SPECPRO 000: NIH Bridges to Baccalaureate Summer Program

Contact Your Librarian

  • Heather Thams
  • heather thams photo

  • Office Hours: Mon/Tues/Thurs 10am-5pm (by appointment)
  • Office Location: 212 Doe Library
  • Contact Info:

About this Guide

A guide for students visiting UC Berkeley to participate in the Bridges to Baccalaureate undergraduate research program, Summer 2013.

Library Buildings on the Cal Campus

The UC Berkeley libraries have a huge variety of resources, both physical and electronic. A few aerial image of the Berkeley campusthings you should know:

- There are more than 20 libraries on the Cal campus, containing more than 10 million books (including the books in offsite storage). All of the Cal libraries have different hours, which change depending on the academic calendar (summer hours are shorter).

- The Bioscience Library in VLSB (Valley Life Sciences Building) is a useful resource for NIH Bridges students; they have plenty of study space, recent editions of biology, biochemistry, and organic chemistry textbooks available for 2-hour loan (ask at the circulation desk), and specialist librarians to help you with searching PubMed and other biomedical literature databases. Their summer hours are 9-5, Monday-Friday. You don't need a Berkeley ID to access the Bioscience Library.

- Doe Library is considered the "main" library (the largest library on campus). Through Doe Library and Moffitt Library, you can access the Gardner Stacks, which is an underground library facility containing more than 3 million books, mostly in the humanities and social sciences. The Gardner Stacks has more than 400 seats for quiet study, and is open later than the other libraries on campus; you can view their June 2013 hours here. You must have a Berkeley ID or a stack pass to access the Gardner Stacks; you must have a Berkeley ID to enter Moffitt Library.

- All the books in all the libraries on campus can be found with one tool: OskiCat, the UC Berkeley library catalog. Some books are stored off-campus (these will give their location as "NRLF"). Always be sure to write down the location as well as the call number for a book you want to locate in the UC Berkeley Libraries. See the "Textbooks" tab of this guide for more help with using OskiCat.

screenshot of OskiCat

Electronic Library Resources on the Cal Campus

In addition to the physical collections of the UC Berkeley Libraries, the Library also has access tostudent getting help at computer over 10,000 electronic journals ("e-journals") and thousands of electronic books. Most of the e-journals that we subscribe to are in scientific fields. For many journals, we have access to the most recent issues electronically, but you will have to go to the library shelves to find older issues; for other journals, we have electronic access all the way back to the first issue. (Our electronic access to Science goes back to 1880, for example).

Because the Library pays publishers and vendors for access to these electronic resources, you will need to authenticate as a Berkeley user in order to use them. When you're on-campus, you're automatically authenticated; you can access any of these resources from any computer on campus (including a laptop connected to AirBears, our wireless network). When you're off-campus, you'll need a current CalNet ID in order to access these resources, and you'll need to set up off-campus access.

Printing and Scanning in the Libraries

All libraries on campus are equipped with "bookscan stations," which allow you to:

Scanning to a USB drive is free.  Moffitt Copy Center sells flash drives.

Scanning documents to print is 8 cents a page (color printing: 60 cents a page).picture of open book

In order to send documents to the printer from any of the public computers in the libraries, you must have the following:

Have more questions? There's more info here.

Beyond the Web

"It's all free on the Internet, right? Why should I go through the library's website to find sources for my paper?"

Library logo

The Web is a great source for free, publicly available information. However, the Library pays for thousands of electronic books, journals, and other information resources that are available only to the campus community. Through the Library website, you can access hundreds of different licensed databases containing journal articles, electronic books, maps, images, government and legal information, current and historical newspapers, digitized primary sources, and more. 

You access these resources through the Internet, using a browser like Firefox, Chrome or Internet Explorer -- but these databases are not part of the free, public Web. Resources like Lexis-Nexis, Web of Science, Academic Search Complete, and ARTstor are "invisible" to Google. You will not see results from most library databases in the results of a Google search.

