Tag: Bioinformatics

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

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

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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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 event is open to anyone selected for the hackathon and willing to travel to Bethesda, Maryland.

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Bioinformatics paper uses NCBI open data to analyze drug response

A study (PMID: 28158543) published in the July 2017 issue of Bioinformatics collects, classifies and analyzes single nucleotide variants (SNVs) that may affect response to currently approved drugs. They identified 2,640 SNVs of interest, most of which occur rarely in populations (minor allele frequency <0.01).

The researchers used protein sequence alignment tools and mined open data from multiple information resources accessed through E-utilities including PubChem Compound (Kim et al., 2016 PMID: 26400175), NCBI Gene (Maglott D, et al., 2014. PMID: 25355515), NCBI Protein (Sayers, 2013), MMDB (Madej et al., 2012 PMID: 22135289), PDB (Berman et al., 2000 PMID: 10592235), dbSNP (Sherry et al., 2001 PMID: 11125122), and ClinVar (Landrum et al., 2016 PMID: 26582918).

Questions, comments, and other feedback may be sent to Yanli Wang.

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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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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November 15 NCBI Minute: Advanced Use of NCBI APIs for High-Throughput Analysis of Genomic Data and Metadata

On Wednesday, November 15, 2017, at 12:00 PM EST, NCBI will present a webinar on advanced applications of the NCBI APIs we previously introduced in our general API webinar in September. This webinar is intended for bioinformaticians, computational biologists and others who are already comfortable with writing scripts to access, download and analyze data.

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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.

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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.

Pittsburgh Genomics Hackathon assisted by NCBI September 25 – 27, 2017

From September 25-27,2017, NCBI will help with a bioinformatics hackathon at the University of Pittsburgh. 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 are 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 non-scientific developers, mathematicians and librarians.

The event is open to anyone selected for the hackathon and willing to travel to the University of Pittsburgh (see below for venue address).

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