Virus hunting in the cloud codeathon, v2


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


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!

Genome context graphic now in virus search results


We have a new and improved search experience for viral genes from select human pathogens. When you search  for a virus such as HIV-1 (more examples below),  you now get an interactive graphical representation of the viral genome where you can see all the annotated viral proteins in context. Clicking on the gene / protein objects allows you to access sequences, publications, and analysis tools for the selected protein. This new feature is designed to help you quickly find information relevant to your research on clinically important viruses.Virus_searchFigure 1. Top: The virus genome graphic result for a search with HIV-1 with access to analysis tools, downloads, and relevant results in the Genome and Virus resources. Bottom: The result obtained by clicking the env gene graphic, which provides links to protein and nucleotide sequences, the literature, analysis tools, and downloads.

Try it out using the following example searches and  let us know what you think!

New Norovirus GenBank Submission Service


Do you have Norovirus sequence data to submit to GenBank? Try out the newly-released improvements in our submission service for Norovirus data! The new service offers the following advantages:

  • Faster processing and shorter time to accession numbers
  • Improved user interface
  • Automatic Feature annotation
Submisssion_portal

Figure 1. The submission portal page showing the new option for submitting Norovirus data.

Begin a new Norovirus submission or see how to get started submitting other data to GenBank.

GenBank accepts a wide range of data to support scientific discovery and analysis on sequences from all branches of life.

Virus Hunting Data Science Hackathon next week in San Diego


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


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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5 NCBI articles in 2018 Nucleic Acids Research database issue


The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

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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.

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NCBI’s Virus Variation Resource Enhancements Include Standardized Search Criteria


NCBI’s Virus Variation resource makes it easy to find genome and protein sequences for a number of viruses – no more stumbling through multiple synonyms to find what you need. Now you can search using standardized biological criteria and intuitive pull-down menus.

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