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.i
    • 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).


  • Project Idea 4: Participating Molecules Widget (Reactome)
    • 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 5: Community-driven curation (WormBase)
    • Brief explanation: [Risky/Exploratory] - Scientific databases that curate the primary literature face an enormous challenge: the number of research papers continues to skyrocket, but the process of curation is slow, tedious, and resource-constrained. One solution is to engage the primary research community in curation of their own data, a strategy referred to as "community curation". At the same time, such strategies require careful and automated quality control to ensure the integrity of submissions and to prevent abuse of the system. We'd like to build a data submission and reviewing system that can be generalized to work on the diverse data types that we curate.
    • Expected results: A Datomic https://docs.datomic.com/on-prem/getting-started/brief-overview.html database that models "under review" content as well as approved content. A REST API for reviewing and approving content, and accessing content that may or may not include those that are under review.
    • Knowledge prerequisites: Clojure, database
    • Skill level: Advanced
    • Mentors: Adam Wright, Sibyl Gao, Matt Russell


  • Project Idea 6: Revision tracking curation database and tools (WormBase)
    • Brief explanation: [Fun/Peripheral] - Serving up-to-date content is critical for repositories like WormBase supporting basic scientific research. Our current workflow consists of periodic integration of multiple databases into a single production database every 2 months. While stable, this impedes real-time publication of new data. Having a live-curated database to power our website motivated our ongoing database migration to Datomic, a transactional database with change tracking and a queryable history. It will enable us to build a live-curated website with an emphasis on change tracking. In addition to having curated content immediately available to users, this website will provide information on what has changed recently along with metadata associated with these updates, such as citations and remarks. We'd like to start by making a prototype that works on the person/lineage data.
    • Expected results: A Datomic https://docs.datomic.com/on-prem/getting-started/brief-overview.html database that models person/lineage data and a REST API for submitting and retrieving content, reviewing change history, and optionally a user interface
    • Knowledge prerequisites: Clojure, database
    • Skill level: Medium
    • Mentors: Adam Wright, Sibyl Gao, Matt Russell


  • Project Idea 7: Multi-container cloud deployment (WormBase)
    • Brief explanation: [Infrastructure/Automation] - Continuously deploying code and data is a long term goal of WormBase. Over the past several years, we have been moving towards a Docker based approach, using AWS' ElasticBeanstalk to deploy individual containers. As we deploy more components of our microservice based architecture, there is an increasing need to coordinate the deployment of the individual services. This project focuses on the devops side of WormBase, creating a prototype of a provisioning system using modern cloud deployment technologies to streamline our workflow.
    • Expected results: A proof of concept, Docker based, system for deploying and maintaining our microservice architecture.
    • Knowledge prerequisites: Docker, DevOps, AWS, Kubernetes
    • Skill level: Medium
    • Mentors: Adam Wright


  • Project Idea 8: Improve search result relevance (WormBase)
    • Brief explanation: [Core development] - An effective search is a critical tool for any large data repository. This project seeks to improve an ElasticSearch-backed service at WormBase with improved code for indexing and search queries. A related component of this project will use analytics to better understand user behavior and how it affects search results.
    • Expected results: Improve the relevance of search result by improving the code that indexes the content and/or queries the search index
    • Knowledge prerequisites: Elasticsearch
    • Skill level: Medium
    • Mentors: Sibyl Gao


  • Project Idea 9: Navigating search with facets (WormBase)
    • Brief explanation: [Core/UI development] - Finding meaningful results in biological data is rarely as simple as conducting a single, basic search. Instead, users often need to step through results with filters to gain new insight into the data. This project aims to add facets, counts, and dynamic graphs to search results stored in our main ElasticSearch database.
    • Expected results: Improve search interface through the use of facets and relevant visualizations.
    • Knowledge prerequisites: Elasticsearch, JavaScript, d3.js
    • Skill level: Medium
    • Mentors: Sibyl Gao, Adam Wright


  • Project Idea 10: User interface re-design and implementation (WormBase)
    • Brief explanation: [Core development] - As we have been actively converting the WormBase website from TemplateToolkit/JQuery to React, we have begun to consider new user interface approaches. For example, the current WormBase website is heavily geared towards per-page customization (see [this page](http://www.wormbase.org/species/c_elegans/gene/WBGene00006763, for example)). This project will review the current website, make suggestions, and create user interface implementations more intuitive.
    • Expected results: Design and implement user interface improvements to make it more intuitive to new users and easier to locate information.
    • Knowledge prerequisites: HTML, CSS, JavaScript
    • Skill level: Medium
    • Mentors: Sibyl Gao, Adam Wright


  • Project Idea 11: CRAM support for JBrowse/Apollo
    • Brief explanation: JBrowse already offers support for several binary formats like BAM, BigWig and tabix formatted files like VCF. The addition of CRAM support would allow several groups with large datasets (like cancer research) to make use of JBrowse and Apollo. This project will likely require a combination of server and client side javascript.
    • Expected results: A client-server tool that parses CRAM files and presents the graphical results in a JBrowse canvas.
    • Knowledge prerequisites: JavaScript (DoJo, Node, React, Canvas)
    • Skill level: Advanced
    • Mentors: Eric Yao, Nathan Dunn, Rob Buels