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Publish Smart, Maximize Impact

Do you have an article you want to publish? Are you trying to decide where to place it? This workshop will examine how journals are ranked for impact (including some of the controversies about ranking systems), and your rights as an author. Are you confused about copyright? Do you want to be able to post copies of your article on your own website? Do you know whether you'll be able to? We will discuss Berkeley funding to support open access publishing, and the movement in academia to make information more accessible.

Friday, October 29, 2010
12 noon - 1:30 pm
Bioscience Library Seminar Room
2101 VLSB

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Catherine Nancarrow: Open Access Goes To Washington

In July 2010, a Congressional Hearing held to inform legislators primed to consider the Federal Research Public Access Act (or FRPAA) offered a unique opportunity for lawmakers to hear the testimonies of 10 witnesses as they spoke to the important implications of expanding public access to the results of federally funded scientific research.  Catherine Nancarrow was a witness at this Hearing. She will summarize the points she made and describe the reactions of the Congressional panel who now, better informed, will be considering the issues in advance of a vote.

Friday, October 22, 2010
12 noon - 1:30 pm
Bioscience Library Seminar Room

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Students for Free Culture Webcast

The Students for Free Culture sponsor this webcast with Nick Shockey of the Right to Research Coalition, a national organization that believes no student should be denied access to research they need because their institution cannot afford the often high cost of access.

Thursday, October 21, 2010
4:00pm - 5:30 pm
Bioscience Library Seminar Room

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Open Access Week at Berkeley, October 18-22, 2010

Open Access Week (October 18-22)  is a global event promoting Open Access as the new norm in scholarship and research. Several Berkeley events are planned for OA week and beyond:

List of Open Access Week events

Students, researchers, faculty and the public are invited to attend. Come early and get a free t-shirt! A limited number of open access t-shirts and PLoS t-shirts will be distributed at each event.)

A reminder to UC Berkeley faculty and researchers: UC Berkeley provides funding for open access publishing fees, if you don't have grant funds to cover the charges. 

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The Marian Koshland Bioscience and Natural Resource Library licenses the BIOBASE Knowledge Library. It is an up-to-date collection of information for characterized and uncharacterized proteins of human, mouse, rat, yeast, pathogenic fungi and worms. We provide access to the following databases:

More information can be found on http://www.lib.berkeley.edu/BIOS/proteomebk.html

Our seminar room accommodates up to 25 people and is equipped with 12 iMacs. You are welcome to bring in your own laptop.

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EndNote Workshop

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.

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PubMed

PubMed is the best resource for locating articles on molecular and cell biology and medicine. It contains bibliographic citations and author abstracts from more than 4,600 biomedical journals.

This introductory workshop will teach you how to:

Follow along on one of our iMacs, or bring your own laptop. No sign-up is needed.

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RefWorks Workshop

Looking for a simple solution for managing your citations and creating bibliographies? RefWorks is a web-based citation management application that's free to UC Berkeley students, staff, and faculty. During this hands-on session you'll learn the basics of RefWorks, including:

Work on one of our iMacs, or bring your own laptop. No sign-up is needed.

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Keeping Current

Keeping current with literature, news, and other types of information can be a daunting task. There are convenient services and technologies that can help you gather and organize the information that you need.

This class gives an introduction to:

Work on one of our iMacs, or bring your own laptop. No sign-up is needed.

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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.

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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.

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EndNote Workshop

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.

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International Open Access Week, October 19-23

Live Webinar from the Open Access Scholarly Publishing Association (OASPA)

  • Date: Tuesday, October 20
  • Time: 9:00 am - 10:30 am
  • Location: Marian Koshland Bioscience Library Seminar Room, 2101 VLSB

Featuring representatives from five different publishers discussing the promise and perils of Open Access publishing. Participants will include:

  • Pierre de Villiers, African Online Scientific Information Systems
  • Matthew Cockerill, BioMed Central
  • David Hoole, Nature Publishing Group
  • Mark Patterson, Public Library of Science (PLoS)
  • Saskia Franken, Utrecht University Library

