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

Register here: https://bit.ly/2KmH1yO

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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.

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.

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.

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.

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

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.

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.

November 28th NCBI Minute: An update to “API Keys for Better E-Utilities and EDirect Access to NCBI Data”


On Tuesday, November 28, 2017, NCBI will present an update to the webinar originally presented on November 8, 2017 about the new API keys. In this updated webinar, you will learn about the relationships between API keys, NCBI accounts and IP addresses and see additional details about rates of access and server messages. You will also get answers to many important questions asked in the original webinar.

Date and time: Wednesday, November 8, 2017 12:00-12:30PM EST

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

November 8 NCBI Minute: New API keys for better E-utilities & EDirect access to NCBI data


On Wednesday, November 8, 2017, we will present a webinar on API keys for E-utilities. In this webinar, you’ll learn how to get and start using your API key with the E-utilities and the command line EDirect programs.

Date and time: Wednesday, November 8, 2017 12:00-12:30PM EST

After registering, you will receive a confirmation email with information about attending the webinar. After the live presentation, the webinar will be uploaded to the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

September 2017: NCBI to present EDirect workshop at NLM


On September 18, 2017, NCBI staff will offer a workshop on EDirect, NCBI’s suite of programs for easy command line access to literature and biomolecular records. To join the workshop, please register.

NOTE: This is an in-person workshop at the National Library of Medicine on the NIH campus in Bethesda, MD, USA. The course is limited to 22 participants.

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