Bioinformatics

MATLAB Builder for COM enables you to deploy MATLAB algorithms as COM objects, which can be used on any web server on a Microsoft operating system. The MATLAB based COM object will handle your technical computing, while integrating with a front-end web application built using industry-standard... Platforms: Matlab

Performs Mantel-Haenszel's test for k strata of 2x2 tables.Mantel and Haenszel proposed this asymptotic test based on the chi-2 distribution. Assuming no three-way interaction (k independent strata). Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input: X: data matrix... Platforms: Matlab

Bio link contains solutions to some topics in biology and bioinformatics. The solutions will be made available as soon as they are developed. Therefore they may contain bugs. Please let me know if you encounter a bug so that it can be fixed asap. Most tools will be in JAVA. The jar files can be... Platforms: Matlab

This function displays a graph of the inheritance hierarchy of Matlab Object Oriented Code. It finds all classes below the current working directory and all super classes on the Matlab Path and displays the graph using the bioinformatics toolbox biograph function. Platforms: Matlab

This tool searches a given directory and populates a browser window with pertinent information about each discovered class, including properties, methods, and superclasses. Other useful features include opening a class definition file from the browser window, opening a file to the line where a... Platforms: Matlab

Chi-square tests of homogeneity and independence.Computes the P-value for I x J - table row/col independence.Ref.: DeltaProt toolbox at http://services.cbu.uib.no/software/deltaprot/Input:X: data matrix (I x J -table) of the observed frequency cells.method: 'RC': Read-Cressie power divergence... Platforms: Matlab

It is a non-parametric statistical test for discrete data used todetermine if there are nonrandom associations between the two variables.Mid-P values are a reasonable compromise between the conservativeness ofthe ordinary exact test and the uncertain adequacy of large-sample methods.Mid-P values... Platforms: Matlab

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks, including the gene regulatory network. Due to several NP-hardness results on learning static Bayesian network, most methods for learning DBN are heuristic, that employ either local search such as greedy... Platforms: Matlab

This program is a bioinformatics tool developed for helping biologists finding patterns from a set of protein sequences. The method is the first one that fully utilizes the advantages of the Dirichlet mixture models. It starts from a random pattern and iteratively improves the Bayesian log-odds... Platforms: Matlab

A tool for managing and organizing classes, with a simple interface and (optional) tree diagramThis is version 0.4.1+ of Class Inheritance Browser, originally released @ http://www.mathworks.com/matlabcentral/fileexchange/27633. This tool searches a given directory and populates a browser window... Platforms: Matlab

pIcarver is a tool to visualize theoretical distributions of peptide pI on a given pH range, and proposes a fractionation scheme that generates fractions with similar peptide frequencies. This tool has been developed as a service of the Bioinformatics Core Facility for Proteomics, within a... Platforms: Mac

The C++ library for bioinformatics and artificial intelligence. Basic abstractions (like attribute, domain, state, etc.), DNA primitives (Nucleotide, Chain, EnergyNucleo, SecStruct, FoldedChain, FoldedPair, Codon, CodonAminoTable, Nussinov algorithm), population genetics primitives (Allele,... Platforms: Mac

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid... Platforms: Mac

MALDIPepQuant is a tool to quantify MALDI peptides (SILAC) from Phenyx output. This tool has been developed as a service of the Bioinformatics Core Facility, within a collaboration between the Proteome Informatics Group from the Swiss Institute of Bioinformatics (SIB) and the Biomedical... Platforms: Mac

AutoSOME is a new unsupervised multidimensional clustering method for identifying clusters of diverse shapes and sizes from large numerical datasets without prior knowledge of cluster number (BMC Bioinformatics, 11:117). Given the general nature of data clustering, AutoSOME has utility for a wide... Platforms: Mac

A collection of various perl scripts that utilize bioperl modules for use in bioinformatics analysis. Tools are included for processing microarray data, next generation sequencing data, data file format conversion, querying datasets, and general high level analysis of datasets. This tool box of... Platforms: Mac

Biomatters was founded on the principle of creating software that can be used by all researchers in their daily work. Our technology converts raw data into meaningful, visual information, simplifying research and ultimately improving efficiency. Biomatters???*a*? flagship software packages are:... Platforms: *nix

caBIO (cancer Bioinformatics Infrastructure Objects) is a robust resource for accessing biomedical annotations from curated data sources in an integrated view in support of knowledge discovery. The entities that concern the Central Dogma of Molecular Biology are the core of the model. Data for... Platforms: *nix

ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications. Platforms: *nix

Bio2RDF is a software to convert bioinformatics data and knowledge bases to RDF format. It is a kind of generalized rdfizer for bioinformatics applications, and it is a place for the semantic web life science community to develop and grow. Platforms: *nix