The Future of Open Access Publishing

  • Date: Tuesday, October 20
  • Time: 4:00 pm - 5:30 pm
  • Location: Marian Koshland Bioscience Library Seminar Room, 2101 VLSB
  • Speaker: Mike Eisen, UC Berkeley Professor of Molecular and Cell Biology and co-founder of the Public Library of Science (PLoS)
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Article-Level Metrics at PLoS - What they are and why you should care

The Impact Factor of a journal (a measure of the number of citations to an entire journal) is commonly used by scientists and administrators as one indicator of the quality of individual articles within that journal. With the advent of the internet it is now possible to measure the worth of an individual article via so called 'Article-Level Metrics' (metrics which include citations, usage, bookmarks, blog coverage, and post publication commentary for a single article). In this respect PLoS leads the world in providing the data to allow this analysis.

Dr. Peter Binfield, Managing Editor of PLoS ONE—an open access journal, the third largest journal in the world, and the recent winner of a prestigious award for innovation in publishing—will describe PLoS's motivation for creating article-level metrics, how they are being implemented, and why you should care about them.

For more information read about article-level metrics at the PLoS website or watch this short video http://vimeo.com/5696434.

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RefWorks Workshop

Looking for a simple solution for managing your citations and creating bibliographies? RefWorks is a web-based citation management application that's free to UC Berkeley students, staff, and faculty. During this hands-on session, we'll cover creating a RefWorks account, importing records from article databases, organizing references, creating bibliographies, and using Write-n-Cite to format citations according to the style of your choice within your paper or manuscript. Once you start using RefWorks, you'll wonder how you ever got along without it.

Work on one of our iMacs, or bring your own laptop. No sign-up is needed.

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EndNote Workshop

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.

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Keeping Current

Keeping current with literature, news, and other types of information can be a daunting task. There are convenient services and technologies that can help you gather and organize the information that you need.

This class gives an introduction to:

Work on one of our iMacs, or bring your own laptop. No sign-up is needed.

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PubMed

PubMed is the best resource for locating articles on molecular and cell biology and medicine. It contains bibliographic citations and author abstracts from more than 4,600 biomedical journals.

This introductory workshop will teach you how to:

Follow along on one of our iMacs, or bring your own laptop. No sign-up is needed.

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BIOSIS

BIOSIS is the most comprehensive biological sciences database and the best source for literature on plant biology, systematics, and ecology. BIOSIS indexes 6,000 journals and contains references to articles, books, and conference proceedings on a wide variety of biological and biomedical topics.

This introductory workshop will teach you how to

Follow along on one of our iMacs, or bring your own laptop. No sign-up is needed.

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Web of Science

Web of Science indexes over 7,000 major scientific journals in all areas of science. This makes it a good resource for researchers doing multi-disciplinary work. It is an excellent database for finding articles that cite a given reference (cited reference searching).

This introductory workshop will teach you how to

Follow along on one of our iMacs, or bring your own laptop. No sign-up is needed.

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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.

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Library Orientation Tours

Each orientation consists of a brief tour of the facility and an introduction to the collection, library services, and resources. Meet at the Circulation Desk at the entrance to the library, which is located in 2101 Valley Life Sciences Building.

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UC Berkeley campus is changing VPN software

All current VPN users will need to download and install the new version before August 12, 2009, using the instructions linked on the Library VPN help page.

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OskiCat debuts June 24, 2009

OskiCat is the new UC Berkeley library catalog, replacing Pathfinder and GLADIS, and offering more content and convenient, new features.

See OskiCat Help to learn about what you can do with OskiCat.

See the OskiCat announcement for more information.

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Limited Services at the Bioscience Library, June 23

UC Berkeley Libraries are transitioning to a new online system for our circulation and catalog. Materials will not be able to be renewed on Monday, June 22 and Tuesday, June 23.

On June 23, 2009, only limited services will be available at the Bioscience Library:

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Privileges Desk Closed June 22-23

Due to technical limitations during the transition to our new computer system, the Library Privileges Desk is expected to be closed to the public on Monday, June 22 and Tuesday, June 23. For more details, contact Sheehan Grant (510-643-6139).

During this time, the Library will not be able to:

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Coming in Summer 2009: OskiCat

The new UC Berkeley library catalog, OskiCat, will replace Pathfinder and GLADIS, offering more content and convenient, new features.

