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Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic
BioCSharp is an open-source project designed to provide a bioinformatics .NET framework for processing biological data. It will include objects for manipulating sequences, file parsers, DAS, database access and analysis and statistical routines.
TAS (Transcription Analysis System) is a multi-tier framework for running parameterized SQL queries. Users can analyze new data or new combinations of data with a few clicks in a GUI. Potentially complex/repetitive database interaction is all automated
Axero Intranet is an award-winning intranet and employee experience platform.
Hundreds of companies and millions of employees use Axero’s intranet software to communicate, collaborate, manage tasks and events, organize content, and develop their company culture.
A C++ development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read, write, and manipulate sequence and annotation data in several file formats.
GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.
cy.prus is a cross platform simulation environment for medical cybernetics and systems biology.
Its purpose is to provide both a facility for simulating life and a GUI for easily constructing biological information processing structures based on XML.
The Synaptic Simulator is a program which simulates models of single neuronal synapses and compartments, complex constructs of such models. Furthermore the program is able to regain parameters by fitting simulated results with experimental data.
A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.
Safetica Data Loss Prevention Software for Businesses
For companies that want to protect their sensitive data against leakages, insider threats and want to be compliant with regulations.
Safetica is a cost-effective, easy-to-use Data Loss Prevention (DLP) solution. It performs security audits, prevents sensitive data from leaving your company, and sheds light on what is going on in your organization.
A Python interface to the Wordnet database of word meanings and lexical relationships. allows the user to type expressions such as N['dog'], hyponyms(N['dog'][0]), and closure(ADJ['red'], SYNONYM) to query the database for lexical relationships.
ReadSeq is a program and library for conversion of biosequence data from one format to another, useful in various bioinformatics programs and services. It is written in Java, though an earlier version in C remains available.
POSA (Perl Objects for Sequence Analysis) provides an easy-to-use perl interface to handling raw ABI sequence trace files. For example: fasta can be extracted, sequence contigs can be build and putative SNPs and SBE primers can be easily generated.
TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides datastorage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.
Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.
An Evolution Simulator of Single Cells in a Pond. This shows a crosssection of
water with sun shining from above. A single cell is dropped in and has various genes. The cells multipy and evolve. See Files above for download and screenshot.
froi (FS-FAST ROI) is a suite of Perl scripts and modules to provide easy slice-, volume-, and surface-based ROI analysis of functional MRI (fMRI) data analyzed by FS-FAST and Freesurfer (http://surfer.nmr.mgh.harvard.edu).
An application for modelling species distribution and preparing and retrieving locality,climatic and other data for use in species distribution models.
Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
For interactive clustering and visualization, Cluster and TreeView by Mike Eisen are great. XCluster by Gavin Sherlock solves the problem of clustering large numbers of files. Now slcview allows you to script generation of cluster and tree images.