Last year the SRF team was invited to take part in a symposium in Boston called Building Linked Web Communities in Biomedicine to Accelerate Research. The meeting highlighted a new framework designed to facilitate the exchange of information between diverse scientific disciplines. The framework’s creator, Tim Clark of Harvard Medical School, described the Science Collaboration Framework (SCF) as a tool intended for use by biomedical knowledge environments like Schizophrenia Research Forum. As stated on the SCF website, “It enables researchers to publish and discuss on-line content such as articles, news, and perspectives, and to provide shared semantic context for this content using established scientific vocabularies and automated text mining.” So, rather than the traditional silo model where one set of researchers in a specific field has no easy way of knowing if a piece of data or even a theory might be connected to another area of study, the SCF allows for fluidity. For example, content like news articles and research papers could be published to a specific site like SRF. During the publishing process a common format and shared annotation method would be employed. This allows end users associated with other knowledge environments like the Alzheimer Research Forum (ARF) to access overlapping information. The shared data or information would be easy to discern via a search function on both SRF and ARF.
The Resource Description Framework (RDF) is the key to making shared information possible. RDF, created by the World Wide Web Consortium (W3C) is, “…a language for representing information about resources in the World Wide Web. It is particularly intended for representing metadata about Web resources, such as the title, author, and modification date of a Web page, copyright and licensing information about a Web document, or the availability schedule for some shared resource.” The SCF uses Drupal, a content management system, as its platform. Interestingly, Drupal allows developers to leverage existing functionality in the Drupal software to create new modules. These modules interact with the SCF and Drupal directly, both of which are Open Source and can be downloaded free of charge. Tim Clark’s technical team has already created and published modules for public use, and they encourage others to download the framework and start using it to create modules and share with other knowledge environments.
Unless you have been living under a rock for the past few years, you have become surrounded by mobile Internet devices like the iPhone and Blackberry, exploited initially by teenagers (like my son) to play games or busy business people to check emails. Only recently have the applications become useful to a much wider audience, and they appear to have finally reached scientists.
The-Scientist.com recently published an article entitled “iPhone apps every biologist needs” [Free Site Registration Required for Access]. Author Balachandar Radhakrishnan, a slime-mold loving Ph.D. student at the University of Kassel, Germany, writes, “[I]t is high time for academics to embrace the next technological wave that is mobile computing. …[E]merging mobile computing platforms will allow researchers to access and manipulate information no matter where we are.”
Radhakrishnan covers 10 mobile applications that can be used by the researcher on the go, ranging from an app that shows 3-D molecular structures to one that is essentially a lab timer. Many of them appear to be free and the rest are reasonably priced. These applications will now help us get things done, instead of procrastinating…as with those mobile video games we like to play so much. ;-)
Here are a couple of examples:
“iCut DNA: Molecular biologists can typically remember the restriction sites of a couple of enzymes, but it’s tough to memorize the sites for more than 10 or so. That’s where iCut DNA comes in. This app brings New England Biolab’s Restriction Enzyme Database (REBASE) of around 2,000 enzymes onto your mobile device, allowing you to look up the recognition sequence of any type II restriction enzyme available on REBASE. The interface is seamless, and tracking down any enzyme is a snap. The app also lets you to select molecules based on enzyme name (with a handy auto-suggest drop down menu that narrows down enzymes based on your text input) or recognition sequence (again with auto-suggest drop down entries).
Price: $4.99“
“PubSearch Plus: PubSearch Plus gives you the ability to search PubMed from the comfort of your iPhone or iPod Touch, and lets you read and e-mail selected publications. Though the iPhone screen isn’t ideal for viewing high-resolution images in research papers, it definitely helps when you’re looking up a specific piece of information from a particular paper. The app also supports EZProxy so you can connect to journals that are available only through institutional access.
Price: $1.99“