What should you do to prepare?

Watch a short preview movie that shows you what you can do with OskiCat.

See the OskiCat announcement for more information.

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EndNote Workshop

EndNote is a widely-used 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.

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UCSC Genome Browser Workshop

The UCSC Genome Browser is an indispensable tool for biology and medicine researchers seeking genomics information. Explore the human genome reference sequence; find variation in genes important to your research in human and other species.

This introductory tutorial will cover the topics needed to effectively use this powerful, free, publicly-accessible tool, including:

This is a hands-on computer workshop on the UCSC Genome Browser presented by OpenHelix, LLC. OpenHelix provides online tutorials and on-site training on comprehensive genomics programs. More information can be found on http://www.openhelix.com/

Our seminar room accommodates up to 30 people and is equipped with 12 iMacs. You are welcome to bring your own laptop.

The workshop is approximately 3 to 3.5 hours. There will be a brief (10-15 minute) break, as well as time for Q & A.

We look forward to seeing you here!

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BIOBASE Knowledge Library Spring 2009 release is now available

The BIOBASE Knowledge Library Spring 2009 release includes a number of new features:

  1. The identifier Quick Search has been expanded to include BKL identifiers for all data types (i.e. matrix, reaction, etc).
  2. Significant improvements in Biomarker Associations, enabling you to search and identify whether genes to disease associations are causal, correlative, preventative or negative.
  3. A new Quick Search allows you to search directly for disease biomarkers. The Disease Advanced Search has been renamed Disease Biomarkers and now offers the ability to query directly by gene/protein name.
  4. Gene Set Analysis Button in the Quick Search View - allows you to upload a set of genes, statistically analyze them for over-representation by disease, expression, canonical pathways, etc, and to create a customized report summarizing the findings.
  5. Expression information for mammalian genes is provided in a new, tabulated format that makes it easy to see at-a-glance whether the mRNA, the protein, or both have been experimentally detected in each tissue/organ, cell, or tumor type assigned.
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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.

rule

EndNote Workshop

EndNote is a widely-used 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.

rule

EndNote Workshop

EndNote is a widely-used 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.

This workshop will be repeated on Friday, April 10, 2pm-3:30pm.

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Springer e-books Available at UC

The UC campuses have recently obtained perpetual access to a large collection of Springer ebooks published in English and German from 2005 to 2009, including Landolt-Bornstein, the largest compilation of data in physics and chemistry. The collection includes nearly 20,000 books from every scientific discipline and many social sciences. There are a few books from 2005 to 2009 that are not accessible because they are jointly published with another publisher, and excluded from this project.

At the present time, the books can be browsed or searched directly at http://springerlink.com/. This interface searches both books and journals articles and typically your results will include many journal articles. After your initial search, you can limit your results to books using the tools on the right side of the interface. Ultimately, the books will be linked from Melvyl, UC-eLinks and Google Scholar. However it will take some time to get this volume of material into these catalogs.

More information about the UC agreement with Springer can be found at: http://cdlinfo.cdlib.org/blog/2009/02/12/springer-electronic-book-package/

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RefWorks Drop-in Workshop

Looking for a simple solution for managing your citations and creating bibliographies? RefWorks is a web-based citation management application that's free to UC Berkeley students, staff, and faculty. During this hands-on session, we'll cover creating a RefWorks account, importing records from article databases, organizing references, creating bibliographies, and using Write-n-Cite to format citations according to the style of your choice within your paper or manuscript. Once you start using RefWorks, you'll wonder how you ever got along without it.

Work on one of our iMacs, or bring your own laptop. No sign-up is needed.

rule

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.

rule

EndNote Workshop

EndNote is a widely-used 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.


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

-- 

Beth Weil
Head Librarian
Marian Koshland Bioscience and Natural Resources Library
2101 VLSB
University of California, Berkeley
Berkeley, CA 94708
http://www.lib.berkeley.edu/BIOS

U.C. Berkeley Library Web
Copyright © 2014 The Regents of the University of California. All rights reserved. Comment Form. Last update: 11/12/13

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