Zzzoot

This workshop - to be held at Indiana University March 26,27 2009 - examines the question: " given millions of dollars invested in initiating software development, how is software that will be important to the US research and engineering communities identified, maintained, and supported over years to decades? " Of course a question of interest for other countries and their cyberinfrastructure initiatives. Workshop Goals: The goals of the Cyberinfrastructure Software Sustainability and Reusability workshop are as follows: Examine software evaluation and adoption models by individual research labs and virtual organizations Examine models for long-term software sustainability – the ability to obtain the software one wants with assurance, obtain the information required to use the software, obtain the software and hardware environments required to run the software, and use the software. Discuss mechanisms for supporting sustainability, including direct government support, unive...

This paper takes a more semantic web and forward looking view than recent cyberinfrastructure articles: Stein, L. D. (2008).Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges Nat Rev Genet, 9(9) , 678-688. DOI: 10.1038/nrg2414 Things like Semantic Web Pipes - missing from the article - can be found on the wiki page for the article (Thanks Matthias Samwald). Related recent articles: Goble, C., Stevens, R. (2008). State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.01.008 Stockinger, H., Attwood, T., Chohan, S.N., Cote, R., Cudre-Mauroux, P., Falquet, L., Fernandes, P., Finn, R.D., Hupponen, T., Korpelainen, E., Labarga, A., Laugraud, A., Lima, T., Pafilis, E., Pagni, M., Pettifer, S., Phan, I., Rahman, N. (2008). Experience using web services for biological sequence analysis. Briefings in Bioinformatics DOI: 10.1093/bib/bbn029 Garciasanchez, F., Fernandezbreis, J., Valenciagarcia...

Volume 5069 of LNCS titled " Scientific and Statistical Database Management " (20th International Conference, SSDBM 2008, Hong Kong, China, July 9-11, 2008) is just out. Some interesting papers: New Challenges in Petascale Scientific Databases Query Planning for Searching Inter-dependent Deep-Web Databases A Probabilistic Framework for Building Privacy-Preserving Synopses of Multi-dimensional Data ViP: A User-Centric View-Based Annotation Framework for Scientific Data Flexible Scientific Workflow Modeling Using Frames, Templates, and Dynamic Embedding Examining Statistics of Workflow Evolution Provenance: A First Study Adventures in the Blogosphere Ontology Database: A New Method for Semantic Modeling and an Application to Brainwave Data NB: I would be using DOIs for these articles as they are available but they do not seem to be registered yet with doi.org...

...it should probably be this one: Jelinkova, K., Carvalho, T., Kerian, D., Knosp, B., Percival, K., Yagi, S. (2008). Creating a Five-Minute Conversation About Cyberinfrastructure . EDUCAUSE Quarterly, 31 (2), 78-82. Thanks Roy Tennant et al ., Current Cites June 2008 .

This looks like an interesting article ( Libraries in the Converging Worlds of Open Data, E-Research, and Web 2.0 , Stuart MacDonald, March/April issue of ONLINE magazine) but I don't have a subscription so I can't really comment much on it. Ironic that the abstract mentions Peter Suber's Open Access News blog.... ;-) Abstract: " The new forms of research enabled by the latest technologies bring about collaboration among researchers in different locations, institutions, and even disciplines. These new collaborations have two key features -- the prodigious use and production of data. This data-centric research manifests itself in such concepts as e-science, cyberinfrastructure, or e-research. Over the last decade there has been much discussion about the merits of open standards, open source software, open access to scholarly publications, and most recently open data. There are a range of authoritative weblogs that address the open movement, some of which include: 1. DC...

Jean-Claude Bradley's presentation " Open Notebook Science: Implications for the Future of Libraries " is a must-read for all research and science librarians if they want to know how science is starting to be, and will be, done. It should also be read by those who plan the futures of research and science libraries, in order to understand how, for instance, the millennials will be doing science, if they are not already. Fundamental to this future (and present) are Open Access, Open Data, social (research) networking, the blogging/wiki/GoogleDocs/mailing-list dynamics, Wiki versioning (of experimental and other research activities), Second Life for presentations and teaching, and the necessity of machine-to-machine communications and interactions (see my earlier blog entry: New Open Access Criterion: Support access by machines "). Abstract: Open Notebook Science involves a variety of internet-based techniques for sharing of scientific information, from the use of wiki...

At a recent plenary I gave [ earlier post ] at the Colorado Association of Research Libraries Next Gen Library Interfaces conference, I went a little off-script and was educating (/haranguing) the mostly librarian audience about the present-and-near-future importance of the accessibility of full-text research articles to their researchers and scientists. By accessibility of full-text I didn't mean the ability of a human to access the PDF or HTML of an article via a web browser: I was referring to the machine- accessibility of the text contained in the article (and the metadata and the citation information). I was concerned because of the increasing number of discipline-specific tools that use full-text (& metadata & citations) to allow users (via text mining, semantic analysis, etc.) to navigate, analyze and discover new ideas and relationships, from the research literature. The general label for this kind of research is ' literature-based discovery ', where new ...

There is a special issue (Winter 2008) of Journal of Electronic Publishing entitled "Special Issue on Communications, Scholarly Communications and the Advanced Research Infrastructure". It examines from a number of different perspectives and interests the intersection of cyberinfrastructure, scholarship and scholarly communication and how they are impacting -- and will be impacting -- scholarly activities. Overview: Editor's Note . Judith Axler Turner Cyberscholarship: High Performance Computing Meets Digital Libraries . William Y. Arms . When Authorship Isn't Enough: Lessons from CERN on the Implications of Formal and Informal Credit Attribution Mechanisms in Collaborative Research . Jeremy Birnholtz The Virtual Observatory Meets the Library . G. Sayeed Choudhury Triple Helix: Cyberinfrastructure, Scholarly Communication, and Trust . Amy Friedlander Talk About Talking About New Models of Scholarly Communication . Karla L. Hahn Can Universities Dream of Electric She...

Clifford Lynch 's closing keynote to the 2007 Seminars On Academic Computing entitled " The Institutional Challenges of Cyberinfrastructure and E-Research " is now available as a podcast . Abstract: It has become clear that scholarly practice and scholarly communication across a wide range of disciplines are being transfigured by a series of developments in IT and networked information. While this has been widely discussed at the national and international levels in the context of large-scale advanced scientific projects, the challenges at the level of individual universities and colleges may prove more complex and more difficult. This presentation will focus on these challenges, as well as the development of truly institution-wide strategies that can support and advance the promises of e-research.