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Position: Java Developer
Site: MaRS Centre, Toronto
Department: Informatics and Bio-computing Platform
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 seeking a Java Developer for the Informatics and Bio-computing platform. This position will focus 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 ((http://seqware.sf.net). This is used by the institute for sample tracking, performing grid and cloud-based analyses, databasing metadata, and querying unstructured and semi-structured data. The position will have an emphasis on leveraging Hadoop tools, such as MapReduce, HBase, Pig, Hive, Cascading, to streamline the analysis and annotation of our sequencer data. This developer will work closely with other teams at OICR to ensure the tools we build are appropriate and easy-to-use for other bioinformatics developers.
The responsibilities include:
• Developing a novel, innovative query engine to store and search Petascale biological datasets;
• Developing new software tools to support the analysis of these huge datasets;
• Mirroring external databases and annotation sources for use in annotating our biological data;
• Optimizing code to reduce computational time required to produce analysis results;
• Interacting with the production team to hand off released software tools and analysis team for driving tool development;
• Developer API building and documentation writing to support the use of advanced query tools by programmers;
• 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.
QUALIFICATIONS
• B.S. degree in computer science or related field;
• Demonstration of excellent programming skills;
• Proficiency with Java required along with a scripting language (Perl preferred) ;
• Desire to learn new technologies, such as Hadoop/HBase/MapReduce, and to participate in large, open source projects;
• Proficiency with databases (MySQL, Postgres, etc) and the generic SQL language;
• Good working knowledge of Linux is required, this includes 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, R, 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.
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 www.oicr.on.ca.
POSTED DATE: October 3, 2011
CLOSING DATE: November 3, 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.
Site: MaRS Centre, Toronto
Department: Informatics and Bio-computing Platform
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 seeking a Java Developer for the Informatics and Bio-computing platform. This position will focus 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 ((http://seqware.sf.net). This is used by the institute for sample tracking, performing grid and cloud-based analyses, databasing metadata, and querying unstructured and semi-structured data. The position will have an emphasis on leveraging Hadoop tools, such as MapReduce, HBase, Pig, Hive, Cascading, to streamline the analysis and annotation of our sequencer data. This developer will work closely with other teams at OICR to ensure the tools we build are appropriate and easy-to-use for other bioinformatics developers.
The responsibilities include:
• Developing a novel, innovative query engine to store and search Petascale biological datasets;
• Developing new software tools to support the analysis of these huge datasets;
• Mirroring external databases and annotation sources for use in annotating our biological data;
• Optimizing code to reduce computational time required to produce analysis results;
• Interacting with the production team to hand off released software tools and analysis team for driving tool development;
• Developer API building and documentation writing to support the use of advanced query tools by programmers;
• 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.
QUALIFICATIONS
• B.S. degree in computer science or related field;
• Demonstration of excellent programming skills;
• Proficiency with Java required along with a scripting language (Perl preferred) ;
• Desire to learn new technologies, such as Hadoop/HBase/MapReduce, and to participate in large, open source projects;
• Proficiency with databases (MySQL, Postgres, etc) and the generic SQL language;
• Good working knowledge of Linux is required, this includes 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, R, 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.
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 www.oicr.on.ca.
POSTED DATE: October 3, 2011
CLOSING DATE: November 3, 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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