Developing open source software to enable network-based biomedical discovery

The National Resource for Network Biology (NRNB) organizes the development of free, open source software technologies to enable network-based visualization, analysis, and biomedical discovery. Biomedical research is increasingly dependent on knowledge expressed in terms of networks, including gene, protein and drug interactions, cell-cell and viral-host communication, and vast social networks. Our technologies enable researchers to assemble and analyze these networks and to use them to better understand biological systems and, in particular, how they fail in disease. The NRNB mentoring organization includes projects such as Cytoscape, WikiPathways, SBML, and cBioPortal. This is a great opportunity to work at the intersection of biology and computing! For example, Cytoscape is downloaded over 18,000 times per month by researchers. We take mentoring seriously and are proud of our >95% success rate with former students and projects. But don’t take our word for it, read testimonials from prior NRNB students students and mentors. Find out more about the software projects being developed in coordination with NRNB. Also refer to the NRNB GSoC page for additional resources and application tips.

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Technologies

  • java
  • javascript
  • python
  • r
  • xml

Topics

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National Resource for Network Biology (NRNB) 2021 Projects

  • Mohamed Soudy-1
    Adding Multi-omics data support to ABioTrans Plus
    ABioTrans Plus is a web server for transcriptome data analysis and visualization. It supports the analysis of microarray and RNASeq data and performs...
  • Pritam Saha
    Develop a Cytoscape App for the Casual Path Algorithm
    The project is marked as Issue #169 in GitHub. The main goal of this project is to visualize the network which is generated from the Casual Path...
  • NIKITA MAHOVIYA
    Develop GUI for ImageJ groovy script calling VCell API
    We have to create a service for VCell users that allows Fiji/ImageJ scripting to directly access the VCell client. We have to expand this service...
  • Javed Ali
    Enhancing ABioTrans Plus using Gene Expression Omnibus database and adding analysis report
    This project aims to add new features to ABioTrans Plus(GeneCloudOmics) that includes the direct import of gene expression data from Gene Expression...
  • Aniket Ranjan
    Enhancing the admin panel of openPIP
    This project aims to add improvements in the admin panel of openPIP that is used to upload data and files, post announcements and change global...
  • Noah Liguori-Bills
    Expand ModelBricks.org and VCell API
    ModelBricks is a tool for bioinformatics researchers that allows users to browse, view, and download detailed models of biological processes. I...
  • Maija Utriainen
    Implementing multiple clustering algorithms and dimensionality reduction techniques on clusterMaker2
    Implementing following dimensionality reduction techniques and clustering algorithms to clusterMaker2: UMAP, t-SNE, PCA, PCoA, Louvain, Walktrap,...
  • Pankaj Yadav
    Local DB support for SBGN maps in Newt
    Newt is a web-based tool to analyze biological maps in standard formats such as PD and AF languages of SBGN, SBML, and SIF. This project aims to...
  • Can Alpay
    PD to AF conversion facility in Newt
    Newt supports the Process Description (PD) and the Activity Flow (AF) graphs of SBGN. However, there is no conversion between these two graphs in...
  • Pranav Ballaney
    SBML Simulator in Rust
    Over the last few years, the programming language Rust has seen a surge in popularity. This has primarily been the case due to its more robust memory...
  • Sankha Das
    SBML4Humans - Interactive SBML Report for Humans
    Systems Biology Markup Language (SBML) is a standard format for the representation and exchange of biological models between computers. The...
  • Indraneel Ghosh
    Simple Enrichment Tool for Analysis
    Cytoscape is a highly popular open source bioinformatics software platform for visualizing, analyzing, and publishing graphs or networks representing...
  • Siras Hakobyan
    TumorComparer, updated version
    TumorComparer, updated version The TumorComparer is a computational method for the comparison of different cancer types with cancer cell lines by...
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2021