Search & Peer Publication Updates

If you perform certain literature searches on a regular basis in your specialty, you should be using automatic searches to do this for you.  Most of the major scientific databases have features that allow you to set the terms of a search and have your results sent to you via e-mail monthly, weekly or even daily if you wish.  In PubMed, you can save searches by using MyNCBI.  I have weekly search updates for all publications from our faculty at our medical school, and monthly searches for protein-protein interaction papers.

There are a number of Web applications that allow you to develop and explore your professional connections with other researchers.   LinkedIn is good for job hunting and resume dispersal.  ResearchGate has means by which researchers can share results, even when those results are not significant enough to publish.  My favorite scientific networking site is BioMed Experts, a free feature developed by the Collexis team.  BioMed Experts will send you notifications every time a member in your publication circle of co-authors publishes a new paper.  It’s a great way to keep up with the work of co-authors who may be geographically distant from you.

Citation Management with Zotero

There is absolutely no reason why anyone writing a research paper should still be manually constructing bibliographies.  Excellent software is available for citation management that will make construction of your manuscripts’ reference section a breeze.  Even if you can’t afford some of the licensed reference management packages on the market, you can still organize your citations with Zotero.  Zotero is a Mozilla Firefox browser add-on that allows you to manage citations and build bibliographies.  It also enables you to synch reference libraries across multiple computers and create shared libraries with colleagues.  Zotero works within your browser to export citations from PubMed, Google Scholar, Web of Science and PsychInfo.  Even if you have other reference management software such as RefMan or EndNote, Zotero will integrate citations into these libraries.

File Hosting and Synching Sites

If you work on two computers (one at home and one at your lab), you know it can be annoying trying to keep the current version of a manuscript on each machine.  Sometimes you may forget which version of a paper was updated more recently.  Instead of using a flash drive to carry your papers back and forth to work, you might want to try using a free file-hosting site.  There are many good ones, and a comparison can be found at Wikipedia.  Many of these servers will allow you to maintain a free account with a decent amount of storage space.  I’m currently using Dropbox.  I love the fact that I can work on a manuscript at home, then go to work and have the site automatically update the paper on my work computer.   Dropbox accounts are hosted on their server and linked to your e-mail address.  Any file you put in your Dropbox folder on each computer will be updated to the most current version when your computer is turned on and connected to the Web.  You can also create shared folders with other Dropbox users and you can get extra storage space for recruiting new users to the site.

Electronic Protocols

It used to be difficult to find protocols for new methods and even more difficult to find protocols for more old-fashioned techniques such as cell stains and fixatives.  Now there are a number of protocols available on the Web and collected at a number of free sites.  My favorite site for visual lab methods is BenchFly.  (That’s not a surprise, is it?)  The site has made its protocols easy to find by creating categories (instruments, chemical techniques, DNA/RNA-related, etc.).   I like the fact that very short, seemingly basic techniques are featured alongside more complicated methods.  I was mesmerized by a video demonstration for pulling capillary tubes, recent winner of a BenchFly contest.  BenchFly also has a useful Products section where users can search for reagents and other lab products, plus a lot of fun features such as user polls and a protocol for making an Old Fashioned.

Bioinformatics Hubs

Most researchers at some point find themselves needing to find a protein or RNA sequence, or to find tools for calculating oligo properties, sequence alignment or structure viewing.  While the obvious choice is to start searches at the NCBI or EBI websites, there are two other tools that I rely on heavily to find just the right bioinformatic database or resource.   The first is University of Pittsburgh’s Health Sciences Library System’s Online Bioinformatics Resources Collection (OBRC).  This collection includes over 2000 resources, including those featured in the Nucleic Acids Resources databases and web servers issues.  Search results are clustered by category making them easier to sort through.

.

Pamela Shaw received her Bachelor’s degree in neuroscience from Oberlin College and worked as a neuroanatomy & histology lab tech for many years at Loyola University and Northwestern University.  Upon completion of her Master’s degree in Library & Information Sciences from University of Illinois, she was hired as Biosciences Librarian at the Galter Health Sciences Library at the Feinberg School of Medicine at Northwestern University.  She was awarded a National Library of Medicine Informationist Fellowship and is using it to complete a second Master’s degree in Computational Biology & Bioinformatics at Northwestern University.

.

