Introduction to NCBI tools: BLAST
This session will provide a general overview of the molecular biology resources from NCBI (National Center for Biotechnology Information). Specifically, it will highlight BLAST (Basic Local Alignment Search Tool).
BLAST is a set of programs designed to perform similarity searches on all available sequence data. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify genes and genetic features.
BIOBASE: Proteome Databases Training
The Marian Koshland Bioscience and Natural Resource Library has licensed the BIOBASE Knowledge Library. It is an up-to-date collection of information for characterized and uncharacterized proteins of human, mouse, rat, yeasts, pathogenic fungi and worm. We provide access to the following databases:
More information can be found on http://biobase-international.com
The training room accommodates up to 25 people. Our seminar room is equipped with 12 iMacs. You are welcome to bring in your own laptop.
EndNote is a widely-used, powerful reference management tool. This hands-on workshop will include an overview of EndNote features. You will learn to:
Our seminar room is equipped with 12 iMacs. If you already have EndNote installed on your laptop, you can work on your own computer. No sign-up is needed.
OskiCat is the new UC Berkeley library catalog, replacing Pathfinder and GLADIS, and offering more content and convenient, new features.
Watch the OskiCat Quick Tour that shows you what you can do with OskiCat.
See the OskiCat announcement for more information.
NIH Mandatory Public Access Policy Details
The NIH Public Access Policy affects you if you have a current NIH grant or have students or staff whose salaries are paid by NIH.
On January 11, 2008, the NIH adopted a revised—and now mandatory—Public Access Policy that requires all NIH-funded investigators to submit their final, peer-reviewed manuscripts to the NIH’s PubMed Central (PMC) database (the digital archive of biomedical and life sciences journal literature) upon acceptance for journal publication. PMC will then make these papers freely available to the public no later than 12 months after publication.
The policy applies to all peer-reviewed journal articles that are accepted for publication on or after April 7, 2008.
The requirement applies to any NIH direct funding, including grants, contracts, training grants, subcontracts, etc. In addition, beginning May 25, 2008, anyone submitting an application, proposal, or progress report to NIH must include the PMC or NIH Manuscript Submission Reference Number when citing applicable articles that arise from their NIH-funded research.
Compliance with the policy is a term and condition of all grants and cooperative agreements active in Fiscal Year 2008 (10/1/07-9/30/08) or beyond, and for all contracts awarded after April 7, 2008.
Principal Investigators and their institutions are responsible for ensuring that articles that arise directly from their awards, even if the PI is not an author or co-author, are submitted to PubMed Central in accordance with the policy.
This policy will affect NIH grant recipients in two ways:
1) Articles resulting from your grant must be submitted to PubMed Central either by the journal or by you.
2) The PubMed Central ID number or Submission Number must be referenced in your NIH applications, proposals and progress reports submitted on or after May 25, 2008
Authors must ensure that any publication agreement they sign allows the final, peer-reviewed manuscript to be submitted to PubMed Central in accordance with the policy.
If a journal presents an author with a copyright transfer agreement, theauthor should not sign it if it does not allow the author to submit the final, peer-reviewed manuscript to PubMed Central within 12 months of the publication date.
Authors should attach an amendment to the publisher’s transfer agreement that will allow them to comply with NIH requirements.
Authors and PIs should begin collecting PubMed Central reference numbers as well as NIH Manuscript Submission System reference numbers as proof of deposit. As of May 25, 2008, these numbers will be required in all progress reports, proposals, and grant applications when citing papers that arose from your NIH award.
There are a number of journals that submit articles directly to PubMed Central on behalf of their authors. When you publish in one of these journals, no further action is required on your part to comply. See the list of Journals That Submit Articles to PubMed Central.
UC investigators may enclose a letter signed by William Tucker, Exec. Dir., Office of Tech. Transfer, UCOP, with any articles submitted to publishers for possible publication. This letter gives notice to the publishers that, if accepted for publication, the article will be required by law to be posted on PubMed Central. If this letter is not submitted to the publisher at the time the article is sent in for review it may be submitted along with any publication agreement signed by a UC investigator. (UCOP Guidance)
If there is any question about your rights, add the following language to the publication agreement: "Journal acknowledges that Author retains the right to provide a copy of the final manuscript to the NIH upon acceptance for Journal publication, for public archiving in PubMed Central as soon as possible but no later than 12 months after publication by Journal”
Feel free to contact me with questions
Beth
Important Links
NIH Public Access Home Page
http://publicaccess.nih.gov/index.htm
NIH FAQ
http://publicaccess.nih.gov/FAQ.htm#b1
NIH Submission Process
http://publicaccess.nih.gov/submit_process.htm
List of Journals that Submit articles to PubMed Central
http://publicaccess.nih.gov/submit_process_journals.htm
UC Office of Research Administration and Technology Transfer letter to attach to journal article submissions to ensure you have the right to submit to PubMed Central
http://www.lib.berkeley.edu/scholarlycommunication/letter_to_publishers.pdf
Sherpa Romeo http://www.sherpa.ac.uk/romeo.php
Summary of permissions that are normally given as part of each publisher's copyright transfer agreement
Copyright © 2009 The Regents of the University of California. All rights reserved. Comment Form. Last update:
11/17/09
