Search Results for "x11-basic"

The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format.

MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++. Our source code and wiki lives on GitHub (https://github.com/OpenMS/OpenMS).

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

set of classes used to handle input/outputs of bioinformatics data files and basic operations as multiple alignment and phylogenetic reconstruction.

The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.

XMIPP is an image processing suite for 3D-reconstruction of biological specimens from transmission electron microscopy data. NOTE that stable releases (including binaries) are longer stored at Sourceforge, but are available at http://xmipp.cnb.csic.es

Ezys is a non-linear 3D medical image registration program. Ezys fully exploits the parallel computing power of inexpensive commercial graphics processing units (GPU), resulting in a very fast and accurate program capable of running on desktop PCs and even some laptops. On these systems, non-linear image registrations take less than a minute to complete. Ezys implements a diffeomorphic inverse consistent image registration algorithm with a demons-style regularization based on a...

ProtoMol is an object-oriented component based framework for molecular dynamics simulations.

...Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic networks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems).

GaloisExplorer provides a user-friendly interface for basic functionalities of Formal Concept Analysis (FCA) with different lattice generation algorithms and an interactive viewer to explore a 3-dimensionally laid out lattice.

CaspLab - Comet Assay Software Project Lab is a cross-platform image analysis software to measure level of DNA damage in SCGE (Single Cell Gel Electrophoresis) method called also comet assay method.

This is a semi-automatic high-throughput hypocotyl phenotyping software. It takes as input time-lapsed images of hypocotyls and measures their elongation and bending

CellNet3D is an application for visualising chemical formula in 3D on Linux platform through PDBlib and X11.

Stand-alone software tool for the interactive CE analysis of microarray data. The software is a user-friendly and allows on-the-fly study of CE

PhyloCpp is (will be...) a C++ toolkit designed for the reading, writing and manipulation of phylogenetic trees with an emphasis on comparative methods, ancestral state reconstruction and characterization of the evolutionary process.

Spotfinder is an image processing software tool for microarray image analisys. It is written on C++ with QT GUI toolkit and runs on Windows, X11, and Mac OSX.

Batman-Seq: Basic Alignment Tool for MAny Nucleotides. A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.

Protein Mass Spectrometry: cprobid is a software for identification peptides from MS/MS spectra. The output of this program is compartable with TransProteomic Pipeline software package (sashimi project).

A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.

Working hardware has been built and is in a late beta stage. Software is also available.

The program NAcMoS (Nucleic Acid Modeling System) is a software package that leads to a natural classification of RNAs represented as weighted graphs.

Cell Motility Analysis Package analyzes timelapse sequences of moving cells. Various quantitites characterizing motility are calculated, including normal velocity of the membrane, cell contact area, and spatio-temporal auto-correlation functions.