Check out the new bioinformatics video tutorials, developed by the MIT Engineering and Science Libraries and Harvard’s Countway Library of Medicine. These tutorials aim to bring research help to your desktop.

The first installment of BITS covers the UCSC Genome Browser, which contains reference sequences and working draft assemblies for a large collection of genomes. The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering at UCSC.

Watch these videos to learn more about the UCSC Genome Browser. Learn how to retrieve DNA sequence, display and configure the annotation tracks, identify gene intron-exon boundaries, and use the BLAT tool.

BIT 1.1: UCSC Genome Browser: Getting DNA Sequence (3:57)
BIT 1.2: UCSC Genome Browser: Using Annotation Tracks (5:47)
BIT 1.3: UCSC Genome Browser: Locating Intron-Exon Boundaries (4:56)
BIT 1.4: UCSC Genome Browser: Searching with BLAT (6:14)

Learn at your own convenience and your own pace.

Find the Bioinformatics Tutorial Series (BITS), and many other tutorials, on the video tutorials page.

Questions? Email ask-bioinfo@mit.edu.

Were you unable to attend a Libraries’ sponsored IAP session this January? Wish you could have attended the March workshops on Building an EndNote Library, or the recent class on Google Maps?

The Libraries are pleased to unveil recordings of our popular workshops. The sessions were recorded in cooperation with Academic Media Production Services (AMPS) and are viewable both on and off campus with your MIT Certificates.

To see a list of recordings, go to the MIT Libraries Video Tutorials page and scroll down to Videos of Recent Workshops.

Contact Angie Locknar with any questions.

Citation Surfing: Using Databases to Track Article Citations
Michael Noga

Learn how to find and use information more effectively in our hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

**NOTE that different events will be happening throughout the month of April and early May.**

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, May 2, 12pm (noon)

Have your ever used the Web of Science to find citations? Have you used Google Scholar? Perhaps you have used citation links in journal articles. This session will explore the different ways you can use citation searching to identify literature on a subject.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

The MIT Libraries now subscribe to over 2,000 e-books from CRC Press, adding 7 new subject collections, including chemistry, engineering, energy, materials science and polymers, nanotechnology, and mathematics.

To search all titles available to the MIT Community, visit CRCnetBASE, or go to each individual subject collection to browse titles.  With time, we will add records of these items to our catalog, Barton to make finding them easier.

List of individual CRCnetBASEs added to our collections:

• CHEMLIBnetBASE (all areas of chemistry, about 350 titles)
• CLEANTECHnetBASE (bio-energy, clean technology, renewable energy,…)
• ENGnetBASE (all areas of engineering, almost 900 titles)
• MATHnetBASE (mathematics, almost 300 titles)
• MATERIALSnetBASE (materials science, over 200 titles)
• NANOnetBASE (nanoscience)
• POLYMERnetBASE (polymers)

Previously subscribed: Combined Chemical Dictionary and CRC Handbook of Chemistry and Physics through CHEMnetBASE.

To see other e-books provided by the MIT Libraries, go to Vera, and select the subject “E-Books.”

Introduction to Google Maps API (5 - 6 pm)

Googler Pamela Fox will give a whirlwind tour of the Google Maps API and KML, teaching the basics of each and showing off some of the really fun applications of them (like campus maps, interactive panoramas, and fantasy worlds).

Google Maps Codelab (6 - 7 pm)

Interactive codelabs in the topics addressed in the Introduction to Google Maps API. Codelab participants should come prepared with basic Javascript or XML experience, and will find debugging the Maps API easier if they have Firebug installed.

Both sessions will be held in 14N-132.

Food will be provided

Email gishelp at mit.edu if you have questions.

Have you even been in Building 10 and wondered what exactly Vannevar Bush did to get the Bush Room named after him? Have you ever looked at the names on the buildings around Killian Court and asked yourself, what’s so great about Chladni, Gramme, and Regnault that their names are carved alongside Darwin, Faraday, and Ben Franklin?

