Topic Guides
Cool Library Tools for BioAg Lab Staff

Ruth Gustafson — ragustafson@ucdavis.edu

Librarian Subject Specialist

Ruth Gustafson
ragustafson@ucdavis.edu — (530) 752‑1883 — Research Support Services

Librarian Subject Specialist for: General Biology; Animal Science; Avian Science; Entomology (including Bee Biology and Pollination); Environmental Science & Policy; Environmental Toxicology; Evolution and Ecology; Forensic Science; Nematology; and Wildlife, Fish and Conservation Biology

Want to make an appointment with Ruth? See weekly availability at http://www.lib.ucdavis.edu/ul/forms/officehours/index.php?office=9

Protocol Tools

These online full-text collections cover a wide range of laboratory methods, protocols, practices and other technique standards. This list is organized from largest collections to smaller, more specialized collections.
Current Protocols Series (http://www.currentprotocols.com/) [Restricted] VPN
Covers nearly 16,000 updated, peer-reviewed protocols. UC CDL subscribes to ten major laboratory methods and protocols series covering the areas of molecular biology, nucleic acid chemistry, cell biology, protein science, immunology, neuroscience, human genetics, pharmacology, toxicology, and cytometry. Includes basic, alternate, and support protocols with literature cited and information on suppliers for standard materials and preparation information for reagents and solutions. IMPORTANT NOTE: UC Davis does *NOT* license the following seven protocol titles: "Bioinformatics", "Chemical Biology", "Essential Laboratory Techniques", "Magnetic Resonance Imaging", "Microbiology", "Mouse Biology" (new with very little content) and "Stem Cell Biology".
Coverage: Updated quarterly or more frequently
Springer Protocols (http://www.springerprotocols.com/) [Restricted] VPN
Springer Protocols contains more than 31,000 (as of March 2013) molecular biology and biomedical peer-reviewed protocols, mostly from the classic series Methods in Molecular Biology, formerly published by Humana Press. Other series included are: Methods in Molecular Medicine; Methods in Biotechnology; Methods in Pharmacology and Toxicology; and Neuromethods. Also included are protocols from laboratory handbooks, such as The Biomethods Handbook, The Proteomics Handbook, and the Springer Laboratory Manuals.
Coverage: 1980-present
Related:
  • Ten-page User Guide (http://www.springer.com/cda/content/document/cda_downloaddocument/SpringerProtocolsUserGuide.pdf?SGWID=0-0-45-517798-0)
Cold Spring Harbor Protocols (http://cshprotocols.cshlp.org/search.dtl) [Restricted] VPN

A definitive, interactive source of new and classic research techniques. The database covers specific sections on: Antibodies, Bioinformatics/Genomics, Cell Biology, Chromatography, Computational Biology, DNA Delivery/Gene Transfer, Electrophoresis, Genetics, High-Throughput Analysis, Imaging/Microscopy, Immunology, Laboratory Organisms, Molecular Biology, Neuroscience, Plant Biology, Polymerase Chain Reaction (PCR), Proteins and Proteomics, RNA Interference (RNAi)/siRNA, Stem Cells, and Transgenic Technology. Unique to this resource is the ability to submit a protocol. Other unique features include protocol recipes and protocol cautions.

Coverage: 2006-present
Related:
  • Search Help (http://www.cshprotocols.org/help/search_help.dtl)
Journal of Visualized Experiments (JoVE) (http://www.jove.com/) [Restricted] VPN
Author: MYJoVE Corporation

Journal of Visualized Experiments (JoVE) is a peer reviewed, PubMed indexed journal devoted to the publication of biological, medical, chemical and physical research in a video format.

