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CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.
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Biosphere3D targets interactive landscape rendering based on a virtual globe. It supports DEM, satellite and aerial images, 3D models (Collada), 3D plant models, and Shapefiles.
Download Biosphere3D

SasView is a Small Angle Scattering (SAS) analysis package for the analysis of 1D and 2D scattering data directly in inverse space. The focus was originally on neutron data (SANS) but has been used for X-ray’s as well and includes a tool for determining a slit resolution for the SAXSess instrument. SansView also includes PrView to invert SAS data to P(r), a resolution calculator, and a scattering length density calculator among others tools. A simple plugin mechanism is available for users to add custom models.
Download SasView

XNBC is a full featured application for computer naive neuroscientists. It simulates biological neural networks using graphic tools to edit neurons and networks, to run the simulation and to analyze results. Written in C, it runs on Unix and Windows.
Download XNBC

This is an implementation of an Artificial Neural Network Library which learns by example. You give the algorithm examples of what you want the network to do and it changes the network's weights. When training is finished, it will give you the required output for a particular input. The project includes handwriting recognition demo application, which is an excellent prototype problem for neural networks learning...
Download Nunn

NCE Process Engineering Tools Collection
Collection of process engineering calculation tools put all together. List of tools: NCE-Panel (common application launcher); PipingUtility (fluid flow and pressure drop calculation in piping); TankHeatLosses (thermal losses from a storage tank); LeeKesler (vapor pressure estimation with corresponding states method) EoS (equations of state); DataInterpolation (interpolation/extrapolation with two data points); Viscosity estimation.
Download NCE Process Engineering Tools Collection

An open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.
Download Open3DALIGN

SCIRun is a problem solving environment or 'computational workbench' in which a user selects software modules that can be connected in a visual programing environment to create a high level workflow for experimentation. Each module exposes all the available parameters necessary for scientists to adjust the outcome of their simulation or visualization. The networks in SCIRun are flexible enough to enable duplication of networks and creation of new modules.
Download SCIRun

Tool for Analysis of Surface Cracks (TASC) is a computer program created in MATLAB to enable easy computation of nonlinear J-integral solutions for surface cracked plates in tension by accessing and interpolating between the 600 nonlinear surface crack solutions documented in NASA/TP–2011-217480. The only required inputs are the surface crack dimensions (2c and a), plate cross-section dimensions (W and B), and linear plus power law material properties of elastic modulus, yield strength, and strain hardening coefficient.
Download TASC

SiBELia (Synteny Block ExpLoration tool) is a fast synteny blocks generation tool for many closely related microbial genomes. It assists biologists in analyzing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. SiBELia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. SiBELia is useful in finding shared regions, regions that present in one group of genomes but not in others, and rearrangements that transform one genome to other genomes.
Download SiBELia

Circuitscape is a free, open-source program which borrows algorithms from electronic circuit theory to predict patterns of movement, gene flow, and genetic differentiation among plant and animal populations in heterogeneous landscapes. Circuit theory complements least-cost path approaches because it considers effects of all possible pathways across a landscape simultaneously.
Download Circuitscape

A periodic table written in qt4. Inspired by the great kde app Kalzium. QPeriodicTable is an application which will show you some information about the periodic system of the elements. Therefore you could use it as an information database. Note: Just extract the zip file and launch QPeriodicTable.exe. Place the QPeriodicTable folder where you want, but don't change the internal structure of the folder, or the application will stop working.
Download QPeriodicTable

Reconstruction and Visualization from a Single Projection (ReViSP) tool: a 3D volume rendering method we developed to reconstruct the 3D shape of multicellular spheroids, besides estimating the volume by counting the voxels (3D pixels) fully included in the 3D surface.
Download ReViSP

