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DNA sequencing quality values, base calling and trace processing
Tracetuner is a tool for base and quality calling of trace files from DNA sequencing instruments. Originally developed by Paracel, a Celera Business, this code base was released as open source in 2006. TraceTuner was used by Celera to call 30+ million reads from both Drosophila and human genome sequencing projects. In 2000, Applied Biosystems bundled TraceTuner with ABI3700 Genome Analyzers and shipped it to the customers of these capillary electrophoresis sequencers. Later versions of...
The ProM Import Framework allows to extract process enactment event logs from a set of information systems. These can be exported in the MXML format, which is the standard event log data format for Process Mining analysis techniques.
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.
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Software tools for visual psychophysics research. The focus of these tools is amblyopia research, but they can be used in some related visual neuroscience research tasks.
VT-Layer is a Java library for discrete-event simulation modeling. VT-Layer allows you to create, visualize, and analyze high-performance discrete-event simulations.
JStatCom is a software framework that facilitates the creation of JAVA programs for data based analysis tasks in various domains. It provides ways to call routines from specialized software packages, like Matlab, Gauss, Ox, and possibly others.
Carbon Effective Supply Chain Simulator (CESCS) is a software package for simulating green supply chain. A unique approach is taken to help achieve the optimal balance between carbon footprint, supply chain cost, service level, and product quality.
The CodeTime platform covers every aspect of parallel software from authoring, through distribution, to run-time. Its goals are: high programmer productivity; write once, run high performance anywhere; and wide acceptance.
ScreeningAssistant is a software based on JOELib and dedicated to the management of chemical databases. It allows the user to select a set of compounds for screening tests (High Throughput Screening or Virtual Screening).
XMPP Web Services for Java (XWS4J) is an implementation of machine to machine communication over XMPP. The communicated content is encoded in XML, according to customized definitions of input and output in W3C XML Schemata.
Planning Tool is a tool developed by QualDev Group (Universidad de los Andes, Bogota, Colombia) created to support the planning process and to track project's activities for all the projects worked in the group.
AntManager is a Java-based, multi-threading and easily extensible build engine using Apache ANT to manage the build process of a whole hierarchical software project structure. Enjoy your build with AntManager.
Eclipastie is an open source Eclipse (3.3+) plugin (EPL license) which seamlessly copy and pastes text from within Eclipse to pastebins like Pastie (http://pastie.org) or LodgeIt (http://paste.pocoo.org/)
The Napkin Look and Feel is a pluggable Java look and feel that looks like it was scrawled on a napkin. You can use it to make provisional work actually look provisonal, or just for fun.
UfakPython is a small subset of Python programming language, for small embedded devices, like PICs. UfakPython sources are translated to C by UfakPython Compiler. Small Device C Compiler can then compile the C outputs to the target device's codes.
Framework: Project for Evolutionary Predator Prey Algorithms, used to implement an evolutionary scheme based on the developement by van Laumanns. Implement testproblems, special behaviours, environments, and other yet not known features.
Franklin Math is an open source Java symbolic computer algebra system (CAS), with similarities to commercial math packages such as MATLAB or Mathematica. It allows numeric and symbolic calculations, with built-in functions including plotting commands.