June 2013: COMPLETE ACCESS to all sections now licensed

Coverage: Access currently to JoVE General section and all subsections
Date: 2006-
Methods in Enzymology [Science Direct -- Elsevier] (http://uclibs.org/PID/61958) [Restricted] VPN
Methods in Enzymology is the classic laboratory methods/protocols book series. The complete backfile of the full-text is available back to volume 1 from 1955. Direct article/chapter links are provided from core subject databases such as PubMed and BIOSIS Previews. Contains detailed protocols and descriptions of biochemical and biophysical techniques for research in biological and molecular sciences. More than 300 volumes are browse-able by individual volumes online from 1955 to the present or by searching across the collection by title, author, abstract, and keyword. Full-text access to articles is available in HTML and PDF formats.
Coverage: 1955-
Protocols (http://openwetware.org/wiki/Protocols)
Author: OpenWetWare

Open Access to full-text protocols in three categories of "in vivo", "in vitro" and "in silico" and a general category of other.

Anyone can add their own protocols or review those under development.

Over 200 protocols available.

Encyclopedias

These manufacturing and synthesis encyclopedias provide comprehensive details on BioAg related processes.
Encyclopedia of Reagents for Organic Synthesis (e-EROS) (http://onlinelibrary.wiley.com/mrw/advanced/search?doi=10.1002/047084289X) [Restricted] VPN
The Encyclopedia of Reagents for Organic Synthesis, e-EROS, provides updated information on approximately 3,800 reagents with a database of close to 50,000 reactions. Each reagent entry includes properties such as physical data, solubility, form supplied in, purification, and preparative methods; examples of use in reactions; and literature references. Search options include: name, CAS number, structure and reaction.
Related:
  • Also in print
    PSE Reference QD77 E53 1995
  • Structure and reaction searching require plug-ins, which may not be available on all library computers.
Kirk-Othmer Encyclopedia of Chemical Technology (http://uclibs.org/PID/12129) [Restricted] VPN
Comprehensive online chemical technology encyclopedia with more than 1,000 articles written by a panel of prominent scholars from industry, academia, and research institutions from around the world. Topics covered include: Analytical Techniques; Biochemistry & Biotechnology; Chemical Reactions; Dyes and Pigments; Energy; Environmental Protection and Industrial Safety; Fat, Oil, Food and Feed, Cosmetics; Inorganic Chemicals; Materials; Metals and Alloys; Organic Chemicals; Pharmaceuticals; Polymers and Plastics; Processes & Process Engineering; and Renewable Resources (Monthly updates)
Related:
  • Also in print
    PSE Reference TP9 E685
Ullmann's Encyclopedia of Industrial Chemistry (http://uclibs.org/PID/12130) [Restricted] VPN

Provides excellent overviews on materials used in manufacturing (ionic liquids, amino acids, silylating agents), or processes used in manufacturing (e.g., fermentation, chromatography, dyeing) as well as manufactured items.

Major sections cover: Agrochemicals; Analytical Techniques; Biochemistry & Biotechnology; Chemical Reactions; Dyes and Pigments; Energy; Environmental Protection, Industrial Safety; Fat, Oil, Food and Feed, Cosmetics; Inorganic Chemicals; Materials; Metals and Alloys; Organic Chemicals; Pharmaceuticals; Polymers and Plastics; Processes & Process Engineering; and Renewable Resources.

Related:
  • Also in print
    PSE Reference TP9 U57 1985

E-book Collections

CAB eBooks [via CAB Direct] (http://www.cabi.org/cabebooks/) [Restricted] VPN

CABI ebooks now provides access to over 532 agricultural titles (more than 9,000 individual chapters). The archives from 2000-2007 includes 400+ titles (with over 6,500 individual chapters).

This collection is divided into six core subject collections: Agriculture; Animal and Veterinary Sciences; Human, Food and Nutrition Sciences; Plant Sciences; Environmental Sciences; and Leisure and Tourism.

PLEASE NOTE: This collection does *not* include ALL books published by CABI but selected titles. In particular, the publisher has chosen *not* to include textbooks in this package.

