Tag Archives: STRIDES

Request for proposals: Single Cell in the Cloud codeathon at NYGC in January

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The New York Genome Center is hosting an NCBI  Single Cell in the cloud codeathon from January 15-17, 2020. Submissions for project proposals are due December 2nd.

Please submit your proposal and apply here.

What topics are in scope?

This codeathon will focus on single cell data, including RNA, DNA, and chromatin accessibility.  We are particularly interested in proposals for pipelines and analysis of SRA data, data interoperability, and using machine learning techniques in clustering.  We also welcome proposals for tutorial pipelines and educational tools. You will have access to computational resources in the Cloud to turn your idea into a working prototype.   Visit our website for examples of previous codeathon projects.

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Virus hunting in the cloud: A hackathon story at ASV 2019

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Are you going to ASV 2019?

If you are, join us in a few days for a workshop on the virus hunting hackathon we helped run earlier this year.

Session: Workshop #19: Virus Discovery

Program Number: W-19-8

Time: Sunday, July 21, 7:00 PM CDT

Location: Mayo Auditorium

In this workshop, Dr. Rodney Brister will talk about how 41 scientists from 21 organizations worked to improve the usability of SRA data, identifying datasets that included known viruses and viral signals. Not only is that information now being integrated into a public search interface, but the approach used is also being refined in future hackathons so it can be applied to all SRA datasets.

We hope to see you there!

Bring your own data to the computational virology workshop at LSU New Orleans

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Attention all aspirational computational virologists and cloud-curious bioinformaticians! NCBI is hosting a free workshop in New Orleans, Louisiana April 23 and 24.

Choose your own adventure: participants may bring their own data and/or work with public data housed at NCBI.

Day 1 will consist of a short cloud-onboarding session, introduction to Jupyter notebooks, SRA and BLAST intros, and more! On day 2, we’ll roll our sleeves up in a working session around phylogenetic clustering of sequences where we’ll look for unknown viruses.

BYOD (bring your own data) and apply today! Please fill out the application form in its entirety by Tuesday, April 9th.

Attendee insights will be made publicly available on GitHub.

NCBI Computational Virology Workshop at LSU New Orleans!

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Introduction to NGS Analysis in a Cloud Environment for Novice Bioinformaticians:

We are pleased to announce a free workshop in New Orleans, Louisiana April 23 and 24.  After a short cloud-onboarding session, early career computational virologists interested in extracting sequences from metagenomic samples will be exposed to new, community-generated tools!

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Follow “Pangenomics in the Cloud” hackathon projects on GitHub

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NCBI is on the West Coast this week (March 25 – 27) for “Pangenomics in the Cloud,” a three-day hackathon hosted by the University of California, Santa Cruz.

Graphs are the name of the game here! The teams will be building graphs, managing coordinates between samples and defining and identifying and marking haplotypes, and looking at population specific variants.

Please follow along on our GitHub, fork and make pull requests during and after the event, and stay tuned for updates on the findings.

Pangenomics in the Cloud hackathon, March 25-27, 2019

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We are pleased to announce the first ever pangenomics, graphs and haplotypes hackathon.

From March 25-27, 2019, the NCBI will help run a bioinformatics hackathon in Santa Cruz, California, hosted by the University of California, Santa Cruz (UCSC).  Potential topics include:

  • Building large scale graphs from pangenomes using several assembly methods
  • Simplification of mapping
  • Resolving haplotypes
  • Identification of population-specific structural variants
  • Defining haplotype-specific expression, visualization, and coordination with the GRC

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Announcing the first ever RNA-Seq in the Cloud hackathon!

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From March 11-13, 2019, the NCBI will help run a bioinformatics hackathon in the North Carolina Research Triangle hosted by the University of North Carolina, Chapel Hill (UNC).

Potential topics include:

  • technical metadata homogenization
  • a simple interface for using ontologies to make data searches more sensitive and specific
  • automated data analysis and visualization
  • novel isoform identification and comparison

We’re looking for people who have experience in working with subjects like these. If this describes you, please apply!

This event is for researchers, including students and postdocs, who use bioinformatics data or develop pipelines for large scale RNA-Seq analyses from high-throughput experiments. The event is open to anyone selected for the hackathon and willing to travel to UNC. Continue reading →

Virus Hunting Data Science Hackathon next week in San Diego

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From January 9th – 11th, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University. We reached out to the global computational biology and virology community as part of this effort to make data more accessible.

The hackathon teams look forward to leveraging metagenomic datasets in the cloud to find data based on organismal content and update taxonomy – but most of all – hunt down new viruses!

Follow along with the event with NCBI tweets and see our work on GitHub.

NCBI to assist in Virus Hunting Data Science Hackathon January 9-11, 2019

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We are pleased to announce the second installment of the SoCal Bioinformatics Hackathon. From January 9-11, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research Center at San Diego State University!

We’re specifically looking for folks who have experience in computational virus hunting or adjacent fields to identify known, taxonomically-definable and novel viruses from a few hundred thousand metagenomic datasets that we’ll put on cloud infrastructure. This event is for researchers, including students and postdocs, who are already engaged in the use of bioinformatics data or in the development of pipelines for virological analyses from high-throughput experiments. If this describes you, please apply! The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).

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