NIH is pleased to announce a computational medicine-focused codeathon. To apply, please complete the application form by February 25, 2020. We will also be offering a free workshop, AWS Technical Essentials, the day before the codeathon. Read on for more information about the event. Continue reading
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.
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.
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
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 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
We’ve just released a new version of Magic-BLAST with several new, user-driven enhancements like:
- Nanopore sequence alignment
- Improved multithreading performance
- Support for the new BLAST database version, BLASTDBv5, that allows you to limit your search by taxonomy
- More reliable placements of reads
The new executables are available on the NCBI FTP site.
Magic-BLAST aligns next generation DNA- and RNA-Seq sequencing reads. Read more about the latest version of Magic-BLAST in the release notes.
The NCBI will participate in a one-day conference on June 18, 2019 and a hackathon, June 19-21, 2019 as a part of Rocky Mountain Genomics Hackcon 2019 at the BioFrontiers Institute in Boulder Colorado.
The conference will feature technical speakers in precision medicine, metagenomics, and advanced RNA-Seq analysis, as well as an exhibitor and poster session. The hackathon will focus on creating visualization tools for exploratory data analysis.
Many people who attend these events have experience working with large datasets or the development of informatics tools, code, or pipelines; however, researchers who are in 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.
Please visit the Rocky Mountain Genomics Hackcon 2019 site for more details and information on how to attend.
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