Tag: EDirect

Download Assembled Genome Data Programmatically with NCBI Datasets

As previously announced, NCBI’s Assembly and Genome record pages will be redirected to new NCBI Datasets pages in June 2023. The NCBI Datasets Command Line Interface (CLI) tools provide easy, straightforward programmatic downloads of assembled genome sequence data. We invite you to check them out and let us know what you think!

Features & Benefits of NCBI Datasets

Get assembled genome sequence, annotation, and metadata, including transcripts and proteins, in one easy step.
Querying is easy and flexible! Retrieve data using organism name, assembly accession, or BioProject accession.
Request data for multiple assemblies in one request – it is now simpler and faster to download large amounts of data.
Metadata is derived from multiple databases and metadata schemas are documented.

Continue reading “Download Assembled Genome Data Programmatically with NCBI Datasets” →

A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists

Exciting update! We recently collaborated with the African Society for Bioinformatics and Computational Biology (ASBCB) for their spring OMICS Codeathon, and it was a great success. ASBCB is a professional association dedicated to the advancement of bioinformatics and computational biology in Africa. Codeathons are events focused on technology and software development, where participants work collaboratively to solve problems.

The ASBCB codeathon program serves as a grassroots training initiative for expanding expertise among African life scientists. It aims to equip participants with valuable skills and knowledge in life science and biotechnology by using research projects, public datasets, and peer-to-peer learning. Continue reading “A Successful Codeathon! Collaborating to Expand Expertise in African Life Scientists” →

New NCBI Summer Virtual Workshop Series!

Apply to attend interactive, hands-on workshops

Calling all biology students and educators! Want to learn more about NCBI resources and how to use our high-quality data and cutting-edge tools for your research projects or curricula?

We are excited to announce our upcoming virtual workshop series for Summer 2023. Our interactive, hands-on workshops are taught by experienced NCBI Education faculty. Events are free to attend, and applications are open to the public; however, each workshop will accept a limited number of participants to facilitate the best possible educational experience. Continue reading “New NCBI Summer Virtual Workshop Series!” →

Visit NCBI at the ASCB | EMBO meeting in San Diego, December 9-11, 2018

Going to the ASCB | EMBO meeting? Stop by the NCBI booth (#327) to learn about all that NCBI has to offer, ask questions, and provide feedback on how we can better meet your needs for research and teaching.

Booth #327, Exhibit Hall:

Sunday, December 9, 9:30 AM – 4:00 PM
Monday, December 10, 9:30 AM – 4:00 PM
Tuesday, December 11, 9:30 AM – 4:00 PM

Visit the booth anytime during exhibit hours to discuss any topic or just to say hello. We’re also offering specific times at the booth for focused conversations about using specific sets of NCBI resources in your research and teaching.

Discussion Sessions:

Sunday

12:30 PM NCBI BLAST in research and teaching

Monday

12:30 PM Jupyter notebooks to teach scripting and NCBI resources

Tuesday

12:30 PM EDirect for command-line access to NCBI databases
2:00 PM Jupyter notebooks to teach scripting and NCBI resources

To stay up-to-date about NCBI at ASCB or in general, follow us on Twitter at @NCBI ‏.

July 11 NCBI Minute: Five Teaching Examples with NCBI APIs

Next Wednesday, July 11, 2018, NCBI staff will show you a set of simple exercises that use EDirect to explore aspects of a human gene. You can easily incorporate these examples into your undergraduate biology courses.

Date and time: Wed, July 11, 2018 12:00 PM – 12:30 PM EDT

Continue reading “July 11 NCBI Minute: Five Teaching Examples with NCBI APIs” →

June 20 NCBI Minute: Getting the Genomic Context for BLAST Protein Matches

Do you ever want to see the flanking genes of a protein match from a BLAST search? On June 20th, we’ll show you how to see the genomic context of bacterial proteins using the identical protein report and the graphical sequence viewer. You will also learn to use these reports in detail and how to get these genomic contexts in batch for a set of protein matches using the identical proteins report and EDirect .

Date and time: Wed, June 20, 2018 12:00 PM – 12:30 PM EDT

Click to 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.

June 13 NCBI Minute: Using EDirect to Query a Local Installation of PubMed

Next Wednesday, June 13, 2018, we’ll show you how to use EDirect to install PubMed locally and then search and retrieve records from the local instance. You will also see an analysis example that shows the significant speed improvement with the Local Cache and employs some advanced EDirect xtract options to aid with processing records.

Date and time: Wed, June 13, 2018 12:00 PM – 12:30 PM EDT

Click to register.

April 11 webinar: Getting the most out of web BLAST tabular format

Next Wednesday, April 11, 2018, at 12:00PM EDT, we will present a webinar that will help you enhance and expand your tabular saved BLAST results with basic Unix tools and the NCBI EDirect suite of programs. You will see how to add useful information to tabular format results like taxonomy, sequence titles, and links to sequence records and publications.

The NCBI web BLAST service has many useful download formats, including the traditional pairwise output, tabular formats and highly structured formats. These formats allow you to easily save your BLAST results for later processing, editing and annotating.

EDirect for PubMed starts March 5

Beginning Monday, March 5, 2018, the National Library of Medicine (NLM) will present EDirect for PubMed, part of the Insider’s Guide to Accessing NLM Data.

This newly expanded series of interactive workshops will introduce new users to the basics of using EDirect to access exactly the PubMed data you need, in the format you need. Over the course of five 90-minute sessions (plus an optional “office hours”), students will learn how to use EDirect commands to access PubMed, design custom output formats, create basic data pipelines to get data quickly and efficiently, and develop simple strategies for solving real-world PubMed data-gathering challenges. EDirect requires access to a Unix environment but we will send easy installation instructions for Windows and Mac computers before the class starts. No prior Unix knowledge is required; novice users are welcome! Continue reading “EDirect for PubMed starts March 5” →

February 14th NCBI Minute: How to quickly retrieve a sequence from NCBI

On Wednesday, February 14, 2018, NCBI will present a webinar that will show you how to quickly retrieve sequences in any format from NCBI.

Date & time: Wed, Feb 14, 2018 12:00 PM – 12:30 PM EST

Ever need to quickly grab a protein or nucleotide sequence in FASTA or another format from NCBI? This NCBI Minute will show you how to accomplish this using the nucleotide and protein web pages, an NCBI URL, and – the most flexible way – through the commandline EDirect client that accesses the E-Utilities API.