Bio-Informatics
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(AB)² Simulation Simulation for Physics / Bilogics Systems
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APBSmem APBSmem is a Java-based graphical user interface for Poisson-Boltzmann electrostatics calculations at the membrane. APBS version 1.2.0 or later is required.
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Animal Studies Animal Studies
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Bayesian Network tools in Java (BNJ) Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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Behavioral Monitoring Tool Used to record and analyze some behavioural experiments in neuroscience (using usb webcam). it was developed in collaboration with neuropharmacology lab at Faculty of Medicine, Ain Shams University. it can use(JMF,OpenCV,JMyron & AGCamLib) for webcam
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Ben(Zai)Ten - visual modeling editor Ben(Zai)Ten is a graphical modeling environment for computational and systems biology. It supports the community exchange standards: SBML, SBRML, SED-ML as well as ontologies: MIRIAM, SBO, ChEBI, KEGG, GO
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BioWord A Microsoft Word add-in for biological sequence manipulation
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BioXTAS RAW BioXTAS RAW is a program for analysis of Small Angle X-ray Scattering data. The software enables data reduction from the 2D detector image, data manipulation and masking and provides analysis of 1D data by the Bayesian Indirect Fourier Transform.
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Boon Rules Study the computational basis of human learning and inference
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CBFlib CBFLIB is a library of ANSI-C functions providing a simple mechanism for accessing Crystallographic Binary Files (CBF files) and Image-supporting CIF (imgCIF) files. The CBFLIB API is loosely based on the CIFPARSE API for mmCIF files.
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Comet MS/MS search engine Comet open source tandem mass spectrometry (MS/MS) search engine.
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Critterding Evolving Artificial Life
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DNAsong this is atool that accepts a long DNA sequence and Produces DNA music according to Nucleotide base pair pattern. Helpful for Pattern analysis in Genomic Seqences.
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EDNA Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
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ELECANS Electronic Computational Cancer Systems Biology Simulation Studio
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Entrainer Entrainer is a Java program (JRE 1.7.0_07+ required, available from http://java.sun.com/javase/downloads/index.jsp) which creates binaural beat frequencies with sound, light and animations for the purpose of entraining one's brain waves.
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Febrl Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.
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GUI for DEDA GUI for DEmography Data Analysis
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Gemi PCR oligos / primers design from multiple sequence alignments
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GuiTope Identifies significant regions in proteins from peptide selections.
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Gwyddion A data visualization and processing tool for scanning probe miscroscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry, useful also for general image and 2D data analysis.
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JFinisher JFinisher is software for alignment, editing and manipulation DNA seqs
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JGAP JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included.
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KlustaKwik spike sorting KlustaKwik is an open-source C++ and Java program for automatic clustering of continuous data into a mixture of Gaussians. The program was originally developed for sorting of neuronal action potentials, but can be applied to any sort of data. NOTE (25/04/12): For those interested in trying the new masked version of KlustaKwik designed for large dense electrode array, download KlustaKwik3.0.1 in the maskedKlustaKwik folder. UPDATE (04/07/12): Bugs have been fixed in the new masked version of KlustaKwik. Download KlustaKwik3.0.2 in the maskedKlustaKwik folder. Use the program SpiKeDeteKt to detect spikes from your raw data and to obtain the requisite .mask file.
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LDhat Estimate Recombination Rates from Population Genetic Data
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