Summer 2017 NCBI Hackathon Products

This blog post is for researchers, students, and postdocs, as well as non-scientific developers, mathematicians and librarians.

This summer, we were quite busy running and cohosting hackathons. These events educate participants, allow for networking among computational biologists and produce bioinformatics software prototypes.  Read on for a review of products from our Summer 2017 hackathons.

Colorado hackathon participants pose outside
Figure 1. A few of the Boulder hackathon attendees who ventured outside one day.

At the May 2017 BioFrontiers Hackathon in Boulder, Colorado – the eleventh NCBI-style Hackathon – participants developed eight functional software prototypes, several of which are under active development.

NYGC hackathon participants pose for a picture on the stairs
Figure 2. Many of the NYGC hackathon attendees on the stairs of the Genome Center

Three weeks later, participants at the June 2017 New York Genome Center Hackathon developed eight software projects and a guide for other groups who want to run NCBI-style hackathons. Finally, in August, we came back to NCBI and built 7 products.

Here are short descriptions of a few projects from each event:

RNA-Seq projects

Gene Expression Aging: Modular toolkit for RNA-Seq viewers

SCANT: Derives novel loci and splice variants from single cell RNA-Seq data

MyFavoriteTF: A web interface to identify transcription factor (TF) activity across cell-types

Arvos: A Dockerized database and flask template for presentation of an interactive RNA-Seq results summary

ValR: An R package that provides tools to read and manipulate genome intervals and signals, similar to the BEDtools suite

Bacteria and virus projects

Nastybugs: A simple method for finding antimicrobial resistance genes in metagenomic datasets

Staphviewer: A JBrowse Viewer for Staph aureus genomes

ViromeSniff: Maps NGS data to viral proteins and facilitates discovery of new viruses by mapping to domains

Cancer Projects

Tumorsim: A Python package that simulates the structural variations of cancer genomes

Improved Methodology

GenomicRobots: A robotic encapsulation of a variant calling robot that can return deidentified results

Long read aligner: Aligns long reads generated by the PacBio sequencing platform

SuMu: Feeds genomic data into STAN, a probabilistic programming language for statistical inference written in C++

Educational Tools

Epigenetics_MOOC: A massive, open, online course for beginners to learn about epigenetic analysis

Designing Educational Experiences with Jupyter Notebooks: A template based on Jupyter Notebooks that uses BLAST as an example for documentation for NCBI computational resources

Thanks to all the hackathon participants, and Evan Biederstedt, Danielle Betts (local hosts for NYGC), Dan Timmons and his crew (local hosts for Colorado), Lisa Federer (writing mentor for NCBI hackathons), Sean Davis (multi-team mentor for some NCBI hackathons), and Maryam Zaringhalam (AAAS fellow at NLM that helped with editing the post) and all the other supporters of NCBI Hackathons!

Like what you see?  Check out our guide to running your own NCBI-style hackathon. Feel free to contact for assistance, and keep following NCBI Insights and our social media accounts (Facebook, Twitter, LinkedIn) to join future hackathons.

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