Clarrhmos is a description language and simulator for myocardial structure and electrophysiology. Input to the program is a model file specifying types of cells, action potential shape, refractory period, 3D placement of the cells, relation of parameters to other functions, pacing, electrode placement. Output is a file describing depolarisation and repolarisation of the myocardium and electrograms. A graphic tool for interactive inspection of the output file is also included.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Weka is a collection of machine learning algorithms for solving real-world data mining problems. It is written in Java and runs on almost any platform. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka is also well-suited for developing new machine learning schemes. The development version contains a GUI with visualization tools and direct database access.
EAsea Specification of Evolutionary Algorithms (EASEA), is a high-level language dedicated to the specification of evolutionary algorithms. The language and compiler are quite mature. EASEA compiles .ez specification files into C++ or Java object files, using existing evolutionary libraries. Supported C++ libraries currently are GALib or EO.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
BioCoRE is a collaborative work environment for biomedical research, research management, and training. It features easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.
Asymptopia Flashcard System uses Motif and LaTeX to produce, manage, and use attractively formatted flashcards. You load some or all of your "collections" and set the timer for pop-up frequency. The GUI interface and "Collection Manager" make creating and modifying flashcards as simple as pushing a single button. A knowledge of LaTeX is only required when entering special symbols.
NeoBio is a Java class library of computational biology algorithms. The current version consists mainly of pairwise sequence alignment algorithms, such as the classical dynamic programming methods of Needleman and Wunsch (global alignment) and Smith and Waterman (local alignment). A more efficient approach, due to M. Crochemore, G. Landau, and M. Ziv-Ukelson (2002) is also available. All sequence alignment algorithms support simple scoring schemesm as well as substitution matrices such as standard BLOSUM and PAM matrices with constant (linear) gap penalty functions only. Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction. NeoBio also also provides simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.