December 11 Webinar: Running the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) on your own data


On Wednesday, December 11, 2019 at 12 PM, NCBI staff will present a webinar that will show you how to use NCBI’s PGAP (https://github.com/ncbi/pgap) on your own data to predict genes on bacterial and archaeal genomes using the same inputs and applications used inside NCBI. You can run PGAP your own machine, a compute farm, or in the Cloud. Plus, you can now submit genome sequences annotated by your copy of PGAP to GenBank.  Attend the webinar to learn more!

  • Date and time: Wed, Dec 11, 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.

NIH Biomedical Data Science Codeathon in Pittsburgh, Jan 8-10


NCBI is pleased to announce a Biomedical Data Science Codeathon in collaboration with Carnegie Mellon in Pittsburgh, PA on January 8-10, 2020.

We’re specifically seeking people with experience working with complex diseases, precision medicine, and genomic analyses.  If this describes you, please apply! 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 large scale genomic analyses from high-throughput experiments. The event is open to anyone selected for the codeathon and willing to travel to Pittsburgh.

Potential topics include:

  • Virus Genome Graph tools
  • Image analysis pipelines
  • RNAseq pipelines
  • Cancer graph genomes
  • Complex Disease Analysis

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Structural Variant Hackathon


NCBI is pleased to announce a Structural Variant Hackathon at the Baylor College of Medicine, Houston Texas, immediately before ASHG on October 11-13, 2019.

We’re specifically looking for folks who have experience in working with structural variants, complex disease, precision medicine, and similar genomic analysis.  If this describes you, please apply! 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 large scale genomic analyses from high-throughput experiments (please note that the event itself will focus on open access public human data).

Potential topics include:

  • Mapping structural variants to public databases
  • Calculating the heritability of different types of structural variants
  • CNV effect on isoform expression
  • Assembly accuracy for metagenomics
  • Quality assessment in large cohorts

The hackathon runs from 9 am – 6 pm each day, with the potential to extend into the evening hours each day. There will also be optional social events at the end of each day. Working groups of five to six individuals, with various backgrounds and expertise, will be formed into five to eight teams with an experienced leader. These teams will build pipelines and tools to analyze large datasets within a cloud infrastructure. Each day, we will come together to discuss progress on each of the topics, bioinformatics best practices, coding styles, etc.

There will be no registration fee associated with attending this event.

Note: Participants will need to bring their own laptop to this program. No financial support for travel, lodging, or meals is available for this event.

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New human genome annotation release with MANE Select and other improvements!


There’s a new RefSeq annotation available for the human genome, and it’s quite an update!

About the release

Annotation release 109.20190607 is the first release of our new bimonthly annotation schedule as announced in a previous post.   The annotated sequences are  the latest sequences for the GRCh38, patch 13 assembly, GRCh38.p13 (GCF_000001405.39). The chromosome backbone sequences remain the  same, but we’ve added 45 patch sequences representing novel and improved sequences that the Genome Reference Consortium will incorporate into the primary assembly in the future. The new annotation places the latest curated RefSeq transcripts and functional elements on the genome but keeps the same model dataset as in annotation release 109 except when the models have been replaced by curated RefSeqs or other review. We are also flagging MANE and other RefSeq Select transcripts.  Continue reading for more details on these improvements below. You can download the updated annotation here!

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Presentation on NCBI’s genome browser at Rocky Mountain Genomics Hackcon


On June 18, 2019, NCBI’s Sanjida Rangwala will demonstrate the rich data visualization capabilities of NCBI’s genome browser at a conference that is part of the Rocky Mountain Genomics Hackcon.  As mentioned in a previous post, NCBI staff will also participate in an NCBI-style Hackathon  as part of the larger event.  The genome browser presentation and demonstration will show you how to create visuals that provide insights and show connections among genes, transcripts, variation,  epigenomics and GWAS data from NCBI sources. You will also see  how you can upload your own data and embed NCBI viewers on your own pages.

February 6 Webinar: New Variation Services for Normalizing, Remapping, and Annotating Variants


Join us on Wednesday, February, 2019, when NCBI staff will show you how to use a new set of NCBI variation services that rely on a variant data model called SPDI (Sequence Position Deletion Insertion). These services and data model allow you to inter-convert, map and disambiguate variants in standard formats (RefSNP accessions, HGVS and VCF). Unlike many current variant notation systems, SPDI provides unambiguous, machine-readable definitions of variants. SPDI not only powers SNP build and mapping procedures at NCBI but also our variant sensors that are active in the global search and ClinVar. These services and notation system provide valuable new tools for people who work with sequence variants.additional variant information.

Date and time: Wed, Feb 6, 2019 12:00 PM – 12:30 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.

Apply now to join the Seattle Biological Data Science FHackathon February 4-6, 2019


From February 4-6, 2019, the NCBI will help with a data science hackathon at the Fred Hutchinson Cancer Research Center in Seattle. To apply, complete this form (approximately 10 minutes to complete). Initial applications are due Friday, January 11th by 11 pm ET.

The hackathon will focus on genomics as well as general data science. 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.

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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.