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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
splitsmb is a standalone application for calculating topological convergence diagnostics on MrBayes tree-output files (unrooted only at this point). It calculates the average- and maximum standard deviations of partition frequencies between runs.
MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments. Based upon the Henikoff BLOSUM method.
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The NCD Toolkit is a PHP application to collaboratively manage biological collection metadata that corresponds to the TDWG TDWG Natural Collection Description (NCD v0.8) format. The project was initially funded by GBIF.
EMMA 2 is web-based server application for management, annotation, and analysis of microarray data. It provides mapping of gene expression data onto pathway data extensible analysis and visualization functions and MAGE-ML support.
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Data and animal management software for large-scale phenotype screening Used by GNF for mouse ENU mutagenesis project. Data visualization & analysis, animal husbandry management, & automated QTL mapping. Usable as stand alone animal husbandry system.
The Comparative Genomics Ontology (CGO) is an OWL ontology initially developed to support the integration of comparative genomics data from heterogeneous resources as part of the ComparaGRID project.
Lucy is a program for DNA sequence quality trimming and vector removal. Its purpose is to process DNA sequence data acquired from DNA sequencers to prepare the data for downstream processing applications such as genome assembly.
epiPATH is a platform to store and analyze evolutionary, population and epidemiological data from infectious diseases. It is designed to aid users in daily work with data generated in sequencing projects as well as clinical and epidemiological data.
The Stem Cell Artificial Neural network project entails the analysis and integration of genomics data for extracting the stemness signature of several tissues by training a multiclass single-layer linear artificial neural network.
ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines
MZ-Analyzer is a tool for visualization and analysing of multiple mass spectrometry data in 2D and 3D mode, including the function of quantitating the LC-peak of the specified identified peptides.
LSG is a Windows application framework designed for visual data integration and based on Microsoft .NET 2.0 and CAB. An admin utility manages LSG apps, modules, events, and services, and a client integrates the modules and provides functionality hooks.
A PHP webapp to upload taxonomic checklists as Excel or CSV files to be served as TDWG TCS XML/RDF. It can handle multiple checklists, has a Tapir light webservice and a taxonomic tree of species names created from taxonomy in a checklist can be browsed.
sbmlop is a command-line utility to create, view and manipulate SBML (the Systems Biology Markup Language). It is ideally suited for operating on large batches of SBML files, and can extract and modify information using regular expressions.
Celsius is a data warehouse that provides web services for upload, archival, download, annotation, quantification, and normalization of all Affymetrix microarray platforms.
This set of C++ classes allows the user to load data from custom Affymetrix microarrays. This is a good platform for new method development and it contains several common normalization algorithms.
Open Screening Environment is a open source system for management of High Throughput Screening related experiments. The platform consists of new research tools that will enhance significantly management and analysis of HTS data. More information can be f