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1.  Pathway Processor 2.0: a web resource for pathway-based analysis of high-throughput data 
Bioinformatics  2013;29(14):1825-1826.
Summary: Pathway Processor 2.0 is a web application designed to analyze high-throughput datasets, including but not limited to microarray and next-generation sequencing, using a pathway centric logic. In addition to well-established methods such as the Fisher’s test and impact analysis, Pathway Processor 2.0 offers innovative methods that convert gene expression into pathway expression, leading to the identification of differentially regulated pathways in a dataset of choice.
Availability and implementation: Pathway Processor 2.0 is available as a web service at Sample datasets to test the functionality can be used directly from the application.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3702260  PMID: 23740747
2.  The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways 
Bioinformatics  2011;27(15):2127-2133.
Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions.
Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists.
Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at They are implemented in Java and supported on MS Windows, Linux and OS X.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3137220  PMID: 21653523

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