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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the wild type and mutants (original strain with a set of selected gene deletions).
Cytoscape is an open source software platform for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms.
Toolbox for handling X-ray transmission image data collected using the Xradia TXM system. Features: Xradia file format support; FBP and ART tomo reconstruction; Command script generation for different experimental designs; TXM XANES imaging data analysis; PCA and k-means clustering of TXM XANES data.
Kalypso is an open source application for geospatial modelling and simulation. It is primarily developed to be a user friendly tool for GIS-based modelling and simulation of hydrological and hydraulic numerical models. Features: Hydrological model; Water surface profile model; Unsteady coupled 1D/2D finite element model; Module for flood depth determination; Module for flood risk determination.
OpenChrom Community Edition
OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP. Features: baseline detection; peak detection, integration and identification; mass spectrometric data filter (remove m/z, smooth data, ...); extensibility, modularity; native data file import converter; advanced GUI.
Download OpenChrom Community Edition
Finite Element Method Magnetics (FEMM) is a finite element package for solving 2D planar and axisymmetric problems in low frequency magnetics and electrostatics. The package is composed of an interactive shell encompassing graphical pre- and postprocessing; a mesh generator; and various solvers. A powerful scripting language, Lua, is integrated with the program. Lua allows users to create batch runs, describe geometries parametrically, perform optimizations, etc.
TexGen is a geometric textile modelling software package to be used for obtaining engineering properties of woven textiles and textile composites. Features: 2D Weave Wizard; 3D Weave Wizard; Variable yarn cross sections; Export in various formats including ABAQUS, IGES and STEP.
MetaMIS is the first tool to automatically infer the microbial interactions of microbial community profile in the field of metagenomics. The most distinguished feature of MetaMIS is its ability to retain maximum population of rare species in an ecological interactive network. MetaMIS provides a user-friendly interactive stand-alone graphical interface for scientists without programming skills to investigate the interactions among microorganisms.
PCRaster is a collection of tools and software libraries tailored to the construction of spatio-temporal environmental models. Application domains are amongst others hydrology (rainfall-runoff, global water balance, groundwater), ecology, or land use change. Two scripting languages (PCRcalc and Python) include a rich set of spatial operations for manipulating and analysing raster maps. A Python framework supports Monte Carlo simulations and data assimilation (Ensemble Kalman Filter and Particle Filter).
VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated - change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results.
IDP is a knowledge Base System (KB-system) for the FO(·) language. Using IDP, it is possible to model systems and problems, both from the real world as several artificial intelligence research problems. Solutions to these problems can then be found using one or more inference techniques. One class of real world problems that serves as a nice introduction to IDP is a scheduling problem.
BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc.
Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Combenefit only requires the user to save replicate data in the predefined .xls template files. It is based on an interactive platform which collects all experimental replicates and generates surface analyses for selected models. A wealth of outputs can be obtained and the software populates the project folder with the results.
itom is an open source software suite for operating measurement systems, laboratory automation and data evaluation. One main application of itom is the development and operation of sensor and measurement system for instance in a laboratory environment. Therefore, the software has to be able to communicate with a wide range of different hardware systems, such as cameras or actuators and should provide a diversified and as complete as possible set of evaluation and data processing methods.
Toast++ is a software suite for image reconstruction in diffuse optical tomography (DOT). It contains a forward solver module using the finite element method for simulating the propagation of light in highly scattering, inhomogeneous biological tissues, such as the brain. The inverse solver module uses an iterative, model-based approach to reconstruct the unknown distributions of absorption and scattering coefficients in the volume of interest from boundary measurements of light transmission.
Arabidopsis Motif Scanner
The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting en-hancers and silencers appear to have key roles in regulating gene expression. Arabidopsis Motif Scanner was design to build gene networks by identifying the cis-regulatory elements position in the model plant Arabidopsis thaliana and by providing an easy interface to evaluate gene relations.
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The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
Morpheus is a database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast-up to nearly 5 times faster than OMSSA for large human datasets.
Gimias is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, Gimias provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.
OVITO is a freely available visualization software. Being a single integrated application it covers both the analysis and the visualization of large-scale atomistic datasets produced by molecular dynamics/statics and Monte-Carlo simulation codes. The name OVITO is an acronym for Open Visualization Tool, emphasizing that this software has been designed with flexibility and extensibility in mind.
CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Previously known as PIVOT (Protein Interaction Visualization and Observation Tool).
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.
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...
QBlade is a Blade Element Momentum Method (BEM), Double Multiple Streamtube (DMS) and nonlinear Lifting Line Theory (LLT) Design and Simulation Software for Vertical- and Horizontal Axis Wind Turbines. It also includes tools to setup and simulate the internal blade structure and perform an aeroelastic analysis of a wind turbine rotor in turbulent inflow conditions through a coupling with FAST from NREL.
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
AtomicJ is a Java application for processing of force curves that allows for fast and reliable estimation of mechanical properties of the sample. AtomicJ supports a wide range of contact mechanics models, including the models for blunt tips, the corrections for the effect of finite sample thickness, models of adhesive contact and models of spherical indentation of hyperelastic material. It implements novel procedures for analysis of force curves which allow for greater resistance to model deviations. AtomicJ can process force maps, it generates maps of Young’s modulus, adhesion force, transition indentation, sample height and the deformation. The results of force maps processing can be visualized in 3D. In addition, AtomicJ can also analyze and process AFM images.
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.
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.
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.
MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data.
- label-free protein quantification
- MS1-based quantification
- MALDI ADA (Advanced Data Aquisition).
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.
The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA (2004, 2009, 2013) polarizable atomic multipole force field.
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.
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.
XParallax viu is a free software tool for automated astrometric data reduction of astronomic CCD images. It helps astronomers to perform an accurate astrometric reduction of dozens ore even hundreds of images which can be used in subsequent data analysis process. Fit headers generated by this software are fully compatible with other commonly used image utilities like SAO DS9 or Aladin Sky Atlas.
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Mass-Up is an open-source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. Mass-Up includes the following analyses: Quality Control, Biomarker discovery, Principal Component Analysis, Hierarchical clustering, Biclustering, and Classification analysis.
A collection of cheminformatics and machine-learning software written in C++ and Python. The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
XFLR5 includes the xfoil program for foil analysis, and several 3d analysis methods for planes:
- a non-linear lifting line method for standalone wings,
- two vortex-lattice and a 3d panel method for the analysis of aerodynamic performance of wings and plane operating at low Reynolds numbers.
The latest v6 version introduces stability analysis of planes.
SWAN is a third-generation wave model that computes random, short-crested wind-generated waves in coastal regions and inland waters.
SWAN accounts for the following physics:
- Wave propagation in time and space, shoaling, refraction due to current and depth, frequency shifting due to currents and non-stationary depth.
- Wave generation by wind.
- Three- and four-wave interactions.
- Whitecapping, bottom friction and depth-induced breaking.
- Dissipation due to vegetation.
- Wave-induced set-up.
- Propagation from laboratory up to global scales.
- Transmission through and reflection (specular and diffuse) against obstacles.
Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports many SPM data formats. However, it can also be used for general height field and image processing, for instance for analysis of profilometry data. It aims to provide a modular program for 2D data processing and analysis that can be easily extended by third-party modules and scripts.
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. Cantera provides types (or classes) of objects representing phases of matter, interfaces between these phases, reaction managers, time-dependent reactor networks, and steady one-dimensional reacting flows. Cantera is currently used for applications including combustion, detonations, electrochemical energy conversion and storage, fuel cells, batteries, aqueous electrolyte solutions, plasmas, and thin film deposition.
A computer code for simulation of electron-hydrogen scattering. Contains three (more or less) finished sub-programs:
- 'hex-ecs' which solves the Schrödinger equation in the B-spline basis,
- 'hex-dwba' which computes scattering variables for high energies using the distorted wave Born approximation of the first order and finally,
- 'hex-db' which is a user interface to a plain SQLite database, where the intermediate results are being stored, and which is used to extract derived quantities like a cross section from it.
GridLAB-D is a new power system simulation tool that provides valuable information to users who design and operate electric power transmission and distribution systems, and to utilities that wish to take advantage of the latest smart grid technology. It incorporates advanced modeling techniques with high-performance algorithms to deliver the latest in end-use load modeling technology integrated with three-phase unbalanced power flow, and retail market systems. Historically, the inability to effectively model and evaluate smart grid technologies has been a barrier to adoption; GridLAB-D is designed to address this problem.