Wonder no more! They’re just a few of the more than 5000 scientists and mathematicians profiled in the Complete Dictionary of Scientific Biography. All 18 volumes of the classic work Dictionary of Scientific Biography are now available online, supplemented by the eight volumes of the recently published New Dictionary of Scientific Biography, which adds almost 800 new authoritative profile.

Bioinformatics for Beginners
Amy Stout, Courtney Crummett

Learn how to find and use information more effectively in our hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

**NOTE that different events will be happening throughout the month of April and early May.**

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, April 18, 12pm (noon)

Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

Managing your references: Overview of EndNote, RefWorks and Zotero
Remlee Green, Mathew Willmott

Learn how to find and use information more effectively in our hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

**NOTE that different events will be happening throughout the month of April and early May.**

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, April 11, 12pm (noon)

Using citation management software to create and maintain a collection of references is becoming more common and important in today’s academic world. This session will focus on EndNote, RefWorks, and Zotero, the three major options for bibliographic software at MIT.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

Learn how to find and use information more effectively in these hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Fridays in April (and May), 12pm (noon)

April 11: Managing your references: Overview of EndNote, RefWorks and Zotero
Remlee Green, Mathew Willmott

Using citation management software to create and maintain a collection of references is becoming more common and important in today’s academic world. This session will focus on EndNote, RefWorks, and Zotero, the three major options for bibliographic software at MIT.

April 18: Bioinformatics for Beginners
Amy Stout, Courtney Crummett

Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

April 25: EndNote Basics
Peter Cohn, Anita Perkins

EndNote is a “personal bibliographic software” package which allows you to create and manage a database of bibliographic references.

May 2: Citation Surfing: Using Databases to Track Article Citations
Michael M Noga

Have your ever used the Web of Science to find citations? Have you used Google Scholar? Perhaps you have used citation links in journal articles. This session will explore the different ways you can use citation searching to identify literature on a subject.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

On Wednesday and Thursday, March 26 & 27, sections of the basement in Hayden Library will be closed to the public. Workers will be removing materials with mold damage and cleaning the shelves in the affected areas. Mold remediation will be done by Munters, a firm that specializes in recovery, following protocols that have been reviewed by MIT Environmental Health & Safety. The mold-damaged items will be discarded and replaced by materials donated from other libraries.

Staff at the Hayden Desk will be able to retrieve many items in the closed-off area while the work is in process, but some items will not be available until the work is complete. Hayden Desk staff will retrieve materials from anywhere in the basement for anyone who is concerned about venturing into the area while mold remediation efforts are in process. Technical questions can be referred to Nancy Schrock, the Libraries’ conservator, at 452-4064 or nschrock@mit.edu.

On Friday, April 18, from 1-3pm the MIT Libraries will host a community celebration in honor of the opening of the Maihaugen Gallery. The newly constructed exhibit space will showcase some of the extraordinary items from the MIT Libraries’ collections.

The first exhibit: A Celebration of Gifts will feature rare and unique items donated to the Libraries by MIT alumni, faculty, and friends. Among the treasures that will be exhibited to the public for the first time are items from the collection of the Institute’s founder, William Barton Rogers. The exhibit will also include original notebooks from Harold “Doc” Edgerton, several rare books including a first edition of Walt Whitman’s Leaves of Grass, and a book of illustrations from the 1553 volume Historiae animalium by Konrad Gesner. Also featured will be items from the personal library of architect Charles Bulfinch, balloon prints from the Vail Collection, books by architect Santiago Calatrava with original artwork, works from the Aga Khan Program for Islamic Architecture, and other items given to the Libraries.

The new facility is located adjacent to the Institute Archives (14N-118). The celebration will begin at 1pm with remarks by Ann Wolpert, director of the Libraries. Refreshments will be served. Please join us!

