Cyberinfrastructure Days at the University of Notre Dame

ci daysOn Thursday and Friday, April 29 and 30, 2010 I attended a Cyberinfrastructure Days event at the University of Notre Dame. Through this process my personal definition of “cyberinfrastructure” was updated, and my basic understanding of “digital humanities computing” was confirmed. This posting documents the experience.

Day #1 – Thursday, April 29

The first day was devoted to cyberinfrastructure and the humanities.

After all of the necessary introductory remarks, John Unsworth (University of Illinois – Urbana/Champagne) gave the opening keynote presentation entitled “Reading at library scale: New methods, attention, prosthetics, evidence, and argument“. In his talk he posited the impossibility of reading everything currently available. There is just too much content. Given some of the computing techniques at our disposal, he advocated additional ways to “read” material, but cautioned the audience in three ways: 1) there needs to be an attention to prosthetics, 2) an appreciation for evidence and statistical significance, and 3) a sense of argument so the skeptic may be able to test the method. To me this sounded a whole lot like applying scientific methods to the process of literary criticism. Unsworth briefly described MONK and elaborated how part of speech tagging had been done against the corpus. He also described how Dunning’s Log-Likelihood statistic can be applied to texts in order to determine what a person does (and doesn’t) include in their writings.

Stéfan Sinclair (McMaster University) followed with “Challenges and opportunities of Web-based analytic tools for the humanities“. He gave a brief history of the digital humanities in terms of computing. Mainframes and concordances. Personal computers and even more concordances. Webbed interfaces and locally hosted texts. He described digital humanities as something that has evolved in cycles since at least 1967. He advocated the new tools will be Web apps — things that can be embedded into Web pages and used against just about any text. His Voyeur Tools were an example. Like Unsworth, he advocated the use of digital humanities computing techniques because they can supplement the analysis of texts. “These tools allow you to see things that are not evident.” Sinclair will be presenting a tutorial at the annual digital humanities conference this July. I hope to attend.

In a bit of change of pace, Russ Hobby (Internet2) elaborated on the nuts & bolts of cyberinfrastructure in “Cyberinfrastructure components and use“. In this presentation I learned that many scientists are interested in the… science, and they don’t really care about the technology supporting it. They have an instrument in the field. It is collecting and generating data. They want to analyze that data. They are not so interested in how it gets transported from one place to another, how it is stored, or in what format. As I knew, they are interested in looking for patterns in the data in order to describe and predict events in the natural world. “Cyberinfrastructure is like a car. ‘Car, take me there.'” Cyberinfrastructure is about controls, security systems, storage sets, computation, visualization, support & training, collaboration tools, publishing, communication, finding, networking, etc. “We are not there to answer the question, but more to ask them.”

In the afternoon I listened to Richard Whaling (University of Chicago) present on “Humanities computing at scale“. Given from the point of view of a computer scientist, this presentation was akin to Hobby’s. On one hand there are people do analysis and there are people who create the analysis tools. Whaley is more like the later. I thought his discussion on the format of texts was most interesting. “XML is good for various types of rendering, but not necessarily so good for analysis. XML does not necessarily go deep enough with the encoding because the encoding is too expensive; XML is not scalable. Nor is SQL. Indexing is the way to go.” This perspective jives with my own experience. Encoding texts in XML (TEI) is so very tedious and the tools to do any analysis against the result are few and far between. Creating the perfect relational database (SQL) is like seeking the Holy Grail, and SQL is not designed to do full text searching nor “relevancy ranking”. Indexing texts and doing retrieval against the result has proven to be much more fruitful or me, but such an approach is an example of “Bag of Words” computing, and thus words (concepts) often get placed out of context. Despite that, I think the indexing approach holds the most promise. Check out Perseus under Philologic and Digital South Asia Library to see some of Whaley’s handiwork.

Chris Clarke (University of Notre Dame), in “Technology horizons for teaching and learning“, enumerated ways the University of Notre Dame is putting into practice many of the things described in the most recent Horizon Report. Examples included the use of ebooks, augmented reality, gesture-based computing, and visual data analysis. I thought the presentation was a great way to bring the forward-thinking report down to Earth and place it into a local context. Very nice.

William Donaruma (also from the University of Notre Dame) described the process he was going through to create 3-D movies in a presentation called “Choreography in a virtual space“. Multiple — very expensive — cameras. Dry ice. Specific positioning of the dancers. Special glasses. All of these things played into the creation of an illusion of three-dimensions on a two-dimensional space. I will not call it three-dimensional until I can walk around the object in question. The definition of three-dimensional needs to be qualified.

