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The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io
A Mass Spectrometer B and Y ion labeling software for proteomics researchers. Peptide sequences can be read from a library and b and y ions will be calculated and sequence can be manipulated by the user (chem. mod. or amino acid mod.)
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
JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.
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.
Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)
BioEra is DSP visual designer that can be used to create interfaces between human being and a machine with using bio signals like EEG, QEEG, HEG, EMG, ECG, GSR, EOG, visual/sound entrainment and others.
Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
IslandEv distributes a Genetic Algorithm (like <a href="/projects/jaga">JaGa</a>) across a network (see <a href="/projects/distrit">DistrIT</a>) using an island based coevolutionary model in which neighbouring islands swap migrating individuals every
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).
Alife research platform to study the evolvability of different assembly-like computer languages. It's similar to Tierra and Avida but it's designed to be more general.
BioQuery is a bioinformatics tool that acts as a query builder for genetic, protein, publication, and other biomedical databases. BioQuery is also an update service that periodically resubmits saved searches and sends you new data as it is found.
Cytoscape is a software platform for computational biology and
bioinformatics, useful for integrating data, and for visualizing and
performing calculations on molecular interaction networks
jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk
The library allows to communicate with BioMOBY Registries and implements all operations such as retrieval, search, registration, deregistration of services, data types etc...
A bi-directional BLAST tool for orthologue listing with extended facilities (global alignment; paralogue list; GO onthology; dN/dS; etc) working on Win32 compiled versions of NCBI BLAST,FASTA,EMBOSS, and PAML. FILES AVAILABLE AT THE HOMEPAGE.(JAVA coded)