ITK-SNAP is a software application used to segment structures in 3D medical images. ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, ITK-SNAP offers many supporting utilities. Compared to other, larger open-source image analysis tools, ITK-SNAP design focuses specifically on the problem of image segmentation, and extraneous or unrelated features are kept to a minimum.
AltAnalyze is an easy-to-use application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more).
This software is designed to help users visualize and analyze 3D point clouds with an associated real value, in a fast and flexible fashion. The primary use is in Atom Probe Tomography, which is an atomic imaging technique. However the program may also be useful in other areas, such as geospatial data, lidar, etc. Features: Load and view large point clouds; Slice, query and perform complex computations on points; Integration with external programs; ...
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.
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.
xfemm is a refactoring of the core algorithms of the popular Windows-only FEMM (Finite Element Method Magnetics) to use only the standard template library and therefore be cross-platform. The codes can be used as a library, standalone executables, or through the advanced Matlab/Octave interface, which uses direct data exchange at the memory level rather than the original FEMM ActiveX of file-based interface, for much improved communication speed.
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.
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This is an academic initiative to develop free software for Digital Photogrammetry. The idea behind the E-Foto project was to offer a simple set of software (a free Digital Photogrammetric Workstation) that could help students understand the principles behind Photogrammetry, thus bypassing eventual costs that would have barred many from learning about Photogrammetry. This objective was reached through the development of free and user-friendly photogrammetric software.
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.
ResCalc Master is a resistor calculator outfitted with various tools, meant to aid in work related to resistors. The main window of the program is meant for decoding and coding of resistors with 3 to 6 bands, it includes calculation of resistor value according to color and vice versa, ability to convert resistor value into Ω, kΩ, MΩ, GΩ, automatic calculation, resistor standard calculation as well as a visual and textual display of resistor color.
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Mokka is an open-source motion analyzer software that can read, edit, write and visualize motion capture data (trajectories, model outputs, events, analog, force-plates). Mokka is especially designed for movement science applications like gait analysis, biomechanical research, sport analysis... Mokka is compatible with several file formats used in biomechanics.
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.
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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.
The BioKanga alignment subprocess is a highly efficient short-read aligner which incorporates an empirically derived understanding of sequence uniqueness within a target genome to enable robust alignment of next generation sequencer short read datasets in either colorspace (ABI SOLiD) or basespace (Illumina). Compared with other widely used aligners, BioKanga provides substantial gains in both the proportion and quality of aligned sequence reads at competitive or increased computational efficiency. Unlike most other aligners, BioKanga utilises Hamming distances between putative alignments to the targeted genome assembly for any given read as the discrimative acceptance criteria rather than relying on sequencer generated quality scores.
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.
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.
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.
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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.
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.
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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.
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GeoViewer is a standalone application for viewing geospatial imagery, vector overlays, and LiDAR files. LizardTech GeoViewer enables you to combine, view and export visual layers from varied sources, such as local repositories, Express Server catalogs, and WMS and JPIP servers, and provides tools for visualizing LiDAR data in MrSID and LAS formats. LizardTech GeoViewer supports a wide range of input formats and exports to GeoTIFF, PNG and JPEG. GeoViewer is the most efficient means of viewing MrSID and JPEG 2000 images.
CLC Sequence Viewer
CLC Sequence Viewer is a free software workbench for basic bioinformatics, enabling users to make a large number of bio informatics analysis, combined with smooth data management, and excellent graphical viewing and output options. Some of the many bio informatics analysis are: interactive restriction site analysis, creating and editing alignments, phylogenetics, integrated GenBank searches, and advanced DNA to protein translation.
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Scilab is an interactive platform for numerical computation providing a powerful computing environment for engineering and scientific applications.
Gathering both industrial needs and scientific advances, Scilab covers a wide spectrum of areas: aerospace, automotive, energy, defense, finance, chemistry, biology, medicine...
Scilab includes hundreds of mathematical functions. It has a high level programming language allowing access to advanced data structures, 2-D and 3-D graphical functions.