QXRD is an application designed to control the readout of an amorphous silicon flat panel X-ray detector made by Perkin Elmer, and is intended for use at a synchrotron light source beamline. QXRD acts as a bridge between the dynamic link library provided by Perkin Elmer and the beamline data acquisition software 'spec' and also provides a convenient GUI interface to the detector.
Download QXRD

Snp Viewer
Snp Viewer aims to be a simple, easy-to use program that enables the viewing and analysis of Affymetrix SNP chip data for homozygosity mapping. Snp Viewer requires as input birdseed files generated by the Affymetrix Genotyping Console containing the 'Call Code' field (i.e. the field giving genotype calls as 'AA', 'BB', 'AB' or 'NO CALLS'). If you have these files for your samples of interest you should be good to go.
Download Snp Viewer

SunCalculator is a simple and easy-to-use application designed to enable you to calculate sunrise, sunset and twilight times and presents them as graphically. You can calculate the sunrise, sunset, astronomical twilight, nautical twilight, and civil twilight for every date between 1801 and 2099. The calculations are based on the sunrise function.
Download SunCalculator

Gecko Hamaker
Gecko Hamaker creates a London Dispersion spectra for the materials in the database. The user may then set up the layer configuration for the calculation by creating a project and assigning database materials to layers in the project. Gecko Hamaker then automatically calculates Hamaker coefficients for your project. Hamaker constants represent the London Dispersion Force of the van der Waals attraction between two materials.
Download Gecko Hamaker

The Berkeley Open Infrastructure for Network Computing (BOINC) software is a distributed computing infrastructure originally developed out of the SETI home project, but intended to be useful to fields beyond SETI. BOINC is the information technology infrastructure for distributing work in the form of work units and downloading the distributed applications that process them. BOINC does no useful scientific work itself. Scientific computations are run on user computers and results are analyzed after they are validated and transferred from BOINC into a scientific database.
Download BOINC

WorldWide Telescope
The WorldWide Telescope (WWT) is a visualization environment that enables your computer to function as a virtual telescope - bringing together imagery from the world’s best ground- and space-based telescopes for the exploration of the universe. WWT blends terabytes of images, information, and stories from multiple sources into a seamless, immersive, rich media experience. Explorers of all ages will feel empowered to explore and understand the cosmos using WWT’s simple and powerful user interface.
Download WWT

A collection of command-line tools for atom probe analysis including:
- Point data XML scripting language, load, transform, resize and otherwise alter point data
- Radial Distribution Function analysis tools
- Level-set tools for simulating shape transformations during experiments.
Download APTTools

Seq Format Converter
Seq Format Converter is a lightweight and easy to use program that will allow you to easily load a file that contains nucleotide or peptide sequences you want to convert to different formats. Seq Format Converter supports tab delimited data for output, as well as fasta or fastaq (biological sequence format), so you can simply drag and drop the files to be processed and press the corresponding button.
Download Seq Format Converter

Nuc-End-Remover is a simple and easy to use program that aims to help users who need to modify nucleotide sequence data on the fly. The application is able to scan a loaded FAST or tab delimited sequence file and it will remove automatically any stretches of nucleotides that are placed at the 3' and 5' ends of the target sequence.
Download Nuc-End-Remover

Complement Reverse
Complement Reverse is a very easy to use application that can reverse and make complement of nucleotide sequences you insert in its main window. Insert the sequence in the appropriate section of the main window, select the desired option and press 'Convert and Copy' to have the application to do its job on the spot.
Download Complement Reverse

Unipro UGENE
Unipro UGENE is a free visual software solution for DNA and protein sequence analysis. UGENE provides customizable tools for visualization, analysis, annotation of genetic sequences. Key features are: Integrated MUSCLE alignment tool, Integrated HMMER2 package, OpenGL viewer for PDB macromolecular structures, and Workflow Designer to create and execute custom computational workflows. Description of the view used to visualize and edit DNA, RNA or protein sequences along with their properties like annotations, chromatograms, 3D models, and statistical data.
Download Unipro UGENE

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