Zzzoot

The School of Information Studies (iSchool) at Syracuse University in Syracuse, N.Y., has introduced a new program (in collaboration with Cornell University Library) called " Building an eScience Librarianship Curriculum for an eResearch Future ". It is focused on creating librarians with a better understanding of eScience and the research process, as well as the new types of digital resources - in particular research data and their long term preservation and use - and how to manage them. Right now they have a call out for applications for scholarships that they have for this new program. The lack of eScience and research data savvy librarians is one of the gaps identified by the Research Data Canada and is the focus of its capacity working group.

For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop: Workshop on Semantic Web Applications in Scientific Discourse , October 26, 2009, Proceedings ), part of The 8th International Semantic Web Conference (ISWC 2009) Keynote: Enabling Semantic Publication and Integration of Scientific Information David Shotton. Presentation . A Short Survey of Discourse Representation Models Tudor Groza, Siegfried Handschuh, Tim Clark and Simon Buckingham Shum Paper Presentation Strategic Reading and Scientific Discourse Allen Renear and Carole Palmer Paper 'Confortation': about a new qualitative category for analyzing biomedical texts Delphine Battistelli, Antonietta Folino, Patricia Geretto, Ludivine Kuznik, Jean-Luc Minel and Florence Amardeilh Paper Presentation Hypotheses, Evidence and Relationships:The HypER Model of Representing Scientific Knowledge Anita de Waard, Simon Buckingham Shu...

Microsoft Research has put together a quite amazing collection looking at the revolution that is data intensive research, calling it the fourth paradigm: The Fourth Paradigm: Data-Intensive Scientific Discovery Edited by Tony Hey, Stewart Tansley, and Kristin Tolle

The Journal of Visualized Experiments (JoVE) - which publishes research video-articles - is now indexed by PubMed, as reported in the JoVE blog . Related: Visualize This! Interview with Moshe Pritsker , co-founder and editor-in-chief of JoVE [2008 Feb] Troy, T., Arabzadeh, A., Enikanolaiye, A., Lariviere, N., Turksen, K. (2008). Immunohistochemistry on Paraffin Sections of Mouse Epidermis Using Fluorescent Antibodies. Journal of Visualized Experiments DOI: 10.3791/552 . A JoVE video article from University of Ottawa and Ottawa Health Research Institute (I work in the Ottawa area).

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...

The Microsoft Research Faculty Summit 2008 included Publishing and Research Tools for Academics that allows for archival annotation and structuring of Microsoft software produced documents, as well as supporting PubMed Central format . Additional sessions of interest: The Cyberspace Connection – Impact on Individuals, Society, and Research New Developments in Scholarly Communication Reflections on Directions in Artificial Intelligence What Will Be the Impact of Cloud Services on Science? Spotlights on Interdisciplinary Artificial Intelligence Research AI, Sensing, and Optimized Information Gathering: Trends and Directions Ontological Myths: Reducing the Confusion Social Networking and Semantics Toward Situated Interaction Statistical Machine Translation Research at Microsoft Research Interactive Machine Learning: Challenges, Methods, and Applications Information Extraction from Documents and Queries Contexts in Computer Science Education The Future of Research Clouds REAssess: Resou...

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...

" Is posting raw results online, for all to see, a great tool or a great risk? " Scientific American article . Read it. Nuff said.

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...

Related to my last posting ( FREE THE ARTICLES! (full-text for researchers & scientists and their machines) ) and in the light of Peter Murray-Rust's recent annoying discovery that he cannot text-mine Pubmed Central ( Can I data- and Text-mine Pubmed Central? ), I would like to suggest an additional criterion to the definition of Open Access: Open Access must include access by machines : At minimum one must allow crawls of the site/content or (to reduce the impact of badly configured crawlers) create a compressed XML file containing all metadata and either content, or direct links to content and make it available for download (and if bandwidth is still an issue put it on a P2P network like BitTorrent ). Preferable is to offer some kind of API (OTMI) or protocol (OAI-PMH) to get at content and metadata and citations. Better is to offer access to the XML of the articles in addition to the PDF and/or HTML; if the XML actually has some semantic content, then we are approaching th...

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 ...

It is very exciting that the Places and Spaces: Mapping Science exhibit from Indiana University will be on display at NRC-CISTI from April 3 - June 27 2008. This is the first time this collection of amazing maps of science is on display outside the U.S. The diverse and creative collection includes traditional cartographic maps, concept maps and domain maps. These are all physical paper (+other media) maps, and also includes some hands-on maps made specifically for children to interact with. Congrats to all involved at NRC-CISTI and in particular my CISTI Research colleague Jeff Demaine who was the originator and champion of this initiative. References: Boyack, K.W., Klavans, R., Börner, K. (2005). Mapping the Backbone of Science . Scientometrics, 64 (3), 351-374. Update: 2008 April 15: Indiana University SLIS Events News: Mapping Science Exhibit at the National Research Council - Ottawa, Canada

The Canadian government's House of Commons Standing Committee on Industry, Science and Technology has released a press release describing a consultation which is looking for submissions from various sectors and regions in the following areas: Science advice to government; Commercialization, venture capital and intellectual property; Federally funded research performed in government and higher education; and “Big science” projects and Canada’s position in global science and technology. Submissions must less than 5 pages in length, and emailed in by April 18 2008. No indication of what file formats are accepted.

The First Workshop on Extremely Large Databases was held at the Stanford Linear Accelerator Center , October 2007. Many of the heavy hitters were there (Google, Yahoo, Microsoft, IBM, Oracle, Terrasoft, SLAC, NCSA, eBay, AT&T, etc) from industry, academia and science (? their classification). A report is available and I thought I'd touch on some of the more interesting things I found in it: Scale : Most have systems with > 100TB of data, with 20% of scientific databases > 1PB of data; All from industry reps had >100PB of data, with all having at least one system with >1PB Industry had single tables with > 1 trillion rows; science ~100 times smaller. Need for multi-trillion-row tables in Peak ingest: 1B rows per hour; 1B rows per day common " All users said that even though their databases were already growing rapidly, they would store even more data in databases if it were affordable. Estimates of the potential ranged from ten to one hundred times current...

When Google and IBM last October announced their Internet-Scale Computing Initiative - which looked to dedicate a cluster of 1600 computers for the use of researchers, for free - it was not clear (to me) whether this was a U.S.-only initiative, or was also available (or would eventually become available) to non-U.S. researchers: The University of Washington was the first to join the initiative. A small number of universities will also pilot the program, including Carnegie Mellon University, Massachusetts Institute of Technology, Stanford University, the University of California at Berkeley and the University of Maryland. In the future, the program will be expanded to include additional researchers, educators and scientists. Now with the NSF's announcement that they are partnering with Google and IBM in this initiative in what they are calling the Cluster Exploratory (CluE), it is even less clear (or maybe more clear that is only available to U.S. researchers??), with the NSF re...