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This project is no longer hosted on sourceforge, please go to https://github.com/jodersky/sims instead.
A library for rigid body simulation written in Scala. This project was created under the terms of a one-year project at school (Gymnase de Burier). Another program for testing and visualizing SiMS, Graphyx, is included.
ARTADE (ARabidopsis Tiling-Array-based Detection of Exons) is a standard tool for the automatic annotation of genome-wide tiling-array data in Arabidopsis. ARTADE is a program originally written by Dr. Tetsuro Toyoda, RIKEN, Japan.
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...
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Re-searcher is the system for recurrent psiblast searches. It enables timely detection of new proteins on the protein sequence databases. Searches can be done on a local server or at NCBI. It has a user-friendly web interface.
MobHealth is an extensible mobile health framework/API written in JavaME. The current version supports two sensor-data formats (e.g. used by AliveTec). It already provides higher-level classes for data recognition like body position or hypoxia-detection.
Java framework for face detection and face recognition based on different plugin and filter types. Includes Eigenfaces in pure Java, OpenCV detection via JNI, integration of the Betaface.com Web Service, skin color filter, Adobe XMP Export and a nice GUI
ABPS - Advanced Branch Prediction Simulator - allows: branch prediction simulation using multiple predictors (GAg,PAg,PAp,GShare,Perceptron) and detection of unbiased branches. Results can be seen using charts. Used benchmarks: Stanford, SPEC2000, CBP2.
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JTextPro: A Java-based Text Processing tool that includes sentence boundary detection (using maximum entropy classifier), word tokenization (following Penn conventions), part-of-speech tagging (using CRFTagger), and phrase chunking (using CRFChunker).
The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.
The Network Security Response Framework (NSRF) allows for testing different computer security response engines and methodologies. It supports simulated and real: Intrusion Detection Systems (sensors), Attacks, and Responses.
A Java-based client-server architecture for processing network intrusion detection data. The server receives XML alerts from Snort sensors buffers them for review by clients. The console provides a real-time view of IDS activity.
idyuts is \"I Dare You to Use This Shell\"; a pre-hibernate approach to replacing an ORM written with jython functors into a pure-Java language command pattern. The \"pipeline codegen artifacts\" are simple IoC templates, and trivial to adapt
Grok is a library of natural language processing components, including support for parsing with categorial grammars and various preprocessing tasks such as part-of-speech tagging, sentence detection, and tokenization.