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Old 06-06-2011, 09:49 AM   #1
Location: Downtown Toronto

Join Date: Nov 2010
Posts: 37
Default Bioinformatics Pipeline Developer

Position: Bioinformatics Pipeline Developer
Site: MaRS Centre, Toronto
Department: Informatics & Bio-computing
Reports To: Manager and Senior Software Architect
Salary: Commensurate with level of experience
Hours: 35 Hrs/week
Status: Full-time, Permanent

The Ontario Institute for Cancer Research (OICR) is in the forefront of cancer research and is participating in the International Cancer Genome Consortium and other large-scale sequencing projects. These cutting-edge studies provide an extraordinary opportunity to study the molecular basis of cancer and to implement cutting-edge computational tools in the process. Specifically, this position is focused on developing software tools to aid in the analysis of sequence data produced by OICR. This position is primarily focused on software development to support the SeqWare open source project ( which is used by the institute for sample tracking, performing grid and cloud-based analysis, databasing metadata, and querying unstructured and semi-structured data with Hadoop tools (such as MapReduce, HBase, Pig, Hive, Cascading, etc).

The responsibilities include:
Work with OICR developers and scientists to build robust pipeline systems for analyzing thousands of sequence samples;
Develop new software tools to support sequence analysis, algorithm evaluation, and data retrieval;
Work with the production team at OICR to ensure sequence data is automatically processed in a reliable and complete fashion;
Develop web applications to provide an interface to the sequence analysis system;
Follow excellent coding practices for open source development including managing code in source control, writing unit tests, providing documentation on both public and private sites.

B.Sc. degree in computer science or related field;
Masters/PhD in related field preferable;
Demonstration of excellent programming skills;
Desire to learn new technologies, such as Hadoop/HBase/MapReduce, and to participate in large, open source projects;
Proficiency with a scripting language (Perl preferred) and compiled language (Java preferred);
Proficiency with databases (MySQL, Postgres, etc) and the generic SQL language;
Good working knowledge of Linux is required, including common command line tools and the Bash shell environment;
Excellent interpersonal skills and the ability to work with a diverse group of individuals both locally and remotely;
Dedication to follow software development (agile programming) best practices and methods (testing, code reviews, etc);
Proficiency in both written and spoken English with excellent communication skills (presentations, reports, etc);
Must be detail-oriented and focused;
Experience with clusters (either traditional grid and/or Hadoop MapReduce);
Familiarity with other scripting languages (Python, Javascript, etc) and compiled languages (C, C++, etc);
Experience with Linux system administration and networking;
Experience with the Globus Toolkit, Condor, and/or Pegasus;
Experience with unit testing and code optimization;
Background in biology, molecular biology, or biochemistry;
1+ years of experience working as a software developer (graduating college students will be considered);
Please provide references on request.

OICR is an innovative cancer research institute located in the MaRS Centre in the Discovery District in downtown Toronto. OICR is addressing significant challenges in cancer research with multi-disciplinary, multi-institutional teams. New discoveries to prevent, detect and treat cancer will be moved from the bench to practical applications in patients. The OICR team is growing quickly. We are innovative, dedicated professionals who bring expertise to each of our roles. We are looking for individuals interested in being part of a culture of excellence that will result in Ontario being recognized internationally as a leading jurisdiction for cancer research.

Launched in December 2005, OICR is an independent institute funded by the Government of Ontario through the Ministry of Research and Innovation.

For more information about OICR, please visit the website at

POSTED DATE: May 31, 2011
CLOSING DATE: June 30, 2011

Interested candidates may apply here

OICR has a diverse workforce and is an equal opportunity employer.

The Ontario Institute for Cancer Research thanks all applicants. However, only those under consideration will be contacted. Candidates will be expected to provide their current employer as a reference.

Resume Format: If you elect to apply, you will need a text or HTML version of your resume so that you can cut and paste it into the application box provided. Before you submit the completed application, you will be asked to attach one or two files to your application. Please attach your resume as a .doc file.
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