Photos by: L. Barry Hetherington, Bottom photo: Copyright Harold E. Edgerton 1992 Trust

Donna Kirking, a representative from EndNote, will offer basic-intermediate training on building a library and using Word with EndNote. All members of the MIT community are welcome to attend one or both sessions, and no sign up is necessary.

2:00-3:30: Building an EndNote Library

3:45-5:00: Using EndNote in Word

Training will be held in the Libraries’ Digital Instruction Resource Center (DIRC), in 14N-132. If you have EndNote installed on a laptop, you’re welcome to bring it and follow along. If you’re already an EndNote user, feel free to come with questions.

Questions? Contact cite-help@mit.edu.

If you’re unable to attend the training, you may want to check out our guide on EndNote at MIT, or the Overview of Bibliographic Software.

Need analysis of medical technology markets? Want data on on biotech and pharmaceutical deals? Try Windhover’s MedTech Insight and Strategic Transactions Database, now available through the MIT Libraries. Access both via the Windhover Archives platform at: http://libraries.mit.edu/get/windhover (certificates required).

• MedTech Insight includes analyses of US markets for a variety of therapeutic categories and medical technologies. Articles can be browsed or retrieved by keyword search.
• Strategic Transactions Database provides data on biotechnology, pharmaceutical and device deal making activity, from 1991 to date. To access Strategic Transactions at the platform, highlight Browse or Search in the navigation bar and then choose Deals.

Note: MIT certificates are required (even on-campus) and access is limited to two simultaneous users. Feel free to contact Maggie Bartley, mbart@mit.edu with questions or comments.

MIT Geoweb provides a web interface to search, view, and download GIS data and view metadata from the MIT Geodata Repository, an international collection of GIS data maintained by MIT GIS Services.

http://web.mit.edu/geoweb

Questions, comments, or suggestions: email gishelp@mit.edu

Did you know there are many ways to access the licensed copies of e-journals that we subscribe to? The methods below work from anywhere as long as you have MIT certificates installed or are using MIT’s VPN client.

1. Go to Vera and type the title in the search box.
(Our database called “Vera” has been the primary way to access e-journals since 2000).

2. Go to http://libraries.mit.edu/ejournals and type the title in the search box
(This page is part of a new version of Vera, which is currently in beta).

3. Go to our Full Text Finder: http://libraries.mit.edu/fulltext
If you have a complete citation to an article, you can enter it and go directly to the article (in most cases).

4. Search for an article using Google Scholar. Set your preferences to say that you want the MIT Libraries links. Then follow links that say “full text - MIT Libraries.” For details, see Making Google Scholar work for you. (Google Scholar does not index ALL of our licensed e-journals, so try Vera if you don’t find it in Google Scholar).

5. Go directly to the journal’s web site. Insert our proxy server string by typing it in front of the URL and then reload the page. See: Manually inserting the proxy string.

6. Install our bookmarklet in your browser toolbar. Go to the journal web site and then click on the bookmarklet, which inserts the proxy string automatically. See Inserting the proxy string with a bookmarklet.

7. In Firefox, install our LibX toolbar. Go directly to a journal’s web site. Right click on the page and select “reload this page via MIT Libraries’ proxy.” See a video of how this works. (A version of LibX for Internet Explorer is under development).

8. In Firefox, install our search toolbar widget for Vera:
see: http://mycroft.mozdev.org/download.html?name=MIT+vera
For more info, see: Search for journals in Vera with the new Firefox search bar.

9. If you install MIT’s VPN client and log in before you visit a journal’s web site, you will be able to access our subscription e-journals. (It will see you as if you are coming from ON CAMPUS). See VPN: an alternative off-campus option. With this method, #5, 6, and 7 above are not needed.

10. Within our licensed databases, such as Web of Science or SciFinder Scholar, look for buttons that say “Get this - MIT”. Those links will take you directly to our licensed copies of articles using our “open URL resolver” which is called SFX. To see a list of our licensed databases, see Vera shortcuts.

—

These methods work only if you are ON CAMPUS:
1. Go to our Barton catalog and search for the title. Links in Barton work only from ON-CAMPUS . (A project to change this is in the works).