Coverage: 2000-present
Related:
Safari Tech Books Online (http://uclibs.org/PID/33109) [Restricted] VPN
A collection of computing books that includes the full text of over 300 O'Reilly Press books dating from 2004 to the present. Safari will grow to include all new O'Reilly titles, including the popular In a Nutshell books on important computing topics. The full-text is searchable across titles and searches can be limited to code fragments. Books can also be browsed by topic. Books can be read online, or individual chapter sections can be printed out or emailed. Access is limited to 28 simultaneous UC connections. Coverage: 2004-present.
Coverage: 2004-present
Related:
Springer eBooks Package (http://springerlink.com/books/) [Restricted] VPN
UC-wide licensed three-year (2013-2015) package for Springer eBooks and includes more than 55,000 titles in English (and selectively in German) from every scientific discipline and many social sciences. This online interface enables all books to be searchable at the full-text level. Scope (textbook areas are starred) ranges from Architecture and Design, *Behavioral Science, *Biomedical and Life Sciences, *Business and Economics, *Chemistry and Materials Science, *Computer Science, *Earth and Environmental Science, *Engineering, *Humanities & Social Sciences and Law, *Mathematics and Statistics, *Medicine, *Physics and Astronomy, to Professional and Applied Computing. NEW books are added monthly.
Coverage: 2005-2014
Wiley Online Library Ebook Collection (http://wileyonlinelibrary.com) [Restricted] VPN

NOTE: Interface does not separate ebooks from Wiley ejournals.

Over 2,000 books with 2011-2014 publication dates. The Wiley ebook license comes with broad and favorable rights for scientific, scholarly and educational uses. The collection serves a wide range of research needs in the life, health and physical sciences, social sciences, and the humanities. EXCLUSIONS to the Wiley collection are textbooks, major reference works, some professional and trade titles, and consumer books. The 2014 books continue to be added to the collection throughout the year as they are published simultaneously in both online and print.

Coverage: 2011-2014

Subject Guides

Subject guides lead one to library resources for nearly every major or department on campus. Whether you have library research or recreational info needs (music, dance, sports?), subject guides can help you locate core resources and the librarian to contact for questions.
Subject Guides (http://www.lib.ucdavis.edu/ul/research/subjects/)
Use the Subject Guides to identify additional databases to search for information on your topic.

Databases

BIOSIS Previews [via Web of Science] (http://isiknowledge.com/BIOSIS) [Restricted] VPN
More than 23 million records in all life science areas, including agriculture, biochemistry, biomedicine, biotechnology, ecology, environmental sciences, genetics, microbiology, plant biology, veterinary medicine & pharmacology, and zoology. Indexes over 6000 journals, serials, books and book chapters, conference proceedings and patents.
Coverage: 1926-present
Related:
CAB Abstracts [via OvidSP] (http://ovidsp.ovid.com/ovidweb.cgi?T=JS&MODE=ovid&NEWS=N&PAGE=main&D=cabz) [Restricted] VPN

NOTE: default UCD Search Type set to Advanced Ovid Search. Citations and abstracts to the international agricultural literature, including veterinary medicine, human and animal nutrition, forestry, rural development, as well as other related topics such as tourism and human ecology. Covers over 11,000 journals & conference proceedings and selected books in agriculture. Produced by CAB (Commonwealth Agricultural Bureaux) International (CABI) with more than 9.0 million records as of 10/27/10.

HISTORICAL SCOPE: Archive abstracts added in August 2005 go back to 1910 with 1,860,000 additional records.

CAB DATABASE PDFs: As of January 2009, hard-to-find literature may be available as CAB Database PDFs (so noted *below* the UC-eLinks button). Currently, ONLY Internet Explorer (PC platform) or Safari/Google Chrome (Mac platform) loads these PDFs. These CABI Full Text items give users automatic access to over 187,000 (as of March 2013) journal articles, conference papers and reports - 80% of which are not available electronically anywhere else.

