Open Genome Informatics
Open Genome Informatics represents the efforts of many bioinformatics projects.
The Open Genome Informatics group is organizing the joint efforts of Dockstore, Galaxy, GBrowse, GMOD, Informatics and Bio-computing (OICR), JBrowse, and Reactome. This is a great opportunity for students to contribute to the work of these established bioinformatics projects.
Dockstore: An open source project to bring together bioinformatics tools encapsulated in Docker with machine- and human-readable descriptions in the Command Workflow Language (CWL) or the Workflow Definition Language (WDL). Link: http://dockstore.org/.
Galaxy: An open, web-based platform for accessible, reproducible, and transparent computational biomedical research. Link: https://galaxyproject.org/.
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: http://gmod.org/wiki/GBrowse.
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: http://oicr.on.ca/informatics-and-bio-computing/.
Reactome: A manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. Link: http://www.reactome.org/.
SequenceServer is 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: http://sequenceserver.com.
Open Genome Informatics 2016 Projects
Biological Graph VisualizationsThe proposed project deals with the development of two Drupal modules, for storage and visualizations of Complex Biological Graph. Both the proposed...
Interactive visualisation framework for genome mutations in gene and protein networksI have wrote a set of thoughts expanding the original proposal "Interactive visualisation framework for genome mutations in gene and protein...
Lightweight chat plugin for the JBrowse genome browserThis project will deliver a lightweight socializing plugin for JBrowse using OAuth2 and the Faye pub/sub framework. Users will be able to chat, share...
Using Go-Docker to enhance Galaxy functionalitiesGo-Docker is a cluster management tool using Docker as execution/isolation system. It can be seen like Sun Grid Engine/Torque/… Using Bioinformatics...
Visualisation for BLAST resultsBuild a Standalone library / tool to visualise the BLAST results. This tool will be build on Ruby as command line tool. Types of visualisation ...
Work with the Dockstore Team and the GA4GH to Enable Cross Docker Repository SharingWith the development of software container technology, developers can manage and deploy their software effectively. The software can start up and run...