Search Results for "gnu linux"
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Showing 53 open source projects for "gnu linux"
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Systems Biology Markup Language (SBML)
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more. -
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KARDIA ("heart" in Greek) is a Matlab software with a graphic user interface designed for the analysis of cardiac interbeat interval data.
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PsPM
A matlab suite for Psycho-Physiological Modelling
PsPM is a powerful tool for psychophysiological modelling. It includes linear convolution models and non-linear models for SCR, and allows for modelling of other signals, too. A flexible import interface and many utilities make this software a standalone tool. IMPORTANT: As of 04.11.2019, the official code repository for PsPM has been moved to https://github.com/bachlab/PsPM . In order to check the latest releases, discussion and bug reports, please refer to our new repository. Although... -
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De_Lux
Deconvolution of luminescence cross-talk in microplate reader data
An algorithm to deconvolve the luminescence cross-talk in high-throughput gene expression profiling to recover the true luminescence activity of a microplate. -
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BWTT
BIOTACT Whisker Tracking Tool
The BWTT is an artefact of the EU Framework 7 Project BIOTACT 215910. It is an extensible software framework that runs under Matlab (Mathworks, TM) providing for the computation of whisker tracking algorithms for small mammal observation. Other tracking algorithms (e.g. snout tracking) can also be included. The software is released with a number of algorithms included, allowing rapid whisker tracking with no other software required (other than Matlab). -
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EigenMS is a normalization method implemented in R (and older version in Matlab) available as a set of two functions that should be used in a sequence. Please download EigenMS.zip file (latest version). Latest version uploaded in October 2017 has a bugfix for single treatment group normalization. Rescaling has been omitted from 2015. EigenMS utilizes SVD to detect bias trends in the data and eliminates them. EigenMS eliminates effects from known and unknown factors and can be...
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BioRec:Bird Census field data annotation
Recognizing biological data from a notebook.
This project helps to digitize field data for a certain Bird Census method. Namely, bird census based on personal inspection or small (~10 km^2) regions with recording birds' position and behaviour on paper. This project makes it easy to annotate such field data and to make this data available for statistical analysis. -
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All future developments will be implemented in the new MATLAB toolbox SciXMiner, please visit https://sourceforge.net/projects/scixminer/ to download the newest version. The former Matlab toolbox Gait-CAD was designed for the visualization and analysis of time series and features with a special focus to data mining problems including classification, regression, and clustering.
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SoundRuler is a tool for acoustic analysis, graphing and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing and didactic modules.
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PB-sQF_BacterialTyping
Bacterial Typing from either assembled or raw short reads file
Probability Binning - signature Quadratic Form, PB-sQF, types unknown sequence to one of the 628 bacterial library genomes which gives the smallest test statistics thus most similar library strain. The input file is the k-mer counts of the unknown assembled genome sequence or raw short reads file in decimal format generated by KAnalyze developed by P. Audano et al. (https://sourceforge.net/projects/kanalyze/). The download included the library index, the library name and sample unknowns. -
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This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
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FieldTrip
The MATLAB software toolbox for MEG and EEG analysis
FieldTrip is the Matlab toolbox for EEG and MEG data. It includes algorithms for simple and advanced analysis, such as importing, preprocessing, time-frequency analysis, source reconstruction, statistical testing and connectivity analysis. -
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NBT is an open source Matlab toolbox for the computation and integration of neurophysiological biomarkers. NBT allows for easy implementation of new biomarkers, and incorporates an online wiki with extensive help and tutorials.
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math lib for .NET. n-dim arrays, complex numbers, linear algebra, FFT, sorting, cells- and logical arrays as well as 3D plotting classes help developing algorithms on every platform supporting .NET. Sources from SVN, binaries: http://ilnumerics.net
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SysGenSIM is a bioinformatics toolbox to create artificial gene expression datasets by simulating Systems Genetics experiments.
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EXIMS
EXploring Imaging Mass Spectrometry data
EXIMS: an improved data analysis pipeline based on a new peak picking method for EXploring Imaging Mass Spectrometry data. -
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An implementation of the Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method for MATLAB and R. The supplied functionality includes e.g. cross-validation, kernel parameter optimization, model diagnostics and plot tools.
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OpenFlux2 is an extended version of OpenFLUX (https://sourceforge.net/projects/openflux/) - the modern MATLAB-based modelling software for 13C flux analysis (MFA). The following features were implemented in OpenFLUX2, which were not present in original software: integrated support for calculation and analysis of parallel labeling experiments (PLE), extended statistical analysis of parameter estimation results, calculation of fluxes and measurements correlation, structural identifiability...
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Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
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PlaTypUS
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes. -
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FluxModules
Module Computation for Metabolic Networks
Genome Scale Metabolic Networks are complex systems, Modules help to break them down and hence ease understanding and algorithmic complexity. FluxModules is a toolbox with code for module detection and module visualization. -
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MCTIMME
Microbial Counts Trajectories Infinite Mixture Model Engine
MCTIMME is a nonparametric Bayesian computational framework for analyzing microbial time-series data.The current implementation is in Matlab. -
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KYM is a MATLAB / GNU Octave set of functions that implements a wavelet-based automated procedure of quantification and characterization of biological signals. In particular it has been thought for the analysis of the oscillatory component of cytosolic calcium concentration time course.
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abc-sde
approximate Bayesian computation for stochastic differential equations
A MATLAB toolbox for approximate Bayesian computation (ABC) in stochastic differential equation models. It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. Variance components for the "measurement error" affecting the...
