Aims to support real-time infectious disease outbreak investigations and pathogen surveillance using genomic data. IRIDA is a platform for analytics and visualizations of whole genome sequencing (WGS)-based microbial pathogen investigations that: (1) allows data management and controlled, collaborative data sharing, (2) provides analysis pipelines for public health genomics, enables data integration by implementing ontologies, and (3) permits data visualization.
Computes comprehensive DNA features based on the built-in and user-defined physicochemical properties. repDNA aims to simplify the studies of DNA and nucleotides. It can be adapted and allows users to construct their own predictors. This tool is based on machine learning packages and holds very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis.
Allows storage of matrices of experimental results, which are commonly produced by sequencing and microarray experiments. SummarizedExperiment is an R package that contains two classes: (1) SummarizedExperiment, a matrix-like container and (2) RangedSummarizedExperiment, the child of the SummarizedExperiment. The software is suitable to a variety of experiments, particularly sequencing based experiments such as RNA-Seq and ChIp-Seq.
Allows users to manage microarray core. SLIMarray serves for the management of inventory, sample processing and charging information. It automates the construction of interrelated data records where appropriate. This tool can track multiple lab groups' inventories of different chip types, with records of every transaction such as purchasing or using microarrays. It permits users to create records of hybridizations.
Facilitates the submission of large microarray experiment datasets to the public repository database ArrayExpress. Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. The software provides a script that can parse data files in several formats, and a data file checking script. It can also generate MAGE-ML for data exchange.
Makes accessible the contents of maxdLoad2 database. maxdBrowse is a program available through the web-browser, the command-line and the web-service environments. It allows users not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. This web interface also permits users to review annotated experiments in a simple manner at any time, without needing maxdLoad2.
Provides a resource for investigating patent documents to find biological sequences. PatSeq is a platform that provides five different modules for retrieving, analyzing and exploiting sequences and their contexts. The toolkit is composed of two databases: (i) PatSeq gathers data collected from national patent offices and (ii) PatSeq Text Search retrieves sequence from patent documents; and three applications: (iii) PatSeq Finder compares sequences (iv) PatSeq Analyzer compares patenting activities; and (v) PatSeq Explorer analyzes specific sequences.