The final presentation of the day took place after dinner. The talk, “The Transformation of modern science” was given virtually by Edward Seidel (National Science Foundation). Articulate. Systematic. Thorough. Insightful. These are the sorts of words I use to describe Seidel’s talk. Presented remotely through a desktop camera and displayed on a screen to the audience, we were given a history of science and a description of how it has changed from single-man operations to large-group collaborations. We were shown the volume of information created previously and compared it to the volume of information generated now. All of this led up to the most salient message — “All future National Science Foundation grant proposals must include a data curation plan.” Seidel mentioned libraries, librarians, and librarianship quite a number of times during the talk. Naturally my ears perked up. My profession is about the collection, preservation, organization, and dissemination of data, information, and knowledge. The type of content to which these processes are applied — books, journal articles, multi-media recordings, etc — is irrelevant. Given a collection policy, it can all be important. The data generated by scientists and their machines is no exception. Is our profession up to the challenge, or are we too much wedded to printed, bibliographic materials? It is time for librarians to aggressively step up to the plate, or else. Here is an opportunity being laid at our feet. Let’s pick it up!

Day #2 – Friday, April 30

The second day centered more around the sciences as opposed to the humanities.

The day began with a presentation by Tony Hey (Microsoft Research) called “The Fourth Paradigm: Data-intensive scientific discovery“. Hey described cyberinfrastructure as the new name for e-science. He then echoed much of content of Seidel’s message from the previous evening and described the evolution of science in a set of paradigms: 1) theoretical, 2) experimental, 3) computational, and 4) data-intensive. He elaborated on the infrastructure components necessary for data-intensive science: 1) acquisition, 2) collaboration & visualization, 3) analysis & mining, 4) dissemination & sharing, 5) archiving & preservation. (Gosh, that sounds a whole lot like my definition of librarianship!) He saw Microsoft’s role as one of providing the necessary tools to facilitate e-science (or cyberinfrastructure) and thus the Fourth Paradigm. Hey’s presentation sounded a lot like open access advocacy. More Association of Research Library library directors as well as university administrators need to hear what he has to say.

Boleslaw Syzmanski (Rensselaer Polytechnic Institute) described how better science could be done in a presentation called “Robust asynchronous optimization for volunteer computing grids“. Like Hobby and Whaley mentioned (above), Syzmanski separated the work of the scientist and the work of cyberinfrastructure. “Scientists do not want to be bothered with the computer science of their work.” He then went on to describe a distributed computing technique for studying the galaxy — MilkyWay@home. He advocated cloud computing as a form of asynchronous computing.

The third presentation of the day was entitled “Cyberinfrastructure for small and medium laboratories” by Ian Foster (University of Chicago). The heart of this presentation was advocacy for software as a service (SaaS) computing for scientific laboratories.

Ashok Srivastava (NASA) was the first up in the second session with “Using Web 2.0 and collaborative tools at NASA“. He spoke to one of the basic principles of good science when he said, “Reproducibility is a key aspect of science, and with access to the data this reproducibility is possible.” I’m not quite sure my fellow librarians and humanists understand the importance of such a statement. Unlike work in the humanities — which is often built on subjective and intuitive interpretation — good science relies on the ability for many to come to the same conclusion based on the same evidence. Open access data makes such a thing possible. Much more of Srivastava’s presentation was about DASHlink, “a virtual laboratory for scientists and engineers to disseminate results and collaborate on research problems in health management technologies for aeronautics systems.”

Scientific workflows and bioinformatics applications” by Ewa Deelman (University of Southern California) was up next. She echoed many of the things I heard from library pundits a few years ago when it came to institutional repositories. In short, “Workflows are what are needed in order for e-science to really work… Instead of moving the data to the computation, you have to move the computation to the data.” This is akin to two ideas. First, like Hey’s idea of providing tools to facilitate cyberinfrastructure, Deelman advocates integrating the cyberinfrastructure tools into the work of scientists. Second, e-science is more than mere infrastructure. It also approaches the “services against text” idea which I have been advocating for a few years.

Jeffrey Layton (Dell, Inc.) rounded out the session with a presentation called “I/O pattern characterization of HPC applications“. In it he described how he used the output of strace commands — which can be quite voluminous — to evaluate storage input/output patterns. “Storage is cheap, but it is only one of a bigger set of problems in the system.”

By this time I was full, my iPad had arrived in the mail, and I went home.


It just so happens I was given the responsibility of inviting a number of the humanists to the event, specifically: John Unsworth, Stéphan Sinclair, and Richard Whaley. That is was an honor, and I appreciate the opportunity. “Thank you.”

I learned a number of things, and a few other things were re-enforced. First, the word “cyberinfrastructure” is the newly minted term for “e-science”. Many of the presenters used these two words interchangeably. Second, while my experience with the digital humanities is still in its infancy, I am definitely on the right track. Concordances certainly don’t seem to be going out of style any time soon, and my use of indexes is a movement in the right direction. Third, the cyberinfrastructure people see themselves as support to the work of scientists. This is similar to the work of librarians who see themselves supporting their larger communities. Personally, I think this needs to be qualified since I believe it is possible for me to expand the venerable sphere of knowledge too. Providing library (or cyberinfrastructure) services does not preclude me from advancing our understanding of the human condition and/or describing the natural world. Lastly, open source software and open access publishing were common underlying themes but not rarely explicitly stated. I wonder whether or not the the idea of “open” is a four letter word.

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Eric Lease Morgan

Artist- and Librarian-At-Large