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Librarian Subject Specialist

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Ruth Gustafson
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Biological, Agricultural & Environmental Sciences
Reference Librarian
Shields Library, 3rd Floor

Phone: (530) 752‑1883
ragustafson@ucdavis.edu

Cool Library Tools for BioAg Lab Staff | Table of Contents

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 [Wiley]  
      
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    Covers over 20,000 updated, peer-reviewed protocols. UC CDL/UCD Library subscribes to THIRTEEN major laboratory methods and protocols series including the classic comprehensive work "Current Protocols in Molecular Biology" with other titles being CP in: Bioinformatics; Cell Biology; Cytometry; Human Genetics; Immunology; Microbiology; Mouse Biology; Neuroscience; Nucleic Acid Chemistry; Protein Science; Pharmacology; and Toxicology. 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 FIVE protocol titles: "Chemical Biology", "Essential Laboratory Techniques", "Magnetic Resonance Imaging", "Plant Biology" (new as of May 2016 with very little content) and "Stem Cell Biology".
    Updates: Quarterly or more frequently
  • Springer Protocols  
      
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    Springer Protocols contains more than 34,000 (as of September 2014) 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
    Ten-page User Guide
  • Cold Spring Harbor Protocols  Icon
    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 {RG 12/11/13}
    Search Help
  • Journal of Visualized Experiments (JoVE)  
      
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    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.
    July 2014: JoVE Science Education section in process for licensing {still not accessible September 2014}
    Coverage: Access currently to JoVE General section and all journal subsections
    Date: 2006- (General) 2013- (subsections)
  • Nature Protocols  
      
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    Author: Nature Publishing Group
    Nature Protocols is an interactive online resource for experimental and laboratory protocols for bench researchers primarily in biology and chemistry. Protocols are presented in a ’recipe’ style providing step-by-step descriptions of procedures that users can take to the lab bench and immediately apply in their own research. Protocols on the site are fully searchable and organized into logical categories to be easily accessible. Together, ’Nature Protocols’ and the interactive ’Protocols Network’ create a dynamic forum for scientists to upload and comment on protocols. Also includes Stem cell series, Stepwise blog, Discussion Forum, Tools & reagents, and Featured videos.
    Coverage: v.1-present
    Date: 2005-present
  • Methods in Enzymology [Science Direct -- Elsevier]  
      
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    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. As of 2017, videos are selectively being added to accompany the written methods. 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 500 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.
  • Bio-protocol
    A rapidly growing collection of peer-reviewed, life science protocols organized by 11 different fields of study and 10 different organisms. Protocols are organized chronologically with a detailed guide on how to reproduce a given experiment. Each protocol also contains an interactive and moderated Q & A section to facilitate open communication between protocol authors and the research community. Coverage: Jan 2011 – present.
  • 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)  Icon
    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  Icon
    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  Icon
    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

  • Ebooks at the UC Davis University Library
    This guide provides details on the various methods and licenses the UCD University Library employs to provide access to electronic books.
  • Springer eBooks Package  
      
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    Springer eBooks include more than 60,000 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: 2005-2017
  • CAB eBooks [via CAB Direct]  
      
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    FARMED OR DOMESTICATED ANIMALS. 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
    Scroll down to see CABI's ebook coverage in the various eBooks packages (Front file & backfile packages)
  • Safari Tech Books Online  Icon
    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.
    RSS feed of new titles in Safari
  • Wiley Online Library Ebook Collection  
      
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    NOTE: Interface does not separate ebooks from Wiley ejournals.

    Over 2,000 books with 2011-2016 publication dates. The Wiley ebook license comes with broad and favorable rights for scien ptific, scholarly and educational uses. The collection serves 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 2015 books continue to be added to the collection throughout the year as they are published simultaneously in both online and print.
    Coverage: 2011-2016

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
    Use the Subject Guides to identify additional databases to search for information on your topic.

Databases: Current Awareness/Updates Feature

Citation Tools

EndNote

  • EndNote Intro for BioAgEnvi Sciences Researchers [Library Guide]  
      
    Author: Ruth Gustafson

    This webpage is the step-by-step guide for the bi-monthly in-person EndNote Intro course taught in Shields Library.
  • EndNote Online or my.endnote.com
    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
    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

Data Management Plans for Grants

  • Ten Simple Rules for the Care and Feeding of Scientific Data
    Date: April 24,2014
    Excellent PLoS Computational Biology article about getting started with managing your data.
  • Primer on Data Management [DataOne]
    Date: 2012
  • Best Practices Database {for Data Management} [DataOne]
    Provides individuals with recommendations on how to effectively work with their data through all stages of the data lifecycle.
  • Data Management [LibGuide]
    Detailed resource guide for data management plans, data sharing and data archiving.
  • DMPTool  
      
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    Author: UC Curation Center (UC3)
    Build your Data Management Plan using the DMPTool which 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 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.
  • Webinar Series
    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.
  • Dash (UCD is not yet participating)  
      
    Author: UC Curation Center (UC3)

    DASH is a new self-service tool for researchers to describe, upload, and share their research data. It is designed to be a simple self-service curation tool for researchers, and helps them perform the following tasks:
    •Prepare data for curation by reviewing best practice guidance for the creation or acquisition of digital research data.
    •Select data for curation through local file browse or drag-and-drop operation.
    •Describe data in terms of the DataCite metadata schema.
    •Identify data with a persistent digital object identifier (DOI) for permanent citation and discovery.
    •Preserve, manage, and share data by uploading to a public Merritt repository collection.
    •Discover and retrieve data through faceted search and browse.
  • EZID
    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  Icon
    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
    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]
    This is a list of digital image collections for all disciplines.
  • ARTstor  Icon
    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 hundreds of thousands of 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.

    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 Client VPN or the Proxy Server.

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