We’ll be exhibiting next week at the 2019 Experimental Biology conference in Orlando. Stop by the NCBI booth (#446) (April 7-9, 9 AM – 4 PM) to meet NCBI staff, to see live demonstrations of NCBI molecular and literature databases and tools, ask questions and provide feedback. We’ll also be showcasing important updates to BLAST, PubChem, and PubMed!
Attention all aspirational computational virologists and cloud-curious bioinformaticians! NCBI is hosting a free workshop in New Orleans, Louisiana April 23 and 24.
Choose your own adventure: participants may bring their own data and/or work with public data housed at NCBI.
Day 1 will consist of a short cloud-onboarding session, introduction to Jupyter notebooks, SRA and BLAST intros, and more! On day 2, we’ll roll our sleeves up in a working session around phylogenetic clustering of sequences where we’ll look for unknown viruses.
BYOD (bring your own data) and apply today! Please fill out the application form in its entirety by Tuesday, April 9th.
Attendee insights will be made publicly available on GitHub.
- The 2.9.0 programs handle the new four character identifiers for chains of 3D structure records from RCSB Protein Data Bank (PDB). The previous version of the BLAST databases and programs do not support these identifiers. See the MMDB News for additional details about the PDB change and the impact on NCBI Structure resources.
- Another important improvement in 2.9.0 is the ability to configure the output separator for tabular and CSV output formats. See the BLAST Manual for details.
More improvements and a few bug fixes with this release are detailed in the release notes.
For more information on new database version, BLASTDBv5 (download), see the previous NCBI Insights article and the recording of our webinar. We will continue to update the BLAST databases in their current version (BLASTDBv4) until September 2019.
NCBI is excited to host our first Women-led Hackathon, a collaborative biodata science event organized by women on the NIH Campus in Bethesda, Maryland!
NIH has a strong interest in enhancing the diversity of the scientific workforce, and women in particular are underrepresented in data science. This women-led NCBI initiative strongly encourages researchers, especially women, at any stage of their data science journey to apply for this inaugural event. Past hackathon participants have ranged from students and postdocs with a working knowledge of scripting (e.g. Shell, Python, R) to those already engaged in the use of large datasets or in the development of informatics tools, code, or pipelines.
Potential topics include:
- An open store for variant and gene prioritization tools
- Variable Tracking and Schema Capturing to make Biomedical Research Data ‘FAIR’
- Molecular language: discovery of cell-to-cell communication molecules from RNA-Seq data
- dsVirus variant discovery and annotation pipeline
- Design of ICD-9 to 10 conversion function for the R package ‘icd’
- Hiding in plain sight — unannotated structural variants in public genomic data sets
We’ve been making improvements to the NCBI genome Assembly resource. Highlights include:
- Links added between members of a pair of genome assemblies derived from the same diploid individual
- Additional filters now shown on the left-hand side bar
- Annotation status
- Assembly type, including the new types “Unresolved diploid” and “Alternate pseudohaplotype”
- vhost filters on the Advanced page Search Builder that allow selection of virus assemblies with a particular host (e.g. “vhost human”)
- Searching by assembly names with the version unspecified
- Total ungapped length reported in the “Global statistics” table, replacing the less useful total gap length
- Improved N50 & L50 statistics presentation for complex genome assemblies
Introduction to NGS Analysis in a Cloud Environment for Novice Bioinformaticians:
We are pleased to announce a free workshop in New Orleans, Louisiana April 23 and 24. After a short cloud-onboarding session, early career computational virologists interested in extracting sequences from metagenomic samples will be exposed to new, community-generated tools!
In about a week, NCBI staff will join GeneReviews® on their home turf, Seattle, at the Annual Clinical Genetics Meeting hosted by the American College of Medical Genetics and Genomics (ACMG). While there we will have an exhibit booth (#531) where you can meet our staff, get answers to your questions, and pick-up informative handouts on our various resources for clinical practice.
Also, be sure to visit our two posters on Friday, April 5 from 10:30 AM to 12 PM.
The National Library of Medicine (NLM) seeks a Scientific Director with creative vision and strong leadership to guide its Intramural Research Program. One of the 27 Institutes and Centers (ICs) of the National Institutes of Health (NIH), NLM is a leader in computational health sciences research and the world’s largest biomedical library. The successful candidate will oversee a diverse group of some 150 scientific personnel, developing innovative new approaches to data science, biomedical informatics, and computational biology and their application to open questions in basic molecular biology, genomics, health, and healthcare.
NCBI will be updating the human genome RefSeq annotation more frequently to incorporate improvements made to genes and transcripts by RefSeq curation experts. Faster updates will allow us to include the latest datasets.
In the past, we’ve produced a full re-annotation of the human genome about once a year. The last full annotation, Homo sapiens Annotation Release 109, was in March 2018. A full annotation is produced by two main processes:
NCBI is on the West Coast this week (March 25 – 27) for “Pangenomics in the Cloud,” a three-day hackathon hosted by the University of California, Santa Cruz.
Graphs are the name of the game here! The teams will be building graphs, managing coordinates between samples and defining and identifying and marking haplotypes, and looking at population specific variants.
Please follow along on our GitHub, fork and make pull requests during and after the event, and stay tuned for updates on the findings.