Frank

Darn you, flash games! :) - Allyson Lister

148,932 on 3rd attempt... Just a few more hours practice and I should make it into the top 10 :-) - Eric Jain

PLoS Biol, Vol. 7, No. 11. (17 November 2009), e1000242. The authors discuss the value of article-level metrics in determining an article's scientific impact. Cameron Neylon, Shirley Wu - Frank

Applied Ontology, Vol. 3, No. 4. (1 January 2008), pp. 235-245. The role of proteins and their function in pathways is crucial to understanding complex biological processes and their failures that lead to disease. With over 200 pathway databases in existence, it is not possible for biologists to examine a pathway in all of them. The emergence and adoption of Biological Pathways Exchange (BioPAX), a standardized format for exchanging pathway information, provides a unique opportunity to integrate knowledge from multiple pathway databases. We conducted a case study integrating multiple pathway databases using BioPAX and Oracle's resource description framework (RDF) data repository. This integration enables querying across different species and across multiple pathway resources simultaneously. It also enables comparison of the degree of complementarity across different pathway sources. We find that BioPAX and RDF are powerful mechanisms for data exchange and integration and are... - Frank

Sounds interesting... please share your findings later. #openid #publishing #science - Egon Willighagen

To muddy the waters further, this message came via linkedin recently: http://www.linkedin.com/groupAn... not sure of that link will work for everyone 'cause linkedin hates sensible permalinks for some reason - Mr. Gunn

Future Generation Computer Systems, Vol. 25, No. 5. (10 May 2009), pp. 528-540. Scientific workflow systems have become a necessary tool for many applications, enabling the composition and execution of complex analysis on distributed resources. Today there are many workflow systems, often with overlapping functionality. A key issue for potential users of workflow systems is the need to be able to compare the capabilities of the various available tools. There can be confusion about system functionality and the tools are often selected without a proper functional analysis. In this paper we extract a taxonomy of features from the way scientists make use of existing workflow systems and we illustrate this feature set by providing some examples taken from existing workflow systems. The taxonomy provides end users with a mechanism by which they can assess the suitability of workflow in general and how they might use these features to make an informed choice about which workflow system would... - Frank

The Microsoft Biology Foundation (MBF) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework. Currently it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological Web services such as NCBI BLAST. MBF is available under an open source license - Frank

Nucl. Acids Res. (15 September 2009), gkp760. Annotating the function of all human genes is a critical, yet formidable, challenge. Current gene annotation efforts focus on centralized curation resources, but it is increasingly clear that this approach does not scale with the rapid growth of the biomedical literature. The Gene Wiki utilizes an alternative and complementary model based on the principle of community intelligence. Directly integrated within the online encyclopedia, Wikipedia, the goal of this effort is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Previously, we described the creation of Gene Wiki stubs' for approximately 9000 human genes. Here, we describe ongoing systematic improvements to these articles to increase their utility. Moreover, we retrospectively examine the community usage and improvement of the Gene Wiki, providing evidence of a... - Frank

Genome Biology, Vol. 8, No. 4. (30 April 2007), 404. Gene annotation, as measured by links to the biomedical literature and funded grants, is governed by a power law, indicating that researchers favor the extensive study of relatively few genes. This emphasizes the need for data-driven science to accomplish genome-wide gene annotation. Andrew Su, John Hogenesch - Frank

The Web of data for e-commerce. A hands-on introduction to the GoodRelations Ontology, RDFa and Yahoo! SearchMonkey - slides - Frank

Nat Biotech, Vol. 27, No. 10. (01 October 2009), pp. 921-924. Networks in biology can appear complex and difficult to decipher. We illustrate how to interpret biological networks with the help of frequently used visualization and analysis patterns. Daniele Merico, David Gfeller, Gary Bader - Frank