2. Go directly to the journal’s web site.
If you’re ON campus, and we have a subscription, you’ll get in (in most cases).

There has been an explosion of open source and free mapping tools. In this talk we will offer a brief look into the neogeographer’s world of online mapping.

WHEN: Wednesday, January 23, 2 -3 pm

WHERE: 4-231

Complete listing of GIS workshops

Image source: http://www.joomla.org/content/view/4410/74/

Have your ever used the Web of Science to find citations? Have you used Google Scholar? Perhaps you have used citation links in journal articles. This session will explore the different ways you can use citation searching to identify literature on a subject. The concept of citation searching has been around for over 50 years, but it has evolved with the technology. Several methods will be explored including the Web of Science, Journal Citation Reports, Google Scholar, Research Index (CiteSeer), ScienceDirect, PROLA, GeoScienceWorld, and Citation Bridge (US Patents). Come and share your own citation searching methods.

WHEN: Monday, January 28, 2 -3 pm

WHERE: 14N-132, DIRC

Contact Michael M Noga with any questions.

Learn about how to find chemical properties and other new exciting features in SciFinder Scholar by attending this hands-on virtual lab! Go to the link below to join the session, or see more information about the training session, including its agenda.

WHEN: Friday, January 25, 10 am - 12 pm

WHERE: Your office! (via WebEx teleconference)

https://casevents.webex.com/casevents/k2/j.php?ED=90618307&UID=528470787

Training session password: mitscholar

Teleconference: Call 866-469-3239 (Tollfree in US/Canada) or 650-429-3300 (US/Canada Direct)

Session Number: 665 905 421

Web: http://libraries.mit.edu/guides/cheatsheets/sci-finder/index.html

Contact Erja Kajosalo with any questions.

Learn how to use MIT Libraries’ databases and the Internet to uncover energy-related industry overviews, market research, and country statistics.

WHEN: Friday, January 25, 1 - 2 pm

WHERE: 14N-132, DIRC

Enrollment is limited to 27 participants and is on a first-come, first-served basis.

Contact Alex Caracuzzo with any questions.

Are you curious about already-awarded grants in your field of study? Wondering where grant money goes and what for? Want to know what grants NASA, NSF or NIH are funding? This hands-on session will covers the primary web resources of grant funding in the sciences. Attendees will find out what information these resources cover, what data they contain, and how to navigate them. Although this session will not cover how to write a grant, knowing where the money goes will improve your research and grant writing skills.

WHEN: Thursday, January 24, 11 am - 12 pm

WHERE: DIRC, 14N-132

Enrollment is limited to 20 participants and is on a first-come, first-served basis.

Contact Courtney Crummett with any questions.

Make the Libraries work where you do! Search the MIT Libraries from your Facebook or Google page. Learn how the LibX library toolbar can speed up your research. Discover resources at your own pace with web tutorials. Increase Firefox capabilities with cool tools, tips, and tricks.

Come hear about some new web tools that may help you work more efficiently. Learn to organize and share your references, and search seamlessly between library resources and other web sites.

We will demo: del.icio.us, Facebook, Zotero, library-relevant Firefox extensions, and more.

WHEN: Wednesday, January 23, 12 - 1 pm

WHERE: 14N-132, DIRC

Enrollment is limited to 20 participants on a first-come, first-served basis. Contact Remlee Green to sign up or with questions.

Learn about chemical reaction searching in SciFinder Scholar by attending this hands-on virtual lab! To attend this WebEx session with CAS trainer, go to the link below for more information about the training session, including its agenda, or to join the session.

WHEN: Friday, January 18, 10 am - 12 pm

WHERE: Your office! (via WebEx teleconference)

https://casevents.webex.com/casevents/k2/j.php?ED=90618292&UID=528470012

Training session password: mitscholar

Teleconference: Call 866-469-3239 (Tollfree in US/Canada) or 650-429-3300 (US/Canada Direct)

Session Number: 661 033 867

Web: http://libraries.mit.edu/guides/cheatsheets/sci-finder/index.html

Contact Erja Kajosalo with any questions.

