Zzzoot

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

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 ...

Putting the Open (and almost live) back into Science In an effort that will surely challenge both other researchers and the Publishers, the Wiki Paper Experiment ( Jean-Claude Bradley ) is performing the research and writing the paper as they go on a wiki dedicated to the project , with a secondary (primary?) experiment being whether any publisher will pick-up the final paper.