Working in a library in an academic institution is fulfilling but can be frustrating.  At the library, we get many general questions such as “What are the library’s hours?” or “Where can I scan this document?”  However, our researchers don’t know all the resources the library has to offer.   Here’s a list of the top library resources that users should be putting to better use.   Since I work in a health sciences library affiliated with a medical school, some of the resources may vary slightly from other libraries, but most academic libraries will offer similar tools and services.

THE LIBRARY ITSELF

Sounds obvious, right?  Most of the users of the library are either students who want to study (in our case they are medical or graduate students) or visitors.   Most of our other users never set foot in the library.  They get all the information they need electronically through journal and database subscriptions paid for by the library and accessed through the library’s website or via proxy from databases such as PubMed.   This is great and we are happy that our users can access literature easily without having to come to the library itself.   But…

What our users don’t know is that many academic libraries offer space for the research community to reserve and use:  small conference rooms with computer hook-ups and video screens and/or computer classrooms that offer teaching space for hands-on computer training.   Many library computers are equipped with specialized software.  Also, our users can check out computer peripheral equipment such as Mac adaptor cables, laptops and projectors.

THE LIBRARY’S WEBSITE

This again seems obvious, but our library has done extensive usability testing on our website and we know that our users rarely start their searches at the library’s web pages.  This is fine, because information technology staff works hard to make links from databases such as PubMed and Web of Science to full text articles as seamless as possible.   But users don’t know that academic libraries have a lot of great content on their websites, such as step-by-step guides and tutorials on how to conduct literature searches or manage citations, writing guides, lists of core titles in specific disciplines, electronic textbooks and specialized databases–there’s a lot more out there than just PubMed and Google Scholar.

LICENSED SOFTWARE OFFERED BY THE LIBRARY

Many academic libraries pay for software that can save users’ departments loads of money in individual subscriptions.   Libraries may provide users with statistical packages, graphics editing packages or even video editing software.  Medical libraries often pay subscriptions for dissection guides, physical examination guides and atlases that are not available through open sources.  Some libraries pay for specialized software such as biological pathway analysis or microarray analysis packages.  Many libraries also pay for reference management software (such as EndNote or RefMan).

LIBRARY INSTRUCTION

You should check to see if your academic library offers classes or workshops.  Many libraries teach classes in the use of citation management software (including free resources like Zotero); creating scientific posters or slide presentations; efficient search techniques for MEDLINE, Web of Science, SciFinder Scholar, Google Scholar; or GIS (geographical information systems).  Additionally, a number of research libraries employ bioinformatics experts who teach classes on finding and aligning protein or nucleotide sequences (BLAST), using genome browsers and structure tools.  These experts are sometimes librarians with a second degree in the sciences (PhDs or Master’s degrees in biochemistry, molecular biology, neuroscience or, in my case, bioinformatics).  They may also be PhD non-librarians who are working from offices in the library—a large number of my bioinformatics colleagues don’t have library degrees at all, but teach classes and have offices in the library.

YOUR LIBRARIAN

Okay, you probably could have predicted that I would make one of those “Librarians are so cool!” statements…so I will.  One of the reasons I decided to leave the bench and become a librarian was that I had met so many really fantastic librarians throughout my academic career.  Librarians work with faculty, staff and students across many departments.  This makes the library an institutional core facility, just like a microscopy & imaging core facility or a biostatistics core facility.  Often librarians can make connections between users who have shared needs or skills.  One of the greatest compliments I ever received was from a user who said that he loved working with librarians because “they connect people to resources, even when those resources are other people”.  I know that I can’t answer every question about managing large sequence datasets or untangling a mass of disparate microarray platform probe identifiers, but I often have a suggestion for my users on whom they should contact for expert assistance, even if it’s not me. The library is probably the most budget-friendly core facility, since most librarians don’t charge their users by the hour for research consultations.

There are lots of things your library has to offer that you never knew about, so you might want to pay a visit or make a call to your librarian—chances are good that they can help make your research more efficient.

Pamela Shaw received her Bachelor’s degree in neuroscience from Oberlin College and worked as a neuroanatomy & histology lab tech for many years at Loyola University and Northwestern University.  Upon completion of her Master’s degree in Library & Information Sciences from University of Illinois, she was hired as Biosciences Librarian at the Galter Health Sciences Library at the Feinberg School of Medicine at Northwestern University.  She was awarded a National Library of Medicine Informationist Fellowship and is using it to complete a second Master’s degree in Computational Biology & Bioinformatics at Northwestern University.