Association of open access genomics and bioinformatics projects.

Since 2011, the Open Genome Informatics group has served as an umbrella organization that represents a number of open-source and open-access bioinformatics projects worldwide.

[Alliance of Genome Resources (Alliance)] (https://www.alliancegenome.org "Alliance"): Develops and maintains sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease.

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

Generic Model Organism Database (GMOD): An open-source project to develop a complete set of software for creating and administering a model organism database).

Informatics and Bio-computing (OICR): Develops new algorithms, software, databases, visualization tools and other necessary components to interpret genome datasets.

JBrowse: 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.

WormBase: An international consortium of biologists and computer scientists providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes.

Please refer to the Open Genome Informatics GSoC page to find out more about the software projects being developed.

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Technologies

  • neo4j
  • python
  • mysql
  • react
  • javascript

Topics

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Open Genome Informatics 2021 Projects

  • Aoji Xie
    Authentication and Authorization Service for the Alliance of Genome Resources
    The Alliance of Genome Resources is a consortium of 6 model organism databases (MODs) and the Gene Ontology (GO) Consortium whose goal is to provide...
  • Prajna
    Bioinformatics with Jupyter Notebooks
    For an open-source tool for bioinformatics like WormBase, it is essential to have thorough documentation of features and use cases. As part of this...
  • Rishabh kohale
    Interactive viewer for systems-biology variant interpretation (Server-side)
    Genomic assays generate lists of genes or proteins statistically associated with a condition, such as being altered in disease. Genes need to be...
  • Lovro Vrcek
    Reactome Pathway Embeddings
    In the last several years, deep learning became widely used in various different fields, ranging from object detection and face recognition to speech...
  • Joao Luiz
    Single-Cell pathway annotation pipeline
    Single-Cell sequencing is a new methodology that provides high-resolution data to understand individual cells. Applied to RNA sequencing, it can...
  • Lokesh Rana
    Visualization Of Systems-Level Gene Annotation (UI-Side)
    This GSoC project proposes to create the UI side of a network-based hierarchical viewer to visualize gene annotation at various levels of systems...
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2021