NCBI to hold Developers' Forum September 28th
On Wednesday, September 28th, at 3 PM EDT, NCBI will hold a developers' forum for those who use large amounts of NCBI data. The forum will help us provide you with better access to NCBI data. (Source: NCBI Announcements)
Source: NCBI Announcements - September 23, 2016 Category: Databases & Libraries Source Type: news
October 4-6: Stream the University of Michigan NCBI workshops
On October 4th, 5th, and 6th, the University of Michigan ’s Taubman Health Sciences Library will host a series of NCBI workshops that can also be streamed remotely. The workshops are: Navigating NCBI’s Molecular Data Using the Integrated Entrez System and BLAST, A Practical Guide to NCBI BLAST and EDirect: Command Line Access to NCBI’s Biomolecular Databases. Please see the Taubman Health Sciences Library Remote Site Registration Page for details. (Source: NCBI Announcements)
Source: NCBI Announcements - September 22, 2016 Category: Databases & Libraries Source Type: news
Introducing Magic-BLAST
Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Magic-BLAST executables for LINUX, MacOSX, and Windows as well as the source files are available on the FTP site. (Source: NCBI Announcements)
Source: NCBI Announcements - September 22, 2016 Category: Databases & Libraries Source Type: news
Scheduled: Next Round of HTTPS Tests
We have scheduled another round of HTTPS tests, following up from the initial tests performed on September 15. More information can be found on an NCBI Insights Blog post. (Source: NCBI Announcements)
Source: NCBI Announcements - September 21, 2016 Category: Databases & Libraries Source Type: news
NCBI's Bryant and Bolton receive 2016 Herman Skolnik Award for PubChem database
On August 23, Drs. Stephen Bryant and Evan Bolton received the American Chemical Society (ACS) 2016 Herman Skolnik Award for their work in developing, maintaining, and expanding the National Center for Biotechnology Information's PubChem database of chemical substances and their biological activities. The award was presented at the ACS 252nd National Meeting& Exposition in Philadelphia. (Source: NCBI Announcements)
Source: NCBI Announcements - September 19, 2016 Category: Databases & Libraries Source Type: news
September 21st webinar: Update on NCBI's Transition to HTTPS
Next Wednesday, September 21st, NCBI staff will discuss plans regarding the move to HTTPS-only services. This past week, we conducted the first of a series of HTTPS tests; in this webinar, we will talk about this and future tests that will help all of us prepare for this change. We will also briefly discuss circumstances surrounding proxy services and software dependent upon NCBI software, such as the SRA and C++ toolkits. (Source: NCBI Announcements)
Source: NCBI Announcements - September 19, 2016 Category: Databases & Libraries Source Type: news
New video on YouTube: Tree Viewer - Display Large Trees
The newest video on the NCBI YouTube channel, Tree Viewer: Display Large Trees, demonstrates a new functionality in Tree Viewer - the ability to display much larger trees. (Source: NCBI Announcements)
Source: NCBI Announcements - September 16, 2016 Category: Databases & Libraries Source Type: news
Genomes FTP site update (version 1.3) adds new data formats and more
NCBI has released a comprehensive update of all current genome assemblies in the Genomes FTP site, affecting data reported in the /genomes/genbank/, /genomes/refseq/ and /genomes/all/ FTP directories. This update adds nucleotide FASTA sequences of CDS and RNA features computed from the genome sequence, expands the scope of the /genbank/ data to include metagenomes, and more. The FTP content of nearly all "latest" GenBank and RefSeq assemblies was updated to reflect these changes between 5/11/2016 and 6/24/2016. (Source: NCBI Announcements)
Source: NCBI Announcements - September 14, 2016 Category: Databases & Libraries Source Type: news
RefSeq release 78 is now available
RefSeq release 78 is accessible online, via FTP and through NCBI's programming utilities. This full release incorporates genomic, transcript, and protein data available as of September 6, 2016 and contains 107,045,797 records, including 70,427,238 proteins, 16,172,490 RNAs, and sequences from 62,739 organisms. The release is provided in several directories as a complete dataset and also as divided by logical groupings. (Source: NCBI Announcements)
Source: NCBI Announcements - September 12, 2016 Category: Databases & Libraries Source Type: news
New on NCBI Insights: The Future of Existing GI Numbers at NCBI
The latest blog post on NCBI Insights discusses what will happen to existing GI numbers in records now that NCBI is phasing out Sequence GIs. (Source: NCBI Announcements)
Source: NCBI Announcements - September 12, 2016 Category: Databases & Libraries Source Type: news
Leiden Open Variation Database to be retired September 30, 2016
NCBI is retiring the Leiden Open Variation Database (LOVD) on September 30, 2016. LOVD has been used to capture information about novel human variants. We encourage past submitters of human genetic variations to LOVD to transfer their information to the ClinVar database. (Source: NCBI Announcements)
Source: NCBI Announcements - September 8, 2016 Category: Databases & Libraries Source Type: news
New on NCBI Insights: Find, Browse and Follow Biomedical Literature with PubMed Journals
The latest blog post on NCBI Insights presents the new PubMed Journals, the latest experiment from PubMed Labs. PubMed Journals allows you to easily find and browse journals of interest, browse new articles, and more. Learn more about PubMed Journals, try it out, and leave us feedback on the blog post. (Source: NCBI Announcements)
Source: NCBI Announcements - September 7, 2016 Category: Databases & Libraries Source Type: news
September 7th webinar: The E-Utilities in an Age without GI Numbers
Next Wednesday, September 7th, NCBI will present a webinar that briefly describes NCBI ’s future plans for the E-utilities API in a time where GI numbers are no longer used as the primary identifiers for sequence records. You will learn how to convert GI numbers to accession.version identifiers and how to quickly determine the most recent version of an accession. You'll also learn a bout a new E-utility parameter (to be released this fall) that allows these tools to work only with accession.version identifiers. (Source: NCBI Announcements)
Source: NCBI Announcements - September 2, 2016 Category: Databases & Libraries Source Type: news
October 24-26: Hackathon at Cold Spring Harbor Laboratory
From October 24th to 26th, Cold Spring Harbor Laboratory (CSHL), with assistance from NCBI, will host a biomedical data science hackathon immediately before the Biological Data Science Conference at CSHL. The hackathon will primarily focus on writing functional software for advanced bioinformatics analysis of next generation sequencing data and metadata, but also may include analysis of other types of data, such as images or other molecular measurements. (Source: NCBI Announcements)
Source: NCBI Announcements - September 1, 2016 Category: Databases & Libraries Source Type: news
Genomes FTP site data organization to change on September 20, 2016
NCBI is moving the contents of the "all" and "ASSEMBLY_REPORTS/All" directories on the Genomes FTP site. Currently, listing the contents of these two directories is impractical because they contain many thousands of directories or files. (Source: NCBI Announcements)
Source: NCBI Announcements - August 31, 2016 Category: Databases & Libraries Source Type: news
