High-throughput bioinformatic analyses increasingly rely on pipeline frameworks to process sequence and metadata. Modern implementations of these frameworks differ on three key dimensions: using an implicit or explicit syntax, using a configuration, convention or class-based design paradigm and offering a command line or workbench interface. Here I survey and compare the design philosophies of ...

Background Fasting and calorie restriction cause significant metabolic changes as organisms try to maintain energy homeostasis. The mitochondrial NAD-dependent protein deacetylase Sirt3 has important metabolic effects, including promotion of fatty acid oxidation during fasting [1] and repression of glycolysis in cancer cells [2]. We sought to investigate the mechanisms by which Sirt3 is transcr...

We consider the problem of analytically evaluating semantic interoperability in large-scale networks of schemas interconnected through pairwise schema mappings. Our heuristics are based on a graphtheoretic framework capturing important statistical properties of the graphs. We validate our heuristics on a real collection of interconnected bioinformatic databases registered with the Sequence Retr...

* Author for correspondence: Department of Microbiology, Box 357242, University of Washington, Seattle, Washington 98195, Phone: 1-206-732-6122, FAX: 1-206-7326055, [email protected]. Abstract. Cells and organisms are governed by networks of genetic, physical and metabolic interactions between proteins and other their substrates, such as DNA, RNA, and other biologically important molec...

The ESSLLI course material has been compiled by Anke L ¨ udeling and Ulf Leser. Unless otherwise mentioned, the copyright lies with the individual authors of the material. Anke L ¨ udeling and Ulf Leser declare that they have obtained all necessary permissions for the distribution of this material. ESSLLI 2008 and its organizers take no legal responsibility for the contents of this booklet. In ...

We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reprod...

To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Ge...