Want to find out more? Get started exploring the Library's electronic resources, or find out how to get access to licensed resources from off-campus.

PubMed Basics

PubMed (created by the National Library of Medicine in Bethesda, MD) pubmed logois the most important source for scholarly, peer-reviewed articles in molecular biology, cell biology, and all aspects of medicine. Over 5000 scholarly journals from around the world are indexed in PubMed, and new articles are added every day. PubMed also provides links to relevant information in other NCBI databases, such as BLAST (a tool to help you find similarities between proteins), Nucleotide (genome, gene, and transcript sequence data), and PubChem (a database of information about biologically active small molecules).

A few things to remember about PubMed:

pubmed screenshot

Searching PubMed

Searching PubMed is easy. You can just enter your search words in the search box and press the Search button; PubMed will automatically cross-reference your search words to the appropriate scientific or medical terms. For example, if you enter "heart attack causes," PubMed will search for "heart attack causes" but it will also search for "myocardial infarction etiology." You can use the basic search box to combine your terms - you can enter the author's name and the subject terms all in the same box - or you can go to Advanced Search to search specifically by author name, institution, article title, date range, etc.

Searching by topic: just enter your search words (e.g., neanderthal genome, pancreatic cancer genetics). You can then use the filters on the left sidebar to narrow down your results by article type (clinical trial, review article, etc.), date, species (humans or other animals), age group, language, and so on.

Searching by author: enter the last name first, followed by initials with no space between them (e.g., full rj). If you don't enter the author names in this format, PubMed won't know that you're looking for an author name and will return irrelevant results. If you enter the author's full name (no initials) PubMed usually won't understand that form of the name, either.

You can also enter the word "author" in square brackets after the name: full rj [author]. This is especially useful when your author has a last name that's likely to appear in other contexts, like "Cell" or "Heart" (these are actual author names in PubMed)!

Searching by institution: This is useful if you want to see what research is going on in labs at various universities that you might want to transfer to. Because of the way that university names can vary when entered into PubMed (UC Berkeley, Univ of Calif Berkeley, University of California Berkeley, etc.) it's best to search with a ZIP code instead. You can find ZIP codes in Google Maps. UC Berkeley's ZIP code is 94720; so to do a search for all articles in PubMed that have a UC Berkeley-affiliated first author, enter 94720 [affiliation].

More Help with PubMed

PubMed has a lot of help on its website, including links to YouTube tutorials.question mark photo

The Bioscience Library has a brief, printable PubMed guide [pdf].

For more sophisticated PubMed searching, you can search with MeSH (Medical Subject Headings), which is the system of specialized terms that are used to organize and classify articles in PubMed. Here's a YouTube tutorial.

Where's the PDF?

Many article databases contain information about articles (citations or abstracts), not the entire text of the article.  Once you've used an article database to find articles on your topic, you may need to use the UC-eLinks button (UC-eLinks  button)  in order to locate and read the full text of the article. The UC-eLinks button appears in nearly all the databases available from the UCB Library website.

UC-eLinks will link you to the online full text of an article if UCB has paid for online access; otherwise, UC-eLinks will help you locate a print copy on the shelf in the library. If UCB doesn't own the article in print or online format, UC-eLinks can also help you order a copy from another library.

For more information, watch this video tutorial (about 4 min.)

You can also set up UC-eLinks to work with Google Scholar.  For more information, watch this video tutorial (about 2 min.)

Find an Article from a Citation

Here's a citation for an article...how do you find the whole article?

Gaultney, J. F. (2010). The Prevalence of Sleep Disorders in College Students: Impact on Academic Performance. Journal of American College Health, 59(2), 91-97

This citation is for an article by J. F. Gaultney, published in 2010 in the Journal of American College Health, a scholarly, peer-reviewed journal. It's part of volume 59, issue 2 of this journal, and was printed on pages 91-97. There are several ways of determining if the article you're looking for is available at Berkeley, in electronic or printed format:

Option 1: Use Google Scholar to locate a citation for the article, and UC-eLinks to retrieve the full text.

Paste or type the citation into Google and pull down the Google Scholar tool. Here's how:

jing thumbnail

Remember to set up off-campus access if you're off-campus. Here's a brief video that shows what to do if you don't see UC-eLinks in your search results.

Note: Google Scholar does not cover all publishers, and many journals indexed by Google Scholar have partial coverage only (some years/volumes missing). Also, not all articles found through Google Scholar will be available online. If you can't find the full text of your article this way, read on for more options!

Option 2: Look up the journal title in OskiCat or Melvyl.

You can also search for the title of the journal (NOT the article title!) in either OskiCat or Melvyl.  They will tell you:

Click this link for a 45-second demo.

Read more

Engineering Textbooks at UC Berkeley

Click here for a list of engineering textbooks available from the UC Berkeley LibrariExploring Engineering book coveres. Most books are hard-copies (not e-books) and are shelved at the Kresge Engineering Library in the Bechtel Engineering Center.

Bio, Chem, and Medical Textbooks at UC Berkeley

Online Books

Most of the textbooks we buy in the library are in print, not online. We would prefer to buy online textbooks, but textbook publishers have been slow to offer them. You can find a list of freely available, open-source biology textbooks here. You can also find (slightly) older editions of some bioscience/medical textbooks on the PubMed Bookshelf, freely available on the internet; AccessMedicine is a database of full-text medical textbooks that's available to UC Berkeley users.

Print Books

See below for a list of some of the major biology and chemistry textbooks available in the UC Berkeley Libraries. Click the book title link to see the complete description in OskiCat (including location and call number). If a book's location is Reserves (Bioscience Reserves, Chemistry Library Reserves) then it's shelved behind the circulation desk at that library. You'll need to write down the call number and give the call number to the person at the circulation desk, who will retrieve the book for you. You can only check out reserve books for two hours (because of heavy use by other students) but if no one else is in line to check out the book at the end of your two hours, you can renew for another two hours. You must renew in person at the circulation desk of the library where you checked out the book.

You can also search OskiCat directly for textbooks - try searching for "microbiology textbooks" or "biochemistry textbooks." If you want an introductory book on a topic, try including the words "introduction," "principles" or "fundamentals": introduction cancer biology, or fundamentals bioengineering. If you want to restrict your search to online resources, you can select Available Online from the Entire Collection drop-down menu.


Campbell Biology (2011 edition) Read at Google Read at Google


Campbell Biology (2008 edition) Read at Google Read at Google


Lehninger Principles of Biochemistry (2013 edition) Read at Google Read at Google


Study guide and solutions manual for Lehninger Biochemistry Read at Google Read at Google


Chemical Principles (Zumdahl, 2013 edition) Read at Google Read at Google


Foundations of Organic Chemistry (available online) Read at Google Read at Google


Organic Chemistry: Structure and Function (Volhardt, 2011 edition) Read at Google Read at Google

Resources in Molecular & Cell Biology

Bioscience Library website

Molecular and Cell Biology Resources: A selection of books, databases, websites and tutorials for biochemistry, bioinformatics, cell & developmental biology, molecular biology, microbiology, the neurosciences, and more.

Molecular Biology Web Resources: Informational and analytical tools and resources on gene and protein sequences and structures.

Proteome: A database of information on the structure and function of proteins expressed in mammalian species, model organisms, and human fungal pathogens. Content covers diseases, drugs, gene regulation, pathways, and fully annotated genomes.

Online Encyclopedias in Life Sciences (most restricted to UCB users)

Digital Images in MCB, Microbiology, Medicine

Biological Animations and Video Lectures

Biodiversity and Taxonomic Databases (most freely available on the web)

Engineering Resources

Kresge Engineering Library website

Location of the Engineering Library (Bechtel Engineering Center)

E-books in engineering

Databases for articles in engineering (you need to look beyond PubMed!)

