Selection tools for genomics researchers – a Galaxy of fun

The major goal of this project is to put in place a diverse collection of existing industry-standard software tools for the detection of “signatures of selection” in genomic data, using the web-based Galaxy software as a common platform for service delivery.

These tools are targeted at the NZ genomics research community, in particular those involved in the Virtual Institute of Statistical Genetics (VISG), and its sponsor organization, MapNet (NZ genetic mapping community). In addition to putting these tools in place, an important component of the project will involve facilitating access to these tools in a way that allows them to utilize cluster computing resources. This could include the creation of virtual machine appliances able to be deployed easily on institutional clusters, or the use of a job submission system that could submit large jobs to computational cluster queues (e.g., capability available as NeSI institutional allocation).

Students will require a strong background in Unix systems (including sysadmin skills), previous experience with web technologies (Apache, PostgreSQL, FTP, XML, etc) and shell (Bash) and/or scripting languages (e.g., Python), familiarity with open-source projects (e.g., ability to read, test and modify documentation and code) and the willingness to contribute back to them.

There is also a need for strong problem solving ability, as the challenges encountered in implementing software packages within the Galaxy framework are often novel and require non-standard solutions.

It would be helpful for students to have some domain-specific knowledge (in this case familiarity with genetics and genomics), as well as experience in dealing with large datasets and the ability to design user-friendly web interfaces.

Submitted by ehills on