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Open Genome Informatics

Open Genome Informatics represents the efforts of many bioinformatics projects.

This is a great opportunity for students to contribute to the work of these established bioinformatics projects:

Galaxy: An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Link.

Generic Model Organism Database (GMOD): An open source project to develop a complete set of software for creating and administering a model organism database). Link: http://gmod.org/wiki/Main_Page).

GBrowse: The Generic Genome Browser (GBrowse) is a web application for searching and displaying annotations on genomes. Link.

Informatics and Bio-computing (OICR): The Informatics and Bio-computing group at the Ontario Institute for Cancer Research (OICR) develops new algorithms, software, databases, visualization tools and other necessary components to interpret genome datasets. Link.

Intermine: InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Link.

JBrowse: JBrowse is being developed as the successor to GBrowse. It is a modern, fast genome browser implemented almost entirely in JavaScript, with some server-side formatting code in Perl. Link.

Reactome: A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. Link.

SequenceServer: A BLAST server for individual use or for sharing datasets with colleagues and community. Its minimalist, modern and thoughtful design lets user focus on the Biology and getting things done. Link.

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Technologies

  • python
  • java
  • javascript
  • nodejs
  • gwt

Topics

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Open Genome Informatics 2017 Projects

  • Samyadeep Basu
    Development of a Statistical Framework to Identify Similar Nodes in InterMine
    InterMine is a large graph containing entities(Genes, Transcription Factors etc. ) with important relationships between them. The main aim of the...
  • Konstantinos Kyritsis
    Expansion of functionality and creation of detailed and exciting bioinformatics R demos for InterMineR package
    InterMine constitutes a data warehouse framework, which provides the ability to access, retrieve and analyze rapidly a variety of biological data...
  • Leonardo Kuffo
    InterMine Registry
    The InterMine Registry will allow users to obtain and search, by consuming a RESTful API, basic information about existing InterMine instances. This...
  • Nadezda Yudina
    iOS InterMine app
    InterMine has an Android application and is looking to make it available on iOS as well. Native iOS application will allow researchers to have access...
  • Alan Cleary
    Pan-Genome Module for the Genome Context Viewer
    With the number of sequenced and annotated genomes continuously increasing, there is a need for new algorithms and tools for comparative analyses...
  • aniarya82
    Performance and user-centric upgrade to Afra
    The primary goal of the project is to upgrade Afra's annotation editing code, to provide it performance upgrade. Afra's annotation editor is built...
  • yasharmaster
    Prototype a new RESTful API querying Neo4j database
    Description InterMine is an open source data warehouse which is used to store complex biological data. It is currently using PostgreSQL as the...
  • Ayushya Chitransh
    Stand-alone Reactome server in a Docker image
    The goal of this project is to produce a Docker image that contains everything that an end-user needs to run Reactome on his/her own workstation....
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2017