Zzzoot

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).

The U.S. National Science Foundation (NSF) has announced the four 2007 grant ($10M over 5 years) awardees of its Expeditions in Computing . The funded projects are: Understand, Cope with, and Benefit From Intractability Computational Sustainability: Computational Methods for a Sustainable Environment, Economy, and Society Open Programmable Mobile Internet 2020 Molecular Programming Project

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 Association of Research Libraries (ARL) and the Coalition for Networked Information (CNI) are hosting a forum " Reinventing Science Librarianship: Models for the Future" , October 16 2008 in Arlington, Virginia.

Ethics In Science And Enviromental Politics Vol. 8, No. 1, Special Issue: The Use And Misuse Of Bibliometric Indices In Evaluating Scholarly Performance is an extensive set of papers on bibliometric indices. I have as yet to read them, but they look interesting and significant: Browman, H., Stergiou, K. (2008). Factors and indices are one thing, deciding who is scholarly, why they are scholarly, and the relative value of their scholarship is something else entirely. Ethics in Science and Environmental Politics, 8 , 1-3. DOI: 10.3354/esep00089 Campbell, P. (2008). Escape from the impact factor. Ethics in Science and Environmental Politics, 8 , 5-7. DOI: 10.3354/esep00078 Lawrence, P. (2008). Lost in publication: how measurement harms science. Ethics in Science and Environmental Politics, 8 , 9-11. DOI: 10.3354/esep00079 Todd, P., Ladle, R. (2008). Hidden dangers of a "citation culture". Ethics in Science and Environmental Politics, 8 , 13-16. DOI: 10.3354/esep00091 Taylor, M...

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...

the scholarly kitchen has a very interesting discussion (" The importance of being first ") that looks at the various biases impacting article readership at arXiv . Based on two recent articles[ 1 , 2 ], biases introduced by the email announcement schedule (sent out at 4PM North American Eastern Time) of arXiv (geographical bias) as well author game- or evolutionary theory strategies of self-promotion ( Submit as close to 4pm so as to appear at the top of the email announcement, thus increasing readership... ) can significantly change the readership and citation rate of an article. Interesting and clearly something that needs to be reduced/taken-in-to-account/monitored at similar sites. I would be surprised if there weren't already EBay sniping-(bidding)-bot -like bots out there that can automatically submit articles to arXiv in the last 10 seconds of 4pm. [1] Dietrich, J.P. (2008). The Importance of Being First: Position Dependent Citation Rates on arXiv:astro-ph. Pub...

It is encouraging to see a session at the upcoming Genome Canada conference ( Genome Canada Third International Conference, 2020 Vision: The Impact of Science on Society, Vancouver, October 22 - 24, 2008) entitled " Commercialization, Data Release, and Open Access: Incompatible Objectives? ". Other sessions at the conference: Human Genetic Variation Science should be on Tap not on Top: the Role of Government Science Advisers A New Paradigm for Drug Discovery (Round table discussion) Green Genomics Genomics of Childhood Diseases Stem Cells The session: " Science should be on Tap not on Top: the Role of Government Science Advisers " is to be chaired by Arthur Carty , the former president of the National Research Council (NRC) , and the former science advisor to the Canadian prime minister. I was unaware that Dr. Carty had recently been named the first executive director of the Waterloo Institute of Nanotechnology ( web site?? ), as indicated in this news releas...

Here are a number of fairly recent Open Access (OA) references that I have collected that need a home. They are from a number of different perspectives, certainly beyond the usual science, technology, medicine (STM) focus of most of my OA postings, and include Middle East Studies, law publishing, OA activities in China and South Asia, and even Bakhtinian dialogism ! I hope they are useful: Byrne, Alex. 2007. Open Access and development: physician, heal thyself! 73rd IFLA General Conference and Council , Durban, South Africa, 19-23 August 2007. Harper, Georgia K. 2008. NIH Open Access Mandate: A Careful Look at Two Options for Retaining Authors’ Rights – "Do Nothing" and ΄Do it Early and Efficiently‘ . Newsletter of the Center for Intellectual Property , Spring 2008. Kennan, Mary Anne & Kautz, Karlheinz. 2007. Scholarly publishing and Open Access: searching for understanding of an emerging IS phenomenon . The 15th European Conference on Information Systems, University of...

ChemStar (Computed Molecular Data) is an Open Access database of the calculated chemical properties of over 12M substances from PubChem. The process - which demands significant computing power - was done is a distributed fashion using JavaRMI and is described in the paper below. The properties are calculated using three different methods: JChem , JOELIB and MOE . The site allows the perusal of the properties, with a Marvin -based applet for viewing structures. The Java sourcecode for the distributed computing is available . Karthikeyan, M., Krishnan, S., Pandey, A.K., Bender, A., Tropsha, A. (2008). Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. Journal of Chemical Information and Modeling, 48 (4), 691-703. DOI: 10.1021/ci700334f