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Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
The development and curation of a range of XML-based tools
for using Chemical Markup Language (CML), including
XSD XML Schemas for validation, datatyping and constraining CML
documents and XSLT Stylesheets for transforming, filtering and rendering.
h2:www is an easily extendable online interface for bioinformatical command-line tools, providing convenient project-oriented working facilities for multiple users.
GAME stays for Generic Architecture based on Multiple Experts.
Its main purpose is to make easy prototyping, test and release of prediction systems.
Released by IASC group, university of Cagliari
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DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.
PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen
SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
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OmicBrowse, developed with Flash and Java, is a highly evaluated genome browser integrating omics knowledge ranging from genomes to phenomes and is especially appropriate for positional-cloning purposes.
Quantitative Evalution of Blush: a program to assess myocardial reperfusion on coronary angiograms. This program calculates a value that can be used for risk classification of STEMI patients or as a surrogate endpoint in clinical trials.
JRasterCreator allows you to easily & visually build a raster file for the mass spectrometry instrument Bruker Daltonics MS ultraflex II by clicking on various spots/locations.
CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.
Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
FreeLIMS is a Laboratory Information Management System ( LIMS ). Manage samples; create sample types from methods & parameters; easily generate reports & certificates; fine tune user rights. FreeLIMS is Open Source and Free.
Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV