Bioinformatics -- UCSC Science & Engineering Library Subject Guides

Use the databases below to search for articles via keyword, subject, or author. Links to the electronic version of the article are often available. If the article is only available in print, these databases will give you the library's call number (location) for the journal. [more info]

PubMed UC Version [UC Only] - Editor's Choice!
Mid-1960's - present. For biomedical articles and conference papers this is the place to go. This searchable database of citations to biomedical literature is a customized University of California edition of the the National Library of Medicine PubMed database. This edition includes more links to full text online articles than the public version, and provides enhanced access to document delivery, among other things. PubMed citations link to Entrez nucleotide, protein and structure records when available.
Entrez Global Query - a cross-database search option that searches many Entrez databases at one time, including PubMed. The results list the number of records in each database that match your query, and provides links to those records. This is a great tool for database discovery and for uncovering data you might otherwise miss.

BIOSIS Previews [UC Only] Editor's Choice!
1926 - present. Start here for plant biology/genetics and other non-clinical biology and genetics articles and conference papers. More than 2,300 of the journals/serials covered by BIOSIS are not in Web of Science. Good for topic exploration, includes conference papers (unlike Web of Science). What may be helpful is using the Major Concepts field with the term Computational Biology to narrow your topic search to articles discussing computational aspects. You can also search Web of Science and BIOSIS at the same time. Choose the All Databases tab.

Web Of Science (Science Citation Index) [UC Only]
1900-present. This is an index to scientific journal articles that also allows you to search for citations to a particular article, and provides citation analysis tables. You look up the reference to a work that you know about to find more recent journal articles that have cited it. Cited reference searching is a unique way to trace ideas and subjects from past research into the present day. Conference papers are not included directly (they are scanned from article bibliographies but not indexed directly). You can search Web of Science and BIOSIS at the same time. Choose the All Databases tab.

Faculty of 1000 Biology [UCSC Only] Editor's Choice!
This is a highly selective literature awareness tool. Articles are selected and reviewed by top researchers for their impact in all fields of biology. You can browse lists of the very best papers in the Top 10 lists by discipline, or browse the Hidden Jewels list, which displays only papers that have been picked from less obvious journals which you may have missed but rate highly on Faculty of 1000 Biology. Or search by author, title, journal name or subject area. Login to create email alerts.

INSPEC [UC Only]
Covers 1969-present. This is the best choice for comprehensive coverage of journal articles and conference papers in computer science, electrical engineering, and physics. INSPEC includes all of the IEEE, IEE and ACM literature as well as the products of many other publishers.

List of Electronic Full Text Journals
Search by words in the journal title (not in the article title) to find journals which are available in full-text electronic format to UCSC users.

NCBI's Entrez Global Query is a cross-database search option that searches many Entrez databases at one time. The results list the number of records in each database that match your query, and provides links to those records. The Global Query search page also acts as a short Entrez database directory since each database is briefly described (select the question mark icon next to each database).

Nucleic Acids Research: Annual Database Issue (January)
For the past fifteen years the journal Nucleic Acids Research, published by Oxford University Press, has devoted the first issue of each year to listing and describing the most noteworthy molecular biology and bioinformatics databases. In 2007 this special issue is available online only and is being made freely available to the world under NAR's open access model. The Database Issue always includes many informative articles describing selected databases in depth as well as an extensive annotated list of significant databases in the field. See also the companion Web Server Issue of this journal, which comes out in July.

Methods in Enzymology [UC Only]
Online collection of detailed protocols and descriptions of biochemical and biophysical techniques contained in over 400 volumes. You can search across the collection by title, author, abstract and keyword, or browse by individual volume.

CRUZCAT
Catalog for the UCSC Libraries. Includes our library locations for books, journals, conference proceedings, maps, videos and more.

