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Archive for the ‘NCBI Databases’ Category

What I’m Reading

Wednesday, July 16th, 2014

Man with laptop drinking coffee in a cafe

It can be such a challenge to keep up with the literature, blogs, books, and other sources that help you to stay updated in your field. Here’s a short list of what I’ve been reading lately that you might also be interested in.

  • The Accidental Instructional Designer: Learning Design for the Digital Age, by Cammy Bean. I attended a presentation by Ms. Bean at the American Society for Training & Development TechKnowledge conference in January. (You can read a post about her presentation here). Her new book has great tips for both the novice and experienced designer of instruction, with a focus on e-learning. You can read a chapter of the book for free here.
  • Database Resources of the National Center for Biotechnology Information . This 2014 article by the NCBI Resource Coordinators provides updates on the suite of NCBI resources as well as a bit of background on the resources.
  • Fatal Victorian Fashion and the Allure of the Poison Garment,” by Allison Meier on the Hyperallergic blog. Interesting read on the dangers of style for both the wearers and the makers. And you can learn more about the toxicity of substances mentioned in the new TOXNET interface.
  • Getting Started with File Naming Conventions,” by Jake Carlson on the e-Science Community Blog. Very useful advice for someone like me who has been guilty of using “final” in a file name.

What interesting things are you reading lately? Let me know on Twitter @nnlmntc or Facebook!

Save the Dates: 2015 “A Librarian’s Guide to NCBI” Course

Thursday, July 10th, 2014
“This course was a great idea and very well executed! I learned a lot and am much more confident going back to my institution and teaching these resources as well as starting an information service. It’ll take time to become proficient but this was a great start!”
“The singularly most useful and interesting class I’ve taken in years.”
               — Comments from recent class participants

Attention health science librarians in the United States who wish to initiate and/or extend bioinformatics services at your institution! The National Center for Biotechnology Information (NCBI) and the NLM Training Center (NTC) will be offering “A Librarian’s Guide to NCBI” course in 2015. Participants who complete the class will be eligible for Medical Library Association (MLA) Continuing Education credits. The course is free, but travel costs are at the expense of the participant.

There are two parts to the course, and applicants must take both parts:

  • Part 1: “Fundamentals in Bioinformatics and Searching” is a six-week, online (asynchronous) pre-course.
  • Part 2: A five-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland.

Important Dates:
Monday, September 29, 2014 – Watch for a detailed announcement about the course and application process here in the NLM Technical Bulletin.
Monday, November 17, 2014 – Application deadline
Monday, December 15, 2014 – Acceptance notifications e-mailed
Monday, January 12, 2015 – “Fundamentals in Bioinformatics and Searching” pre-course begins
Monday, March 9, 2015 – “A Librarian’s Guide to NCBI” five-day in-person class begins at NLM

Mark your calendars for this training opportunity.

Questions?  E-mail ntc@utah.edu.

NCBI turns 25!

Wednesday, November 6th, 2013

On November 4, 1988 Congress established the National Center for Biotechnology Information (NCBI) to develop new information technologies to aid in the understanding of the molecular processes that control health and disease. Since then, the number of tools and databases at NCBI has grown enormously. It can be difficult to keep track of which database does what, so NCBI provides a handy overview of selected NCBI databases. You can download the printable factsheet with short descriptions of each resource or database.

If you’d like to learn more about NCBI resources, check out their Educational Resources page and YouTube videos.  They have a wealth of resources, but you don’t have to learn them all at once! Maybe you’d like to challenge yourself to take 30 minutes a week to discover and explore one of their resources. You can learn a lot in just a few minutes. For example, the short video below describes how to locate all of the genetic sequences of an organism.

PubChem Blog

Friday, September 6th, 2013

What is PubChem?

PubChem is a free chemical database and an open archive of the biological activities of millions of substances. PubChem is a part of the National Center for Biotechnology Information (NCBI), a division of the U.S. National Library of Medicine. PubChem provides information on the biological activities of small molecules. PubChem is organized as three linked databases within the NCBI’s Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool.

Links from PubChem’s chemical structure records to other Entrez databases provide information on biological properties. These include links to PubMed scientific literature and NCBI’s protein 3D structure resource. Links to PubChem’s bioassay database present the results of biological screening.

PubChem recently started a blog, as well as accounts on Twitter, FaceBook, and Google+ to post information about new PubChem features and data updates.

Blog link: http://pubchemblog.ncbi.nlm.nih.gov/

Librarian’s Guide to NCBI Presentations

Wednesday, July 10th, 2013

Participants from the “Librarian’s Guide to NCBI” hybrid class taught in April 2013 recently gave presentations about their experience in the class for the Pacific Southwest Region (PSR) and MidContinental Region (MCR).  “Librarian’s Guide to NCBI” consisted of a 3-week online asynchronous class called “Fundamentals of Bioinformatics and Searching” followed by a five-day in-person workshop in Bethesda, MD.

Both presentations were recorded:

Pacific Southwest Region “Mid-Day at the Oasis,” June 19, 2013

MidContinental Region, May 21, 2013

Now Available: NCBI Insights Blog!

Monday, January 28th, 2013

NCBI has just released a new blog called NCBI Insights at ncbiinsights.ncbi.nlm.nih.gov. We created NCBI Insights to provide an insider’s perspective to help you better understand us and our resources, explore issues of scientific interest that drive our resource development, and demonstrate how you can use our resources to help enhance your research.

We will post articles in four categories:

* NCBI Explained – provides an insider’s perspective on our resources and policies to help you better understand us and avoid some common misconceptions and misunderstandings.
* What’s New – introduces our new and updated resources and include specific examples that demonstrate how you can use these to enhance your research.
* Quick Tips & Tricks – explain hows to perform specific tasks using our website. Selected topics will be chosen based on questions you have asked and suggestions you have provided.
* Science Features – explores current topics in science and demonstrate how you can find relevant data or resources on our website for further exploration.

This blog is a complement to our existing education and outreach efforts, such as News and Social Media publicity, Webinar and Workshop training programs, and Help Desk user support.

Be sure to check in to the NCBI Insights Blog every week or so and let us know what you think!

Send in Your Application to Participate in a New Bioinformatics Training Course: “A Librarian’s Guide to NCBI”

Thursday, December 13th, 2012

In sponsored partnership, the National Center for Biotechnology Information (NCBI) and the National Network of Libraries of Medicine (NN/LM) National Library of Medicine Training Center (NTC), are pleased to invite participation of health sciences librarians in a new bioinformatics training course: “A Librarian’s Guide to NCBI.” Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo.

The course provides basic knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Attending this course will improve your ability to initiate bioinformatics services at your institution and/or extend current initiatives. Prior knowledge of molecular biology and genetics is not required. Participants who complete the class will be eligible for MLA Continuing Education credits. The course is free but travel costs are at the expense of the participant.

For more information and a link to the application, visit the Technical Bulletin article dated December 13, 2012 here:
http://www.nlm.nih.gov/pubs/techbull/nd12/nd12_training_ncbi_application.html