Search Results for "physics"
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Showing 43 open source projects for "physics"
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PhysiCell
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations. -
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Gwyddion
Scanning probe microscopy data visualisation and analysis
A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis. -
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PDPBioGen
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20
NOTICE OF CONSOLIDATION & PARTNERSHIP PENDING As of April 2026, the 20 pipelines of the QCAUS/PDPBioGen suites are undergoing consolidation for high-scale institutional research. Core 'Ford 2026' algorithms remain the proprietary IP of the Ford Peace and Justice Foundation. Academic users at partner institutions are currently performing validation; all other commercial inquiries must contact the author -
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'isotope' is a small command-line utility to calculate the isotope pattern for a given chemical formula. It allows to run calculations interactively, in batch mode, via the command line, or (using a webserver) via a web interface.
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bruread is a program to read and display NMR data in the Bruker XWIN-NMR format. The program has a command-line interface and a graphic display based on gnuplot. - Note that this is only an NMR spectrum *viewer*, not a full-fledged data evaluation suite
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cdfread is a program for people wirking with mass spectrometry datasets. cdfread implements the routines to read mass spectra and mass chromatograms from data files in netCDF ("Andi-MS") format. Centroid and profile data are supported.
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MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
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SPIRE
A tool to compute projections of membrane structures
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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CvMob is an Open Source tool to automatic visual analysis of human movement. The software calculates the optical flow to generate data about trajectory, velocity and acceleration using low-quality videos. For more informations, please visit our website: http://www.cvmob.ufba.br/
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS... -
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ImagingAnalysis
Direct tissue-level image quantification package for Mathematica
ImagingAnalysis is a Mathematica package that performs grid-based analysis of time-lapse imaging data saved in a sequence of TIFF files. This package requires Mathematica 7.0. Revised on 14 May 2017: Bugs are fixed and incompatibility issues are resolved. The current version runs on Mathematica 11. -
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PPTT
Planning PhotoThermal Therapy
The project serves as a simulator of photothermal therapy that efficiently destroys tumours. -
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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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Muninn
A software package for estimating generalized ensemble weights in Mark
We have moved to GitHub: https://github.com/muninnorg/muninn As of July 2015 we have moved to GitHub. The SourceForge page will preserved, with the old releases. Muninn is a software package for estimating generalized ensemble weights in Markov chain Monte Carlo (MCMC) simulations. The method is full automated and makes use of the generalized multihistogram (GMH) equations for estimation the density of states [1]. The package is implemented in C++ and has a convenient interface. -
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gMol
gMol molecular graphics
We've moved to https://github.com/tjod/gMol/wiki gMol is an interactive visualization system used to display and manipulate 3-dimensional models of scientific data, such as molecular structures and surfaces. It contains both OpenGL and web browser widgets that enable flexible user interfaces. -
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This library aims to provide support for D-dimensional images in Java and to enable high-level implementation of algorithms in dimensionally-invariant manner. Major features: the dimensionality and the access to primitive data types are abstracted.
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RaTrav
mean first passage times and node occupancies calculations
RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single or multiple final states in network-like systems are used. The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation... -
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Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
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The Blue Obelisk Data Repository lists many important chemoinformatics data such as element and isotope properties, atomic radii, etc. including references to original literature. Developers can use this repository to make their software interoperable.
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A shareware for build realtime photoacoustic tomography image using NVidia Geforce GPU. Can work in both offline mode or online mode.
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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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The igraph library
Library for creating and manipulating graphs
This is a library for creating and manipulating graphs with focus on speedy operations for large, sparse graphs.