Finding physical and chemical data

Research guides:

Chemistry Resources

Chemistry and Chemical Engineering Library website

Location of the Chemistry Library (Hildebrand Hall)

E-books in chemistry

Reaxys (database of compounds, structures, properties, reactions)

Finding Physical and Chemical Properties

PubChem (biological properties of small molecules)

Help with searching PubChem (series of short video tutorials)

Chemistry basics from Khan Academy

Organic chemistry basics from Khan Academy

Formatting Citations

Citation Management Tools

Citation management tools help you manage your research, collect and cite sources, and create bibliographies in a variety of citation styles.  Each one has its strengths and weaknesses, but any are easier than doing it by hand!

  1. Zotero: A free plug-in that works exclusively with the Firefox browser: keeps copies of what you find on the web, permits tagging, notation, full text searching of your library of resources, works with Word, and has a free web backup service. A guide is available.
  2. RefWorks - free for UC Berkeley users. It allows you to create your own database by importing references and using them for footnotes and bibliographies. Use the RefWorks New User Form to sign up. A guide is available.
  3. EndNote: may be purchased from UC Berkeley's Software Central.

It's always good to double check the formatting -- sometimes the software doesn't get it quite right.

What is Peer Review?

Your instructor may want you to use "peer reviewed" articles as sources for your paper. Or you may be asked to find picture of thinking student"academic," "scholarly," or "refereed" articles. What do these terms mean?

Let's start with the terms academic and scholarly, which are synonyms. An academic or scholarly journal is one intended for a specialized or expert audience. Journals like this exist in the sciences, social sciences, and humanities. Examples include Nature, Journal of Sociology, and Journal of American Studies. Scholarly/academic journals exist to help scholars communicate their latest research and ideas to each other; they are written "by experts for experts."

Most scholarly/academic journals are peer reviewed; another synonym for peer reviewed is refereed. Before an article is published in a peer-reviewed journal, it's evaluated for quality and significance by several specialists in the same field, who are "peers" of the author. The article may go through several revisions before it finally reaches publication.

Magazines like Time or Scientific American, newspapers, (most) books, government documents, and websites are not peer-reviewed, though they may be thoroughly edited and fact-checked. Articles in scholarly journals (in printed format or online) usually ARE peer-reviewed.

How can you tell if an article is both scholarly and peer-reviewed?

Read more

Get Help in the Library

"There are no dumb questions!" student at reference desk

 

 

That's the philosophy of reference librarians, who are here to save you time and trouble. If you get stuck, you can talk to a reference librarian at any campus library

Ask a Librarian 24/7 Chat


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You can type your question directly into this chat window to chat with a librarian. Your question may be answered by a reference librarian from Berkeley, from another UC campus, or another academic library elsewhere in the US.  We share information about our libraries to make sure you get good answers.

If the librarian can't answer you well enough, your question will be referred to a Berkeley librarian for follow-up.

Have fun chatting!

More Help with PubMed

PubMed has a lot of help on its website, including links to YouTube tutorials.question mark photo

The Bioscience Library has a brief, printable PubMed guide [pdf].

For more sophisticated PubMed searching, you can search with MeSH (Medical Subject Headings), which is the system of specialized terms that are used to organize and classify articles in PubMed. Here's a YouTube tutorial.

Library Workshop: Research 101

Unsure how to start a paper or research project? Think maybe you could stand to brush up ostudent with laptopn search strategies?

If this sounds familiar, Library Workshop: Research 101 has you covered. This interactive tutorial explores six stages of the research process. You can view it from start to finish, or focus on specific sections as needed:

1: Begin Your Research

Starting strategies, from choosing a topic to finding the right keywords.

2: Knowledge Cycle

The publication timeline, scholarly vs. popular sources, and differences in academic disciplines.

3: Finding Books

Search for books and other items in OskiCat, Cal's local library catalog.

4: Finding Articles

Locate and access articles in library research databases.

5: Make Citations

How to cite your sources correctly.

6: Basic Search

Common techniques for constructing searches that yield useful results.

7: Advanced Search

Specialized search strategies for targeting specific topics.

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