Flash movie tutorial: Searching for a Known Journal Title (2:40 min)

O'Reilly Books Online (via Safari) [UCSC Only] - Please log off when done!
Desktop access to over one hundred O'Reilly & Associates technical books, cover to cover. Topics include Java, Linux/Unix, Networking, Perl, Programming, Software Engineering, Web Development, XML, Bioinformatics, etc. There is a 10-minute "time-out" period for each user session. If there is no activity on the interface for 10 minutes the user will be logged out, thus making the system available for another user.

Melvyl Catalog
Catalog for the entire UC system. Includes location information for books, journals, conference proceedings, maps, videos and more. Faculty, staff and students can REQUEST items to be sent to you from other libraries. [more about document delivery]
Melvyl User Guides

Books and Other Materials on Reserve for Classes
Students: Course reserves are listed in the CRUZCAT online catalog. You can search by course name or instructor to find items on reserve for your class. More information about reserves is also available.
Instructors: How to place materials on reserve.

Bioinformatics Links Directory
"The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. The links listed in this directory are selected on the basis of recommendations from bioinformatics experts in the field. We also rely on input from our community of bioinformatics users for suggestions. Starting in 2003, we have also started listing all links contained in the NAR Webserver issue."

Books about technical writing available at the Science Library
Here is a list (from CRUZCAT) of recent books on technical writing (i.e., how to write lab reports and scientific articles) that you can checkout at the Science Library. Check the list to see what's available.

UC Copyright Education Web Site
The site provides information on copyright policies and laws, and how to apply them to academic and scholarly work . Also provides access to a variety of clearly written resources about copyright in general and its importance to higher education.

LaTeX and BibTeX Resources
LaTeX is not a word processor, but rather a typesetting language. LaTeX is based on Donald E. Knuth's TeX language. LaTeX was first developed in 1985 by Leslie Lamport, and is now being maintained and developed by the LaTeX3 Project. BibTeX is a tool for formating lists of references used in LaTeX.

EndNote & EndNote Web
EndNote (available for purchase at an academic discount at the UCSC Bay Tree Bookstore) is a database manager that allows you to create your own personal library to store and manage references to documents. It works with Word and WordPerfect, and with other common word processors, to insert citations into papers and to format bibliographies in any of hundreds of styles. EndNote can import search results from many article databases such as PubMed, BIOSIS and Web of Science.

EndNote Web is the new web version of EndNote that is freely available to UCSC students, faculty and staff. Its particularly easy to use from within Web of Science and Biosis because links to EndNote Web are included in those databases.

Teaching Support - From the UCSC Libraries - Editor's Choice!
Learn about the wealth of services the library can offer in support of teaching. You can request instruction sessions and materials tailored for your class, put materials online or on reserve, borrow maps, videos, slides, or books for your classes, and more.

NetTrail Information Literacy Tutorial (University of California, Santa Cruz) - Editor's Choice!
Here your students will learn the information skills that will help them succeed academically. NetTrail contains six modules, each covering an important area of information use: Types of Information, Choosing a Topic, Library & Web, CRUZCAT, Find Articles, and Info Ethics (including plagiarism). It is possible for an instructor to assign the online course to students through successful completion of the Quiz.

National Center for Case Study Teaching in Science
A refereed national clearinghouse for case studies in science, including many in molecular biology/genetics and engineering. The use of case studies develops students' skills in group learning, speaking, and critical thinking, and since many of the best cases are based on contemporary--and often contentious--science problems that students encounter in the news (such as human cloning), the use of cases in the classroom makes science relevant.

The Bioinformatics Librarian

Christy Hightower is the Bioinformatics Librarian at UCSC. She can help you with:

Suggestions for bioinformatics books or journals for the library to purchase,
Library instruction for your classes, lab or research group (topics are tailored to your interests, ranging from basic computer searching to the use of specialized resources in engineering),
Tips and techniques for more effective use of our article databases, MELVYL or CRUZCAT.

Christy can be reached via christyh@ucsc.edu, phone x94708, or campus mail to Christy Hightower, Science & Engineering Library.