Tag: Codeathon

NIH Data Science Collaborative Hackathon April 16 – 18, 2018

NIH Data Science Collaborative Hackathon April 16 – 18, 2018

The NCBI will assist with a data science hackathon to take place on the NIH Campus in Bethesda, Maryland, from April 16-18, 2018.

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 Bethesda, Maryland.

Continue reading “NIH Data Science Collaborative Hackathon April 16 – 18, 2018”

NCBI-UCSC Genomics Hackathon April 2-4, 2018

NCBI-UCSC Genomics Hackathon April 2-4, 2018

From April 2 -4, 2018, the NCBI will help with a bioinformatics hackathon in Northern California hosted by the University of California, Santa Cruz (UCSC)!  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 UCSC.

Working groups of five to six individuals will be formed into five to eight teams.  These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure.  Potential subjects for this iteration include:

  • Developing a framework for nesting containerized bioinformatics workflows in cloud infrastructure.
  • Extending the GA4GH API to map fastq files
  • Machine learning pipelines for germline rare variants linked to phenotypes
  • A simple, open-source mapper for nanopore data
  • An automated pipeline for named entity recognition from biomedical literature

Please see the application form for more details and additional projects. Continue reading “NCBI-UCSC Genomics Hackathon April 2-4, 2018”

North Carolina Research Triangle Hackathon March 12-14, 2018

North Carolina Research Triangle Hackathon March 12-14, 2018

The UNC Curriculum in Bioinformatics and Computational Biology and NCBI will host a data science hackathon from March 12-14, 2018 on the campus of the University of North Carolina at Chapel Hill. Projects addressed during the hackathon will involve general bioinformatics and genomic analyses in addition to text, image, and sequence processing.

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 may involve other non-scientific developers, mathematicians, or librarians.

To be considered for the event, you must apply and be able to travel to the UNC campus in Chapel Hill (see details below).  Applications are due Monday, February 12th, 2017 by 11:59 pm ET.

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Feb 7 webinar “How to Run an NCBI-style Hackathon at Your Institution”

Feb 7 webinar “How to Run an NCBI-style Hackathon at Your Institution”

On Wednesday, February 7, 2018, NCBI will present a webinar that will show you how to plan and run an NCBI-style hackathon at your own institution.

Date & time: Wed, Feb 7, 2018 12:00 PM – 1:00 PM EST

Register here: http://bit.ly/2zYU7Kp

NCBI organizes 2-3-day hackathons at sites throughout the United States. In these events, participants work in small collaborative groups on workflows, scripts or applications to create bioinformatic solutions to problems in fields such as text mining, next-gen sequence analysis, medical informatics, and many others. Code from Hackathon projects is available on the public NCBI Hackathon GitHub site.

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.

NIH Data Hackathon on campus – January 22-24, 2018

NIH Data Hackathon on campus – January 22-24, 2018

From January 22-24, 2018, the NCBI will help with a data science hackathon on the NIH campus in Bethesda, MD. The hackathon will focus on general data science analyses, including text, image and sequence processing. 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 the NIH campus (see below).  Applications are due Friday, December 22nd, 2017 by 9 pm EST.

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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.

Continue reading “Summer 2017 NCBI Hackathon Products”

NCBI to assist in Southern California genomics hackathon in January

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).

Continue reading “NCBI to assist in Southern California genomics hackathon in January”

Two new videos on YouTube: SRA RunSelector & NCBI Hackathons

Two new videos on YouTube: SRA RunSelector & NCBI Hackathons

We’ve uploaded recordings from two recent NCBI Minute webinars on the NCBI YouTube channel.

The first, “Using the SRA RunSelector to Find NGS Datasets”, shows you how to filter the SRA database using metadata details from submitted datasets.

 

Continue reading “Two new videos on YouTube: SRA RunSelector & NCBI Hackathons”

August 30 NCBI Minute: NCBI Hackathons, a framework for rapid prototyping of pipelines for bioinformatics, biomedical informatics and genomics

August 30 NCBI Minute: NCBI Hackathons, a framework for rapid prototyping of pipelines for bioinformatics, biomedical informatics and genomics

NCBI regularly organizes hackathons throughout the United States, where participants work in teams to apply their data science experience with public datasets. In this NCBI Minute, you will hear highlights from recent hackathons, see examples of the software created in these events, and learn how you can participate in future hackathons.

Date and time: Wednesday, August 30, 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.