To facilitate clinical and translational research, we are developing caBench-to-Bedside (caB2B). caB2B will be used to query caGrid data services and will analyze this data using caGrid analytical services. In the first year, the scope of caB2B is confined to the query, analysis and visualization of microarray expression data.

caTissue Core is a web-based biospecimen inventory and tracking tool that may be used by biospecimen resource facilities, regardless of the nature of biospecimen transactions that occur or the type of biospecimens involved in the transaction. In the next version of caTissue, it will support integration with associated free-text surgical pathology reports (SPR) and discrete clinical and pathology annotations

Chip Import Utility (CIU) is a tool to upload metadata, raw and analyzed data in our database CHIPDB for the microarray experiments (expression and SNP chips) performed by investigators at Washington University

CRS is developed to facilitate compatibility reviews by the Vocabularies and Common Data Elements (VCDE) and Architecture (ARCH) workspaces. Currently we are developing version 2.0 that will contain tools for compatibility self-checks by developers and reports that determine the true CDE reuse.

Function Express or FE- To analyze microarray expression data, FE allows end users to filter, normalize, cluster, and classify gene expression data. Available algorithms include Significance Analysis of Microarrays (SAM), k-means, hierarchical, and SOM clustering, GenePattern (Consensus Clustering, Comparative Marker Selection, and Weighted Voting), and R modules (SVM and PCA). FE will also allow end users to view gene networks created using co-expression, transcription factor binding site, pathway, interaction, and literature-based data

Examine gene expression in the context of functional annotations such as biological processes or molecular functions from Gene Ontology, across different microarray experiments of one or more species. Filter genes on the basis of annotations or expression data. Cluster probesets /samples using different supervised / unsupervised clustering techniques.Export /import data to/from another analysis applications

GeneConnect allows users to input one or more commonly used genomic identifiers (e.g. Entrez Gene ID, Ensembl Gene ID, or UniProtKB Accession Number) and returns linked identifiers from other databases (e.g. RefSeq mRNA or Protein ID or GenBank mRNA/Peptide ID).

LIMS, an application for data management is being developed for the Proteomics core. The application is designed to handle sample curation, processing, image analysis and data reporting.

Mascot Viewer or MaV- To analyze proteomics data, MaV allows users to view a 'clickable' gel and to click on relevant spots to view consolidated (i.e. multiple mass spectrometry [MS] runs on one or more machines) MS and MS/MS results.

Mutation Viewer or MuV- To analyze re-sequencing data. We are refining the MuV pipeline to allow users to design primers in high throughput using a web interface, to analyze sequence traces for mixed peaks and indels using multiple analytical tools, and to visualize mutation information in the context of genomic annotation (e.g. exon-intron boundaries, protein domains, and known SNPs).

The Promoter Analysis Pipeline (PAP) is a web-based workbench for identifying transcription factor binding sites in a set of coexpressed genes in mammals. PAP is based on a statistical model which predicts the transcriptional factors and their regulatory targets in the genome using overrepresentation of binding profiles in promoter sequences.

Webtools for microarray data retrieval and analysis allow registered users to download raw data files and annotated microarray chip data files. Chip privileges can also be assigned to other registered users. The gene search utility allows users to query annotations for genes/probesets from Entrez Gene, UniGene, Gene Ontology, and dbSNP and to view expression profile information for genes of interest. Users also have access to microarray raw data files and annotated data for all publications authored by Washington University researchers.