director for Xenbase.

To Apply:

Please go to, select the "viewing all
opportunities" link then in the Basic Job Search, search for the keyword
"Bioinformatician". Select the link to the Job Id 1907. On the job
description page press the "Apply Now" button.

Additional Information

This position is part of the AUPE bargaining unit, and falls under the
Technical Job Family, Phase III.

To find out more about our competitive salaries and benefits, and why we
are A Great Place to Work and Learn, please see:

About U of C

The University of Calgary is a leading Canadian university located in
the nation's most enterprising city. The university has a clear
strategic direction 'Eyes High' to become one of Canada's top five
research universities by 2016, grounded in innovative learning and
teaching and fully integrated with the community of Calgary. For more
information, visit

Calgary is a major cosmopolitan, multicultural and business center with
a population over one million. It is located 1.5 hours, by car, from
Banff National Park in the Rocky Mountains and a number of world class
ski facilities. Calgary offers plentiful opportunities for outdoor

The University of Calgary respects, appreciates, and encourages diversity.

Contact Information

If you have questions please contact Jeff Bowes at [hidden email].

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