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


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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November 13 NCBI Minute: Resources for next-gen sequence analysis


On Wednesday, November 13, 2019 at 12 PM, NCBI staff will present a webinar on NCBI resources for next-gen sequence analysis.  You will learn about key  resources that support multiple aspects of next-gen sequence analyses, including quality control, alignment, data visualization and interpreting results. You will also see how to access and apply these resources for both SRA and your own RNASeq/DNASeq datasets. Whether you’re embarking on your first analysis or already have a background in bioinformatics, you’ll find tools that meet your needs!

  • Date and time: Wed, Nov 13, 2019 12:00 PM – 12:45 PM EDT
  • Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

NCBI at ASHG 2019: Two Data CoLabs Demonstrate How to Analyze NextGen Sequence Data and Access Genetic Variation Population Data


NCBI will be attending the American Society of Human Genetics (ASHG) 2019 in Houston Texas on Oct 15-19.

This year, we will be presenting two CoLabs – interactive sessions where you can learn about new NCBI tools and resources. Read on below for a description of each CoLab and join us at ASHG next week!

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


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

Florida (USF) Biological Data Science “IronHack” February 25-27, 2019


From February 25-27, 2019, NCBI will help with a Data Science hackathon at USF in Tampa Florida!

The hackathon will focus on the genomics of Iron-linked Rare Diseases as well as large scale RNA-Seq indexing and analysis. This event is for researchers, including students and postdocs, who have already engaged in the use of large datasets or in the development of pipelines for 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 Tampa.

Working groups of five to six individuals will be formed into five to eight teams. These teams will build or expand on pipelines and tools to analyze large datasets within a cloud infrastructure. Example subjects for such hackathons include:

  • Integrative pipelines to analyze large scale RNA-Seq experiments
  • Visualization tools for mapping phenotypes to genotypes
  • Rapid clinical diagnostics tools
  • Structural variant mining with single molecule sequencing data

Please see the application form for more details and additional projects.  The project list will continue to evolve and will be updated on the application form.

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NCBI to assist in Southern California genomics hackathon in January


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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August 23 NCBI Minute: Using the Run Selector to Find Relevant Next-Generation Sequencing (NGS) Datasets


Do you have trouble searching the NCBI webpage for relevant datasets? Wish you could filter the search results more precisely? You can with SRA Run Selector.

In this NCBI Minute, you’ll learn how to filter the SRA database using the metadata details captured for each submitted dataset. This is easily done in a spreadsheet format that displays all recorded metadata for each SRA Run. The user-friendly interface allows you to selectively filter datasets down to the most relevant data for your research question and then export it in a spreadsheet.

Date and time: Wednesday, August 23, 2017 12:00 PM – 12:30 PM EDT

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.