MIT Libraries News

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.

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.

Please be aware of the scheduled upgrade which will result in limited access to the IEEE site. This is the official message from IEEE:

Dear IEEE subscriber,

We are writing to inform you that an IEEE Xplore environment upgrade is scheduled for Saturday, 15 March, 2008. During this upgrade, the system will be unavailable for up to four (4) hours beginning at approximately 10:00 am EDT (UTC/GMT - 4 hours). We apologize for any inconvenience this may cause.

If you have any questions, please contact us at onlinesupport@ieee.org.

IEEE thanks you for your support, and we look forward to providing you with excellent service in the years to come.

Regards,

IEEE Online Support
onlinesupport@ieee.org

MIT faculty, students, and staff have access to the Society of Automotive Engineer’s technical papers over the web again, because the SAE listened to MIT and other universities when they spoke out against the imposition of Digital Rights Management (DRM) technology.

Last spring, the MIT Libraries cancelled their web access to the (SAE) technical papers, because the society was imposing a DRM plug-in called FileOpen that seriously impeded normal scholarly use.

Professor of Mechanical Engineering and SAE fellow Wai Cheng presented MIT’s concerns at the SAE’s Publication Board meeting in April 2007, which resulted in an immediate stay of DRM implementation on university campuses, and ultimately (November 2007) in a changed policy: FileOpen would not be required for university access to the SAE Digital Library.

While the MIT Libraries have not been able to get all the assurances we would like regarding SAE’s plans for implementing other DRM tools in the future, after consulting with faculty we have decided, as Professor Cheng put it, to “work with SAE in good faith,” reentering what we hope will be a productive partnership.

Access to SAE technical papers (requires MIT certificates on and off campus).

Details about access to SAE technical papers

If you have comments or questions, please contact:

Tracy Gabridge, Co-Head, Engineering & Science Libraries, tag@mit.edu

Ellen Finnie Duranceau, Scholarly Publishing & Licensing Consultant, MIT Libraries, efinnie@mit.edu

In the new episode in the series of podcasts on scholarly publication and copyright, we hear from Professor John H. Lienhard V, Professor of Mechanical Engineering here at MIT.

Professor Lienhard’s research interests include Heat and Mass Transfer and Fluid Mechanics, among other areas. He is the recipient of several teaching awards at MIT as well as research awards from the American Society of Mechanical Engineers.

He speaks about making his text book — the 3rd edition of A Heat Transfer Textbook — openly available on the web, with no charge to readers. This text was coauthored with Professor Lienhard’s father, John Lienhard IV, who is a professor at the University of Houston. It was published by Prentice Hall in two print editions in the 1980s, and remained in print until the mid 1990s.

In the podcast, Professor Lienhard, whose goal was to “explore the impact that free textbooks could have on higher education,” reflects on how the project came about and what it has meant to those who have downloaded the text, as well as to him.

Download the audio file. (15:10 minutes; 11.1 MB)

Beyond the podcast: More about A Heat Transfer Textbook

Professor Lienhard’s experiment was a remarkable innovation at the time. Certainly its astounding success could not have been foreseen back in 2001, when he and his father launched the open access version. That was before ebooks were widespread, before OpenCourseWare had made the idea of freely accessible educational materials a hot topic, and when internet connections were still slow enough that it took quite a commitment to download the 8 - 10 MB book. Yet the downloads built quickly and the rate has not let up.

One of the unexpected outcomes of this experiment with open textbook publishing was that the freely downloadable 3rd edition reached a completely different and much larger audience than the first two print editions had. The Prentice Hall editions were not marketed internationally, and the buyers were largely American college students, and American college professors. Professor Lienhard estimates that the sales were perhaps 10,000 for each of the first two print editions, a very respectable number for a printed textbook.

In contrast, the open access version has been downloaded more than 150,000 times from more than 150 countries — so the scale of the audience has increased by an order of magnitude. The recipients of the open access version are not primarily American students or professors; they are practicing engineers in the U.S. and elsewhere, and, to an overwhelming extent, students in the developing world who have little to no access to quality textbooks in engineering and science. Professor Lienhard discusses the moving testimonials he’s received from these students in the podcast.

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The other episodes in the podcast series are available on the scholarly publication website.To subscribe to the MIT Libraries’ Podcasts on Scholarly Publishing, paste this link into iTunes or another podcast reader:http://feeds.rapidfeeds.com/6772/We encourage and welcome your feedback, which you may direct to:Ellen Finnie Duranceau / Scholarly Publishing and Licensing Consultant / efinnie@mit.edu

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.

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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/

In the new episode in the series of podcasts on scholarly publication and copyright, Tracy Gabridge, Associate Head of the Barker Engineering Library (as well as a graduate of MIT), speaks about a project she is leading in which a group of librarians is determining which conferences MIT Engineering faculty publish in, whether the MIT Libraries have access to the proceedings from these conferences, and whether the digital access appears to be vulnerable.

Download the audio file. (14:35 minutes; 10.2MB)

The other episodes in the podcast series are available on the scholarly publication website.

To subscribe to the MIT Libraries’ Podcasts on Scholarly Publishing, paste this link into iTunes or another podcast reader:

http://feeds.rapidfeeds.com/6772/

This is the first series of podcasts created by the Libraries specifically for this format. We encourage and welcome your feedback, which you may direct to:

Ellen Finnie Duranceau / Scholarly Publishing and Licensing Consultant / efinnie@mit.edu
Nicole Hennig / Web Manager / hennig@mit.edu

What’s an RSS feed? How can I use it to keep up with new information in my field? We’ll show you how RSS and other current awareness tools can help you stay up to date!

This will be a hands-on session on Windows PCs. You are also welcome to bring your own laptop.

WHEN: Wednesday, January 30, 4 - 5 pm

WHERE: 14N-132 (DIRC)

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

Contact J. Darcy Duke 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.