Tag: Data science

NLM announces rescheduled Curation at Scale Workshop

Data curation plays a critical role in today’s biomedical research and ensures scientific data will be accessible for future research and reuse. In the time of pandemics, the need to get scientific information to researchers, medical personnel, and the public as quickly as possible is greater than ever before. In response to the need for increased curation speed, scale, and reliability, computer automation/assistance is becoming increasingly desirable.

The National Library of Medicine (NLM) is pleased to announce a rescheduled three-day Curation at Scale (Virtual) Workshop, to be held on March 28-30, 2022.

Poster abstract submission, deadline: March 7, 2022
Registration, deadline: March 21, 2022

The NLM workshop will feature invited speakers, bring together biocurators, developers of automated curation methods, and other stakeholders, and will offer an opportunity to learn more about the current status of biomedical data curation, to share your research and your challenges, and to discuss the implementation of advanced computational techniques in scientific data curation. We invite participants from academia, government, publishers, and industry interested in the methods and tools employed in curation of biomedical data to register and attend this exciting workshop. Participants are encouraged to submit an abstract for consideration for poster presentation.

Find SRA datasets in the cloud using BigQuery Taxonomy Analysis tables!

Now that the Sequence Read Archive (SRA) is publicly available on the cloud, you can harness the power of high-performance cloud computing to analyze all the data you wish without having to download a single byte. To help you programmatically find datasets of interest to you, we’ve loaded BigQuery with the SRA Metadata Table, which contains the descriptive information supplied at the time of sequence submission. Searches of the SRA Metadata Table are dependent on the quality and consistency of the metadata as submitted which means it can sometimes be a challenge to identify a complete and relevant set of suitable sequences. However, the Taxonomy Analysis Table can be a useful tool to overcome this challenge. Here’s why.

NCBI indexes SRA runs with one or more taxonomy terms when species-specific sequence k-mers are matched in the submitted sequences. The Taxonomy Analysis Table (tax_analysis) thus becomes a catalog of all taxonomic IDs detected in every run, based on the specificity and accuracy characteristics of these unique hashes sampled from reference genomes. We have now added the Taxonomy Analysis Table to BigQuery so you can filter hundreds of thousands of runs by this calculated taxonomic content to gather target datasets. Use this in conjunction with the BigQuery Taxonomy Table (which connects scientific names to taxonomic IDs) and link back to the BigQuery Metadata Table.

Explore/link to these four new tables in BigQuery:

tax_analysis_info: a summary table for the results of the STAT tool
tax_analysis: use the taxonomy analysis table to locate any number of runs based on kmer hits to a particular organism or branch in a taxonomic tree.
taxonomy: NCBI Taxonomy database where you can locate the taxid based on organism names.
kmer: contains kmers mapped to a particular organism and allows you to continue exploring organismal content further. You can leverage kmer tables in your downstream analysis by building custom kmer libraries.

Big_Query_example
Figure 1. SRA runs found using the taxonomy tables and BigQuery for taxid:694002, Betacoronavirus.

Check out our helpful summary information for additional information on taxonomic analysis.

We are actively working on new tools and ways to help you use the cloud to access and compute on SRA data. We are piloting this new feature in BigQuery, and plan to add this information to Amazon Cloud’s (AWS) Athena soon.

If you need help getting started, refer to our  tutorials  and  how-to video playlist  on YouTube!

NLM announces Curation at Scale Workshop

Data curation plays a critical role in today’s biomedical research and ensures scientific data will be accessible for future research and reuse. To improve the speed and scope of manual curation, computer automation/assistance is becoming increasingly desired.

The National Library of Medicine (NLM) is pleased to announce a two-day Curation at Scale Workshop, to be held on April 27-28, 2020 on the National Institutes of Health (NIH) campus in Bethesda, Maryland, USA. The NLM workshop featuring invited speakers will bring together biocurators, developers of automated curation methods, and other stakeholders, and will offer an opportunity to learn more about the current status of biomedical data curation, to share your research and your challenges, and to discuss the implementation of advanced computational techniques in scientific data curation. We invite participants from academia, government, publishers, and industry interested in the methods and tools employed in curation of biomedical data to attend this exciting workshop. Participants are encouraged to submit an abstract for consideration for poster presentation.

Poster abstract submission deadline: March 6, 2020

Registration deadline: April 17, 2020

WEBSITE: https://www.nlm.nih.gov/curationworkshop2020/index.html

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.

Continue reading “Request for proposals: Single Cell in the Cloud codeathon at NYGC in January” →

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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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.

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.

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

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.

Continue reading “Apply now to join the Seattle Biological Data Science FHackathon February 4-6, 2019” →

NYGC NCBI-style bioinformatics hackathon August 6-8, 2018

From August 6-8, 2018, the NCBI will help with a data science hackathon at the New York Genome Center in Manhattan. 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.

Continue reading “NYGC NCBI-style bioinformatics hackathon August 6-8, 2018” →