GSOC Project Ideas 2018

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There are plenty of challenging and interesting project ideas this year. These projects include a broad set of skills, technologies, and domains, such as GUIs, database integration and algorithms.

Students are also encouraged to propose their own ideas related to our projects. If you have strong computer skills and have an interest in biology or bioinformatics, you should definitely apply! Do not hesitate to propose your own project idea: some of the best applications we see are by students that go this route. As long as it is relevant to one of our projects, we will give it serious consideration. Creativity and self-motivation are great traits for open source programmers.

  • Project Idea Name (Project Name/Lab Name)
    • Brief explanation: Brief description of the idea, including any relevant links, etc.
    • Expected results: describe the outcome of the project idea.
    • Knowledge prerequisites: programming language(s) to be used, plus any other particular computer science skills needed.
    • Skill level: Basic, Medium or Advanced.
    • Mentors: name + contact details of the lead mentor, name + contact details of backup mentor.


Here is a list of the proposed project ideas for 2018:

  • Project Idea 1: Incorporating different database searching algorithms into SequenceServer (SequenceServer/Wurmlab)
    • Brief explanation: It is now trivial to generate large amounts of DNA sequence data; the challenge lies in making sense of the data. In many cases, researchers can gain important insights by comparing newly obtained sequences to previously know sequences. SequenceServer (http://www.sequenceserver.com) is an easy to setup and simple to use graphical interface for searching sequence databases and interpreting the results. Based on the type (nucleotide or amino acid) of the query sequences and sequences in the selected databases SequenceServer automatically selects one of the five basic BLAST (https://en.wikipedia.org/wiki/BLAST) algorithms to use. However, depending on characteristics of query and database sequences (e.g., size, error profile, evolutionary distance) other algorithms, or a combination of different BLAST parameters (other than the defaults) can be more appropriate. This goal of this project is to identify the most common use cases and implement the functionality in SequenceServer.
    • Expected results: describe the outcome of the project idea.
    • Knowledge prerequisites: Working knowledge of Ruby and JavaScript (we use jQuery, React, and SystemJS); basic biology and informatics.
    • Skill level: Advanced
    • Mentors: Mentors: Anurag Priyam (anurag.priyam@qmul.ac.uk), Yannick Wurm (y.wurm@qmul.ac.uk)


  • Project Idea 2: Reactome Javascript Widget for Pathway Browser
    • Brief explanation: Reactome (https://reactome.org) is a free, open-source, curated and peer-reviewed knowledge-base of biomolecular pathways aiming to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. The Pathway Browser (https://reactome.org/PathwayBrowser) is Reactome’s primary means of viewing and interacting with specific pathways. (a short introduction video https://youtu.be/-skixrvI4nU). One of the tabs in the details panel currently shows the participating molecules of the selected items in the PathwayBrowser in a tabular fashion. The proposed project is to redesign the way in which participating molecules are shown to improve users experience as well as integrating the interaction data currently fetch from IntAct (https://www.ebi.ac.uk/intact/).
    • Expected results: An improved javascript widget to be integrated in the Pathway browser to improve the participating molecules tab in the Reactome Pathway Browser.
    • Knowledge prerequisites: javascript and java as programming languages, data visualisation skills.
    • Skill level: Medium.
    • Mentors: Antonio Fabregat (fabregat@ebi.ac.uk), Konstantinos Sidiropoulos (ksidiro@ebi.ac.uk).


  • Project Idea 3: Use Galaxy to run Reactome analysis and processes on genomic data
    • Brief explanation: Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education. Galaxy is an open, web-based platform for data intensive biomedical research, which allows users to perform, reproduce, and share complete analyses.
    • Expected results: There are two potential sub-projects. 1) Adding Reactome as a data resource in Galaxy, to enable Galaxy users to use Reactome reaction and pathway annotation data, and 2) Performing identifier mapping and over-representation analysis workflows from Reactome in Galaxy. Reactome Github: https://github.com/reactome/
    • Knowledge prerequisites: Galaxy, Java, web services
    • Skill level: Medium
    • Mentor: Robin Haw (robin.haw@oicr.on.ca) and Joel Weiser (joel.weiser@oicr.on.ca).