Coverage: 1910-present [Archives added for 1910-1971]
Related:
PubMed (http://uclibs.org/PID/17708) [Restricted] VPN
More than 23 million citations and abstracts for articles published in approximately 8,400 journals in medicine, life sciences, health administration, veterinary medicine, nursing, molecular biology and genetics. PubMed is a service of the U.S. National Library of Medicine on the NCBI platform.
Coverage: 1946-present
Related:

Citation Tools

Journal Citation Reports (JCR) (http://uclibs.org/PID/36787) [Restricted] VPN

Journal Citation Reports is an annual publication by Thomson Reuters with each yearly data analysis being completed in the following year. The most recent edition is always published in the summer following the year analyzed.

Journal Citation Reports indicates the most frequently cited journals in a field, the highest impact journals in a field, and the largest journals in a field. JCR Science Edition contains data from over 7,300 journals in science and technology. JCR Social Sciences Edition contains data from over 2,200 journals in the social sciences. NOTE: For disciplines that have longer timespans for citation, consider sorting for ranking by using the 5-year Impact Factor sort.

Coverage: 2007-2012
Related:
Science Citation Index Expanded [via Web of Knowledge] (http://isiknowledge.com/wos) [Restricted] VPN
Multidisciplinary database, with searchable author abstracts, covering the peer-reviewed journal literature of the sciences. It indexes more than 6,650 major journals across 150 scientific disciplines. Search for articles that cite a known author or work.
Coverage: 1900-present
Related:
F1000Prime (http://f1000.com/prime) [Restricted] VPN
Author: Faculty of 1000

F1000Prime is a "literature awareness tool that is updated continuously and comprehensively and systematically highlights and reviews the most interesting papers published in the biological and medical sciences, based on the recommendations of a faculty of leading researchers. Through immediate rating of individual papers by the authors' peers, F1000 [Prime] highlights papers on the basis of their scientific merit rather than that of the journal in which they appear."

Faculty of 1000 (F1000) Biology & Medicine are merged into one and now called F1000Prime. Includes over 40 Faculties (Broad subject areas such as biochemistry, ecology or plant biology), which are further subdivided into over 300 Sections. On average, 1,500 new evaluations are published each month. Faculty members are more than 5,000 experts worldwide (assisted by 5,000 associates) and assess articles from more than 3,500 peer-review journals.

Related:

EndNote

EndNote Online or my.endnote.com (https://www.myendnoteweb.com/EndNoteWeb.html)

EndNote Online (formerly EndNote Web) facilitates collaborative work and using EndNote Web from any internet-accessible location in the world. You may easily transfer references from your EndNote Web to your desktop Endnote or vice-versa. You can "Cite While You Write" from this Web version or your desktop version although CWYW works best from the desktop version.

NOTE: EndNote Web X5 is the first version to enable PDF attachments.

EndNote Instructional Webpage (http://www.lib.ucdavis.edu/dept/instruc/research/endnote/)
Author: UC Davis Libraries
EndNote, licensed for all UCD full-time students, faculty, researchers and staff, is a bibliographic reference manager which enables citations to be stored, searched, and quickly inserted into research papers in the format of many scholarly journals.

Copyright Tools

Copyright and Intellectual Property Resources (http://www.lib.ucdavis.edu/ul/about/copyip/resources.php)
UC-eLinks Menu: Tool to link to PDF
A feature built into many databases that provides a bridge between licensed database content and material that is available to UC Davis library users, either online or in print. Feature to add PDF link is labelled "Copy & Paste Citation or Link"
Related:

Data Management Plans for Grants

Data Management [LibGuide] (http://ucdavis.libguides.com/dmp)
Detailed resource guide for data management plans, data sharing and data archiving.
Webinar Series (http://www.cdlib.org/services/uc3/uc3webinars.html)
Author: UC Curation Center (UC3)
The UC Curation Center archives a wide variety of data management related webinars, with average run time from 30-60 minutes.
DMPTool (https://dmp.cdlib.org/) [Restricted] VPN
Author: UC Curation Center (UC3)

Build your Data Management Plan using the DMPTool. The DMPTool provides a guide for drafting the document that you must submit with your grant application. Users of the DMPTool can view sample plans, preview funder requirements, and view the latest changes to their plans. The tool also permits the user to create an editable document for submission to a funding agency, and can accommodate different versions as funding requirements change.

