Archive for the ‘NCBI Databases’ Category
Friday, December 12th, 2014
On December 17th, NCBI will present a webinar entitled “A Submitter’s Guide to GenBank: Using BankIt for Small-Scale Nucleotide Sequence Submissions”. This presentation will outline the process of using BankIt, a web-based submission tool at NCBI, to submit sequence data to the GenBank® database.
The webinar will demonstrate how to use BankIt forms to complete a submission of a single or a few nucleotide sequences. A second demonstration of BankIt will illustrate how to format and upload text input files needed for submissions of multiple sequences or for sequences with multiple genes.
This webinar will stay at a basic level for sequence submissions; future webinars that illustrate more complex sequence submissions will be considered depending on the feedback received from this presentation.
For more information and to register, check out the latest story on NCBI News:
Monday, September 29th, 2014
Health science librarians in the United States are invited to participate in the next offering of the bioinformatics training course, “A Librarian’s Guide to NCBI,” sponsored by the National Library of Medicine (NLM), the National Center for Biotechnology Information (NCBI), and the National Network of Libraries of Medicine, NLM Training Center (NTC).
The course provides knowledge and skills for librarians interested in helping patrons use online molecular databases and tools from the NCBI. Prior knowledge of molecular biology and genetics is not required. Participating in the Librarian’s Guide course will improve your ability to initiate or extend bioinformatics services at your institution.
Instructors will be NCBI staff and Diane Rein, Ph.D., MLS, Bioinformatics and Molecular Biology Liaison from the Health Science Library, University at Buffalo.
Online Pre-Course and In-Person Course Components
There are two parts to “A Librarian’s Guide to NCBI,” listed below. Applicants must complete both parts. Participants must complete the pre-course with full CE credit (Part 1) in order to advance to attend the 5-day in-person course (Part 2).
- Part 1: “Fundamentals in Bioinformatics and Searching,” an online (asynchronous) course,
January 12-February 13, 2015
The major goal of this part is to provide an introduction to bioinformatics theory and practice in support of developing and implementing library-based bioinformatics products and services. This material is essential for decision-making and implementation of these programs, particularly instructional and reference services. The course encompasses visualizing bioinformatics end-user practice. It places a strong emphasis on hands-on acquisition of NCBI search competencies, and developing a working molecular biology vocabulary through self-paced hands-on exercises.
- Part 2: A 5-day in-person course offered on-site at the National Library of Medicine in Bethesda, Maryland, March 9-13, 2015.
The in-person course will focus on using the BLAST sequence similarity search and Entrez text search systems to find relevant molecular data. The course will describe the various kinds of molecular data available and explain how these are generated and used in modern biomedical research. The course will be a combination of instruction, demonstration, discussions, and hands-one exercises (both individual and group).
Who can apply?
- Applications are open to health science librarians in the United States.
- Applicants will be accepted both from libraries currently providing bioinformatics services as well as from those desiring to implement services.
- Enrollment is limited 25 participants.
What does it cost?
- There is no charge for the classes. Travel and lodging costs for the in-person class are at the expense of the participant.
Important Application Dates
- Application deadline: November 17, 2014
- Acceptance notification: On or about December 15, 2014
How to Apply
- Please fill out the Application Form at https://www.surveymonkey.com/s/guide_2015_app.
- Once you complete the Application Form, you will be directed to download the Supervisor Support Statement (ftp://ftp.ncbi.nih.gov/pub/education/librarian_guide/Forms/Supervisor_Supportv2.pdf). This is to be filled out and signed by your immediate supervisor. This statement describes your current and/or future role in bioinformatics support at your institution and confirms your availability to attend the course if selected.
- Provide your current curriculum vitae (CV). Please use the suggested CV model as a guideline for the type of information desired (ftp://ftp.ncbi.nih.gov/pub/education/librarian_guide/Forms/LibGuide_CV_model.pdf).
The course page with additional information is at: http://www.ncbi.nlm.nih.gov/education/librarian/
Please direct any questions to: email@example.com
Wednesday, July 16th, 2014
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!
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:
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 firstname.lastname@example.org.
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.
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/
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
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!
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: