A pre- and post-processing program for the VASP code
Basic features: 1, Convert POSCAR or CONTCAR to cif or xsf format; 2, Extract the data of DOS and Band; 3, Extract Charge/Spin density (Open with VESTA ); 4, Linear optical properties; 5, Extract Fermi-Surface data; 6, and so on...
The Home of DMSFT, AAFFT, GFFT, and MSFFT.
A collection of sparse Fourier transform codes developed by faculty at MSU. Currently codes for four different prototype sparse FFTs are here: 1.) DMSFT, implemented by Ruochuan Zhang. This is a fast, stable, noise robust, and *fully discrete* improvement on the ideas in GFFT below. It is THE BEST sparse FFT around!!! If you're looking for AAFFT, try this out first. 2.) AAFFT, implemented by Mark Iwen in 2008. This code is easy to use, and documented well, but not implemented very efficiently. It is much slower than it should be. 3.) GFFT, implemented by Ben Segal and Mark Iwen. This code is less easy to use, and also not terribly efficient. But, the *algorithm* itself is significantly simpler and has "essentially no parameters". 4.) MSFFT, implemented by David Lawlor and Bosu Choi. This code is fast, but is not terribly easy to use. The algorithm is robust to some noise, but requires a lot of parameter tuning. Enjoy at your own risk :), Mark Iwen
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Efficient memory management of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. VCF-Explorer presents an easy to use environment where various types of queries for the annotation and the samples can be defined. VCF-Explorer can be run at different environments and computational platforms ranging from a standard laptop to an advanced server.
Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
This project proposes a virtual laboratory for social scientists interested in the modelling, analysis and behavioral simulation of power relationships within organizations and more generally in systems of collective action. This software is grounded on the works lead by Sibertin-Blanc and Roggero on the formalization of the Sociology of Organised Action [Crozier and Freidberg]. Visit the homepage of the project on soclabproject.wordpress.com for tutorials, examples and further theoretical position.
molecular editor and viewer
Luscus is the program for graphical display and editing of molecular systems. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus can also visualize dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to point out a geometrical feature or a physical quantity. The program is developed as a graphical interface for MOLCAS program package, however it's adaptive nature makes possible using luscus with other computational program packages and chemical formats. If you use this program, please cite: G. Kovačević, V. Veryazov, J. Cheminformatics, 7 (2015) 1-10; DOI: 10.1186/s13321-015-0060-z
A MATLAB toolbox for relating neural signals to continuous stimuli
mTRF Toolbox is a MATLAB toolbox that permits the fast computation of the linear stimulus-response mapping of any sensory system in the forward or backward direction. It is suitable for analysing EEG, MEG, ECoG and EMG data. The forward model, or temporal response function (TRF), can be interpreted using conventional analysis techniques such as time-frequency and source analysis. The TRF can also be used to predict future responses of the system given a new stimulus signal. Similarly, the backward model can be used to reconstruct spectrotemporal stimulus information given new response data. mTRF Toolbox facilitates the use of continuous stimuli in electrophysiological studies as opposed to time-locked averaging techniques which require discrete stimuli. This enables examination of how neural systems process more natural and ecologically valid stimuli such as speech, music, motion and contrast. Support documentation: http://dx.doi.org/10.3389/fnhum.2016.00604
This is a suite of mathematical software solvers GUI
This is a suite of mathematical software solvers interface on DLV and other command-line solvers. It helps researchers and students to better comprehend their declarative definitions published on papers. The user can have links to the related papers and to the software of the corresponding definitions.
Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. firstname.lastname@example.org , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).
Pc Calculator is a clever note and formula editor combined with an advanced and strong scientific calculator. Being an editor it is extremely user-friendly allowing all possible typing and other errors to be easily corrected and fast recalculated.
PowerDEVS is an integrated tool for hybrid systems modeling and simulation based on the DEVS formalism.
Synthesizable SystemC Benchmark Suite
S2CBench v.2.0 provides 18 programs written in synthesizable SystemC language. Each benchmark is designed for specific domains such as multimedia, digital signal processing, security, image processing, etc. The programs are provided with the objective to enable researchers analyze their innovative algorithms and techniques and help users compare the quality of results of state of the art commercial High Level Synthesis tools available in industry. You can log in to our Youtube channel to watch some videos about S2CBench and SystemC in general www.youtube.com/DARClabify or visit our labs web page at www.utdallas.edu/~schaferb/darclab To know more about the designs and why they were included in the benchmark suite you can read the following academic paper: B. Carrion Schafer and A. Mahapatra, "S2CBench:Synthesizable SystemC Benchmark Suite for High-Level Synthesis ", IEEE Embedded Systems Letters, 2014
Tool to plot 3d-graphic from an XML, EXCEL or parametrization
"wpf-plot3d" is a tool designed to plot 3-dimensional graphics. It can handle a wide range of graphic types: - Surface: Graphic defined on a Cartesian grid defined via an XML file - Mesh: Graphic defined on a general mesh defined via an XML file - Points: Set of points defined via an XML file - Curve: 3d-curve defined via an XML file - Parametric surface: Parametric surface defined on a cartesian grid - Parametric curve: 3d parametric curve "wpf-plot3d" includes toolboxes: - Camera: Rotation, zoom, ... - Settings: Define own colors, effects, timer to refresh, ... - Pallet: Add comments, arrows, ... "wpf-plot3d" is implemented in C/C# and uses Windows Presentation Foundation (WPF)
The Insecticide Resistance Monitoring Application
Cell impedance analysis software.
MAT-MECAS is used for calculation of impedance parameters of a cell from recorded current responses elicited by bipolar voltage stimuli in a whole-cell patch-clamp experiment. The calculations are based on a FFT deconvolution procedure and on approximation of the reconstructed currents with a theoretical function. The impulse response of the signal path is necessary for the calculations. Read manual first! For testing MAT-MECAS we provide a sample data along with sample stimulation protocols.
Binner for assembled metagenomes
The Metawatt binner is a graphical binning tool that makes use of multivariate statistics of tetranucleotide frequencies and differential coverage based binning. It also performs taxonomic assessment of binning quality (via diamond BLASTx). Created bins can be edited and exported as fasta. The Metawatt is implemented in Java SWING and minimally depends on Diamond, HMMer3.1, BBMap, Prodigal and the Batik library for the export of SVG graphics. Citation: Strous M, Kraft B, Bisdorf R, TegetMeyer H (2012) The binning of metagenomic contigs for microbial physiology of mixed cultures. Frontiers in Microbial Physiology and Metabolism 3:410. doi: 10.3389/fmicb.2012.00410
The math category theory software with diagram graphical user interface.
An Interactive Visualisation for Tabular Data
TabuVis is a comprehensive visual analysis tool that provides a flexible, customizable and interactive visualization for tabular (or multidimensional) data. It utilizes scatter-plot visualization approach to provide comprehensive and interactive views for different attribute mappings. It provides both single scatter-plot and multiple scatter-plots. The project is available at: http://staff.scem.uws.edu.au/~vinh/projects/TabuVis/
The OpenGEREA is a open enrichment analysis framework for gene expression regulation data analysis.
Plane frame static and dynamic analysis
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. New Biotechnology 33:790-796.
Common software for AMS-A
Common software for AMS-A
Blueprint XAS is a Matlab-based suite designed for the processing and analysis of near-edge x-ray absorption spectroscopy (XAS) data. The suite is designed primarily to assist users in exploring reasonable fit solutions while minimizing user bias.
A digital ambient air data logger built on Debian.
This is the California Air Resources Board, environmental digital data logger (CARBLogger) project which develops and maintains an open source, shell-script based digital data acquisition and reporting system.
Direct Protein-SIF: CALgary approach to ISotopes in proteomics
Calis-p (The CALgary approach to ISotopes in proteomics) is a software package to directly extract stable carbon isotope fingerprints (SIFs) of individual species in a microbial community from a metaproteomic dataset. It takes the scored peptide-spectrum match (PSM) tables for samples and the calibration material, and the raw MS data in mzML format as input. In the first step, the software finds the isotopic peaks for each PSM and sums their intensities across a specified retention time window. The identified isotopic patterns (pairs of m/z value + summed intensities) together with the sum formula of the identified peptides are reported and used as the input for the second step of Calis-p to compute delta13C values for all peptides that pass a set of filters, as well as average delta13C values and standard errors for each species. The species delta13C values need to be corrected for instrument isotope fractionation by applying the offset determined using the reference material.