The National Center for Biotechnology Information (NCBI) Entrez family of databases is the foundation of knowledge for molecular level bioscience research. Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

WHEN: Thursday, January 10, 4 - 5 pm
Friday, January 18, 12:30 - 1:30 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 20 participants.

Contact Amy Stout with any questions.

Scientists from BIOBASE will do training on these bioinformatics databases that include Proteome, TransFac, TransPath, and ExPlain, with focus on the new database ExPlain and updates on new features for all of them. The MIT Libraries subscribes to these, and you will find them on VERA. There will be a 2 hour training session plus hands-on time to work on your own research if you wish.

WHEN: Thursday, January 17, 1 - 3 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 30 participants.

Contact Louisa Worthington Rogers with any questions.

EndNote is a “personal bibliographic software” package which allows you to create and manage a database of bibliographic references.

Attendees will create a personal database of cited literature by importing references from resources such as Barton, Web of Science, PubMed, & other sources of published literature. Your database can be used to automatically generate in-text citations and bibliographies in your manuscripts. It can also help you organize and manage your PDF files.

WHEN: Thursday, January 17, 5 - 6 pm
Wednesday, January 23, 5 - 6 pm
Wednesday, January 30, 12 - 1 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 20 participants.

Contact Howard Silver with any questions.

RefWorks is a web-based resource designed to help you to organize references and create a bibliography. RefWorks allows you to search, retrieve relevant citations, and build your bibliography. It allows users to create individual or group accounts, and makes it easy to write papers, or post your results to web pages.

WHEN: Wednesday, January 16, 4 - 5 pm
Tuesday, January 22, 4 - 5 pm
Thursday, January 31, 4 - 5 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 20 participants.

Contact Howard Silver with any questions.

While you won’t come out of this session qualified to be a patent attorney, you will be able to successfully find patent references from all over the world and know how to obtain patent text and diagrams. The session will be a hands-on practicum that will help de-mystify the patent literature and expose attendees to key resources for finding patents through free resources available on the web.

WHEN:
Wednesday, January 16, 5:30 - 6:30 pm
OR
Tuesday, January 22, 12 - 1 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 25 participants.

See http://libraries.mit.edu/patents for more information. Contact Darcy Duke with any questions.

Searching for molecules is possible in PubMed! Come to this session to learn how to find articles about chemicals, drugs and other substances in PubMed by using subject headings and other advanced techniques. We will also demo the NCBI PubChem Substance database that allows you to search by common name, systematic name, molecular weight and more.

WHEN: Wednesday, January 16, 12 - 1:30 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 30 participants.

Contact Louisa Worthington Rogers with questions.

Information on energy is everywhere! How do you find the scientific and technical information you need and keep on the cutting edge of what is published? Attend this hands-on session to find out.

WHEN: Tuesday, January 15, 4 - 5 pm

WHERE: 14N-132, DIRC

Enrollment is limited to 25 participants on a first-come, first-served basis.

Contact Angie Locknar with any questions.

Using citation management software to create and maintain a collection of references is becoming more common and important in today’s academic world. These software packages allow users to search databases, retrieve relevant citations, and build a bibliography to be added to a paper or thesis or stored for future reference. But which software package should you use, and how do you get started? This session will focus on EndNote, RefWorks, and Zotero, the three major options for bibliographic software at MIT. We will include a discussion comparing and contrasting the three softwares, and we will introduce some of the basic concepts and functionality of each program.

WHEN: Tuesday, January 15, 12 - 1 pm
Thursday, January 24, 12 - 1 pm
Monday, January 28, 5 - 6 pm

WHERE: 14N-132, DIRC

20 computers are available on a first-come, first-served basis. Attendees are welcome to bring their laptops.

Contact Remlee Green with any questions.