UNLABELLED: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway data for the relevant protein. A KEGG Pathway Identifier representing a specific human biological pathway initializes the DataBiNS workflow. The workflow retrieves a list of publications, gene ontology annotations and nsSNP information for each gene involved in the biological pathway. Manual inspection of output data from several trial runs confirms that all expected information is appropriately retrieved by the workflow services. The use of an automated BioMoby workflow, rather than manual 'surfing', to retrieve the necessary data, significantly reduces the effort required for functional interpretation of SNP data, and thus encourages more speculative investigation. Moreover, the modular nature of the individual BioMoby Services enables fine-grained reusing of each service in other workflows, thus reducing the effort required to achieve similar investigations in the future. AVAILABILITY: The workflow is freely available as a Taverna SCUFL XML document at the iCAPTURE Centre web site, http://www.mrl.ubc.ca/who/who_bios_scott_tebbutt.shtml.

Abstract Summary: Multi-dimensional Automated Clustering Genotyping Tool (MACGT) is a Java application that clusters complex multi-dimensional vector data derived from single nucleotide polymorphism (SNP) genotyping experiments using mini-sequencing based microarray chemistries such as arrayed primer extension (APEX). Spot intensity output files from microarray experiments across multiple samples are imported into MACGT. The datasets can include four channels of intensity data for each spot, replica spots for each SNP probe and multiple probe types (APEX and allele-specific APEX probes) on both DNA strands for each SNP. MACGT automatically clusters these multi-dimensionality datasets for each SNP across multiple samples. Incorporation of additional array datasets from known samples that have previously validated SNP genotype calls allows unknown samples to be automatically assigned a genotype based on the clustering, along with numerical measures of confidence for each genotype call. Calling accuracy by MACGT exceeds 98% when applied to genotyping data from APEX microarrays, and can be increased to >99.5% by applying thresholds to the confidence measures. Availability: MACGT is open source and is freely available (under a GNU General Public License) from the iCAPTURE Centre web site, . Contact: [email protected] Supplementary information: Additional information, including Supplementary Figure S1, test data and a user's manual, is available from the iCAPTURE Centre web site (see above).