The Laboratory for Optical and Computational Instrumentation (LOCI) is a biophotonics laboratory under the direction of Kevin Eliceiri that develops advanced optical and computational techniques for biological investigations. LOCI collaborates with over 30 UW departments on problems involving the imaging of live dynamic events. It is also involved with various efforts to promote access to research data including a recent collaboration with the UW Libraries’ Forward project. Forward is a portal that allows users to search and browse the library catalogs of the entire UW system as well as other resources like digital images. The goal of the LOCI/Forward collaboration was to provide a means for discovering biological image data by automatically incorporating LOCI datasets into the Forward catalog.

In order for Forward to create catalog records for LOCI datasets, it was necessary to find areas of overlap between the metadata model LOCI employs to store information about microscopy data and the standards Forward uses to describe items in its catalog. LOCI uses the OME-XML model developed by the Open Microscopy Environment (OME) to record important information about image data. The OME-XML model allows information about experiments, experimenters, instruments, and images to be stored along with image files. At LOCI, much of this information is automatically collected from the software and hardware used to acquire the images. Forward uses very different standards including METS and MODS, both maintained by the Library of Congress, to describe the items in its catalog. Thus, it was necessary to identify mappings between equivalent elements in the OME-XML model and the METS/MODS standards. Combining OME-XML and METS/MODS also allowed the strengths of each standard to be utilized. While OME-XML captures detailed scientific information including instrument settings, the METS/MODS metadata allowed descriptive and administrative parameters such as dataset permissions to be stored as well.

It was also necessary to modify LOCI’s image acquisition software to allow researchers to submit datasets to Forward in as few steps as possible. A checkbox was added to the software’s interface to make it possible for users to opt in to sharing data with Forward. When this box is checked, information stored in OME-XML is automatically transformed into a METS/MODS record that Forward can easily process. Another procedure was developed to upload this METS/MODS record and a sample image to a server that Forward accesses on a regular basis. Forward then uses these files to generate a catalog record for each dataset.

With this workflow in place, LOCI researchers have a relatively simple way to expose their data to a wider audience of potential users. Anyone searching or browsing Forward can now discover biological image data alongside traditional library catalog items. In addition, the LOCI/Forward collaboration may serve as a model for other UW researchers, laboratories, and projects interested in having data or other research products appear in Forward.

Typically, the care and keeping of graduate student theses is a fairly routine process. So long as students follow formidable formatting requirements governing details from page headers to paper quality, libraries are usually well-equipped to preserve, catalog, and store them for the benefit of future scholars. In some disciplines, however, theses come in a wild menagerie of forms, and capturing the scholarly record is more an enigma than a routine.

Melissa Cooke, graduate coordinator at the UW-Madson Art Department, knows this well, as art students’ theses, though sometimes made of paper, bear little similarity to the neatly bound volumes resting peacefully in the basement of Memorial Library. Rather than submitting a typed document, master’s and master’s of fine art candidates stage exhibitions of their work, ranging from mounted paintings to interactive installations, in local gallery spaces. Though vibrant contributions to the UW’s body of academic work, once exhibitions end, little more than nail holes remain to document their occurrence. Several years ago, the department took a step toward remedying this situation by collecting digital photos from students following their exhibitions. While they now had a simple solution for capturing evidence of student work, preserving it and distributing it to the academic community presented perplexing challenges.

When the department decided that a web-based collection would serve as an ideal showcase for these images, Melissa called upon a group of graduate students in Dorothea Salo’s Spring 2011 Digital Curation course for support. Dani Taylor, Beth Fox-Corbett, Luke Leither, Liz Krznarich and Samuel Rudin evaluated several software products and campus services as potential platforms for this collection, and ultimately recommended the UW Digital Collections Center (UWDCC). While some of the other platforms offer slicker graphics and more customizable features, UWDCC’s service requires no technical maintenance by its clients and comes at the unbeatable price of…free. Plus, UWDCC’s array of existing collections and integration into the campus library system offers some assurance that the platform will continue to exist well into the future.

Since a collection platform alone – even a full-service option like UWDCC – doesn’t ensure a long and happy life for digital images, the students also created a simple plan for managing the files within the department, including standardizing file formats and names, recording metadata, handling copyright permissions, storing/backing up files, and checking stored files for errors.

With a solid plan in place at the end of the semester, implementation was placed into the hands of group member Liz Krznarich, who will spend the summer working with Melissa and the capable crew at UWDCC to bring the online collection to life, prepare files for long-term preservation, and create an instruction manual to guide future curators of the collection. Come fall, a new graduate coordinator will fill Melissa’s shoes as she departs for new adventures; after a bit of training with Liz, this person will take charge of the collection and help to ensure that art students’ exhibitions remain on permanent display.

Part I: Rigor, Relevance & Practice

Part II: A Socio-Technical Vision

(I especially like the idea of posting raw data sets with a little explanation as potential publishing in and of itself)

The theme of the 2009 meeting is “Real Data in a Virtual World” — appropriate for the content to be presented and its delivery! Starting on Monday, October 5 and running through Friday, October 9, ICPSR will deliver 20 sessions related to social science data and related content, tools, quantitative training/literacy, and still other resources associated with ICPSR and its partners. ICPSR staff will also host several live chats.

We encourage you to visit our meeting site – http://www.icpsr.umich.edu/icpsrweb/ICPSR/or/ormeet/index.jsp – and begin registering for the webinar Sessions & Presentations.  In addition, the first 200 attendees to register for the ICPSR virtual meeting (see the Registration page) will receive a Labtec headset and a packet of ICPSR promotional materials for your institution (limit one headset per person)!

This conference is FREE and open to everyone.

(Thanks to Cindy Severt for the heads up)

MathBio 2008 Highlights

Conversation with Drs. Kawaoka & Katze