It supports data management plans and funder requirements across the disciplines and includes multiple agency requirements. Templates for funders of BioAg and EnviSci interest include: Gordon and Betty Moore Foundation, Gulf of Mexico Research Initiative, Institute of Museum and Library Services, National Institutes of Health, National Oceanic and Atmospheric Administration, NSF-AGS: Atmospheric and Geospace Sciences, NSF-BIO: Biological Sciences (2013- ), NSF-CHE: Chemistry Division, NSF-DMR: Materials Research, NSF-EAR: Earth Sciences, NSF-EFRI: Emerging Frontiers in Reseach and Innovation, NSF-ENG: Engineering, and NSF-GEN: Generic.

NOTE: New version of DMPTool (DMPTool2) is scheduled for May 2014 release

DataUP (http://dataup.cdlib.org/)
Author: UC Curation Center (UC3)

Manage and share tabular data from your spreadsheet(s).

The DataUP tool helps you to: check your data for best practices (such as consistent naming structures); develop metadata (description of your data) using a wizard-style template; retrieve a unique identifier for your dataset from your data repository; and post your dataset(s) and associated metadata to the repository.

EZID (http://www.cdlib.org/services/uc3/ezid/index.html)
Author: UC Curation Center (UC3)

Makes data easy to discover and cite.

Use EZID to: create identifiers for anything, texts, data, bones, terms, etc.; store citation metadata for identifiers in a variety of formats; and update current URL locations so citation links are never broken.

EZID's Off Site programming interface allows for automated operation at scale where you can choose from a variety of persistent identifiers, including ARKs and DataCite DOIs (Digital Object Identifiers).

Merritt (https://merritt.cdlib.org/) [Restricted] VPN
Author: UC Curation Center (UC3)

Archive and preserve your research. Merritt is a UC repository for all subjects.

Merritt is a new cost-effective repository service from the University of California Curation Center (UC3) that lets the UC community manage, archive, and share its valuable digital content. Merritt features: an easy-to-use interface for deposit and update; access via persistent URLs; tools for long-term management; and permanent storage.

Science and Engineering Data Repositories (http://www.cdlib.org/services/uc3/datamanagement/sharing.html#scieng)

Aside from the UC Merritt, there are many subject oriented data repositories available for archaeology to space science data. This shortlist of S&E data repositories covers only large-scale, authoritative repositories.

ALSO check appropriate UCD Library BioAg Subject Guides at http://www.lib.ucdavis.edu/ul/research/subjects/?list=bioag for the category "Datasets, Data Series, Data Repositories, Data Systems".

Images

Find more under the "Digital Images" Subject guide and under respective Subject Guides which may list subject-focused image collections such as "NOAA Photo Library" under the "Marine Biology" subject guide.
Digital Images Subject Guide [via UC Davis] (http://www.lib.ucdavis.edu/ul/research/subjects/index.php?id=139)
This is a list of digital image collections for all disciplines.
ARTstor (http://uclibs.org/PID/44518) [Restricted] VPN
ARTStor is a library of digital images, associated information, and software tools designed to enhance teaching, learning and scholarship. It contains a searchable database of more than 500,000 digital images, covers many time periods and cultures, and documents the fields of architecture, painting, sculpture, photography, decorative arts, and design, as well as many other forms of visual culture.
Related:
  • ARTstor
    For off-campus access, first register with ARTstor from a computer on campus. Then, you may login from off campus with your ARTstor ID by going directly to www.artstor.org. Or, you may use the VPN or the Proxy Server.
  • If you would like to join a UCD community of ARTstor users to share discoveries and help solve problems, please join our ARTstor Users Group on Smartsite.