Tag Archives: metagenomics

Virus hunting in the cloud codeathon, v2

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We are pleased to announce the second installment of the Virus Hunting Codeathon that will take place from November 4-6, 2019 at the University of Maryland in College Park.

The NCBI will help run this bioinformatics codeathon, hosted by the UMIACS and CBCB at the University of Maryland. The purpose of this event is to continue develop techniques, code, and pipelines to identify known, taxonomically definable, and novel viruses from metagenomic datasets 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. We especially encourage people who have experience in Computational Virus Hunting or related fields to participate.  The event is open to anyone selected for the codeathon and willing to travel to College Park (see below).

TOPICS

  • Fast, federated indexing
    • Big Query
  • Metadata features
  • Genome graphs for viruses
  • Approximate taxonomic analysis
  • Domain/HMM Boundary and Taxonomic Refinement
  • Bringing together approximate taxonomy and domain models
  • Sequence data quality metrics
  • Phage-host interactions

We will provide the final list of projects before the codeathon starts.

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NCBI to help with Rocky Mountain Genomics HackCon, June 17 – 21, 2019

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The NCBI will participate in a one-day conference on June 18, 2019 and a hackathon, June 19-21, 2019 as a part of Rocky Mountain Genomics Hackcon 2019 at the BioFrontiers Institute in Boulder Colorado.

The conference will feature technical speakers in precision medicine, metagenomics, and advanced RNA-Seq analysis, as well as an exhibitor and poster session. The hackathon will focus on creating visualization tools for exploratory data analysis.

Many people who attend these events have experience working with large datasets or the development of informatics tools, code, or pipelines; however, researchers who are in earlier stages of their data science journey, including students and postdocs are also encouraged to apply. Some projects are available to other non-scientific developers, mathematicians, or librarians. The event is open to anyone selected for the hackathon and willing to travel to Boulder, Colorado.  

Please visit the Rocky Mountain Genomics Hackcon 2019 site for more details and information on how to attend.

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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Applications for July 2018 post-ISMB Chicago Bioinformatics Hackathon at Northwestern University Feinberg School of Medicine are open

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From July 11-13, 2018, NCBI will help with a data science hackathon at the Northwestern Feinberg School of Medicine campus in downtown Chicago. This hackathon focuses on genomics and general data science analyses including text, image, and sequence processing. The event is for researchers, including students and postdocs, who already use large datasets or develop pipelines for analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians or librarians. The hackathon is open to anyone selected for the hackathon and willing to travel to Chicago.

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NCBI to help with Rocky Mountain Genomics HackCon at University of Colorado BioFrontiers Institute June 18 – 23, 2018

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The NCBI will assist with a plenary session and a hackathon at the BioFrontiers Institute in Boulder Colorado June 18-23rd.

The hackathon will focus on tools for advanced analysis of biomedical datasets including text, images, next generation sequencing data, proteomics, and metadata. Many individuals who attend these events have already engaged in the use of large datasets or in the development of informatics tools, code, or pipelines; however, researchers who are in the earlier stages of their data science journey, including students and postdocs are also encouraged to apply. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to Boulder, Colorado.

Before the hackathon, there will be a one-day Plenary Session, featuring technical speakers in precision medicine, metagenomics and advanced RNA-Seq analysis, as well as an exhibitor and poster session.  Please see https://hackathon.colorado.edu for more details.

There will also be an advanced nascent RNA-Seq workshop, as well as an advanced pipelining workshop, run solely by the University of Colorado, although NCBI personnel may be present.  Please see https://hackathon.colorado.edu for more details.

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Summer 2017 NCBI Hackathon Products

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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.

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NCBI to assist in Southern California genomics hackathon in January

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From January 10-12, 2018, the NCBI will help with a bioinformatics hackathon in Southern California hosted by San Diego State University. The hackathon will focus on advanced bioinformatics analysis of next generation sequencing data, proteomics, and metadata. This event is for researchers, including students and postdocs, who have already engaged in the use of bioinformatics data or in the development of pipelines for bioinformatics analyses from high-throughput experiments. Some projects are available to other non-scientific developers, mathematicians, or librarians.

The event is open to anyone selected for the hackathon and willing to travel to SDSU (see below).  Applications are due Monday, December 11th, 2017 by 3 pm PT (6PM EST).

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NCBI’s First Hackathon: Advanced Bioinformatic Analysis of Next-Gen Sequencing Data

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This blog post is geared toward genomics professionals.

From January 5th-7th, 2015, NCBI, in conjunction with the NIH Office of Data Science, held a genomics hackathon, where genomics professionals gathered to write useful, efficient pipelines for people new to genomics.

After we announced the hackathon, over 130 qualified applicants expressed interest in attending. Four team leads chose 23 attendees from this pool, then assigned initial predefined roles and provided biological guidance for a product in one of four subject areas: DNA-Seq, RNA-Seq, Epigenomics and Metagenomics. Continue reading →