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.
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.
Open Genome Informatics 2017 Projects
Development of a Statistical Framework to Identify Similar Nodes in InterMineInterMine is a large graph containing entities(Genes, Transcription Factors etc. ) with important relationships between them. The main aim of the...
Expansion of functionality and creation of detailed and exciting bioinformatics R demos for InterMineR packageInterMine constitutes a data warehouse framework, which provides the ability to access, retrieve and analyze rapidly a variety of biological data...
InterMine RegistryThe InterMine Registry will allow users to obtain and search, by consuming a RESTful API, basic information about existing InterMine instances. This...
iOS InterMine appInterMine has an Android application and is looking to make it available on iOS as well. Native iOS application will allow researchers to have access...
Pan-Genome Module for the Genome Context ViewerWith the number of sequenced and annotated genomes continuously increasing, there is a need for new algorithms and tools for comparative analyses...
Performance and user-centric upgrade to AfraThe primary goal of the project is to upgrade Afra's annotation editing code, to provide it performance upgrade. Afra's annotation editor is built...
Prototype a new RESTful API querying Neo4j databaseDescription InterMine is an open source data warehouse which is used to store complex biological data. It is currently using PostgreSQL as the...
Stand-alone Reactome server in a Docker imageThe 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....