Search Results for "alpha"

SBEVSL is a collaborative project between Dowling and RIT on the development of a Structural Biology Extensible Visualization Scripting Language, so that users can move freely among various molecular graphics tools, such as rasmol, pymol, raster3d, etc.

lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/

NOTE: Use of this codebase is NOT RECOMMENDED. This project has been migrated to github at http://jaerproject.net (or https://github.com/SensorsINI/jaer for the Java code). Commits have been disabled for the subversion sourceforge repository and new development is being done on the github repository. Java tools for Address-Event Representation (AER) neuromorphic processing. Uses USB hardware. See wiki at https://sourceforge.net/p/jaer/wiki/

AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus...

The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.

Dynamis is a simple ODE solver implemented in C for studying dynamical systems (e.g. population biology).

Open Source project for the development of the IEEE 11073-20601 reference implementation.

This is a project for Andre to share CellML related tools he works on that other people might find useful.

An algorithm to compute molecular graph descriptors considering the stereochemistry of the molecular structure, based on our previously introduced signature molecular descriptor. The algorithm can generate two types of descriptors, one which is compliant with the Cahn-Ingold-Prelog priority rules, and a faster one based on our previous definition of a directed acyclic graph that isaugmented to a chiral molecular graph.

OpenCV powered image stack analyser for data extraction and preparation. Can be used in conjunction with nanocalcFX. You can get sample data at the NISA homepage. Currently in pre-alpha state.

The NovelSeq pipeline is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

The pyBioImage is a python a python based biological imaging suite tailored to the problem of finding Germinal Center "spots" within multidimensional microscopy images as it is described in the research paper: "Software tool for 3D extraction of germinal centers", by David N. Olivieri, Merly Escalona and Jose Faro.

CoactivationMap is a graphic user interface to browse through a map of functional co-activations of the human brain. Click on a region, and observe which other regions are likely to be connected

A set of command-line utilities for annotating and manipulating DNA sequences in FASTA format. Generate restriction fragments, ORF's, translations, reverse complement, etc. . - and tie it all together with Unix pipes for complete virtual cloning.

Similarity / dissimilarity measures for community ecologists, and palaeontologists.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

Foad is an open source software which receive an EKG Signal from scanner, WFDB database or heart sensors. Finding patient disease started by taking Fourier transform (FFT) from input signal and extract a single cycle. Based on some heuristic algorithm the most important feature like P , Q , R , S , T captured and feed to trained neural network. and so the final decision made by CNN library. As mentioned before this software also capable do some image processing on scanned paper to lower...

MTMP is a multi-threaded multiple pattern matching algorithm based on the Wu-Manber algorithm.

This tool is designed to solve generalized pattern matching problem, by which we only find a set of sub-patterns, ignoring the gaps in between the sub-patterns. This tool is extremely fast and also has good tolerance to errors.

Juggernaut is a high throughput out of core sequence assembly algorithm. This program is very useful in assembly projects involving massive number of short reads which originate from high coverage of the genome.

SIPeS - Site Identification from Paired-end Sequencing

The EvoGrid is an effort to develop a distributed simulation system to simulate potential pre-biotic chemical environments.

Opensource software projects for genetics and genomics from Sage Bionetworks.

CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/