John Boyle

..The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing...

..g. security versus speed). This means that an understanding of specific requirements and tradeoffs is necessary before selecting the access technology...

..However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires...

..This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values...

..Here we describe PeptideAtlas and associated methods for mining the data, as well as the software tools necessary to support large-scale integration and mining...

..As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools...

..These tests are necessary to ensure that data is of a minimum necessary standard for use in downstream analysis. In this paper we present the SAMQA tool to rapidly and robustly identify errors in population-scale sequence data...

..To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage...

..By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function...

..We used an established semantic distance measure that is based on the co-occurrence of disease and protein terms in the MEDLINE bibliographic database...

..abstract:..

..It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape...