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Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
OpenChrom Community Edition
OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS 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.
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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.
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). The Aguila tool allows for the interactive visualisation of stochastic spatio-temporal data.
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).
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.
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.
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; ...
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 system for representing knowledge in the logic FO(IDP) and applying reasoning on it. FO(IDP) is a logic consisting of first-order logic, inductive definitions, aggregates, partial functions and arithmetic. Out of the box, the following inferences are supported: grounding; modelexpansion; propagation; evaluating definitions.
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.
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. Additionally, the rapid prototyping of modern measurement and inspection setups requires a system, where parameters or components can easily be changed at runtime, necessitating the availability of an embedded scripting language.
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.
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.
Protospacer allows researchers to build, analyze, and share their own database of CRISPR target-sites. This enables the development of custom libraries and helps to transfer the CRISPR technology to new organisms. Each Protospacer database is a simple catalogue of all possible Cas9 target-sites within a given FASTA sequence, i.e. all NGG/NAG sites. Protospacer then allows the user to sub-select targets from the database by gene ID, by exon/intron/UTR location, by sequence similarity, or by genomic co-ordinate.
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).
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.
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.
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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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.
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.
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.
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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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.
The Tonatiuh project aims to create an open source, cutting-edge, accurate, and easy to use Monte Carlo ray tracer for the optical simulation of solar concentrating systems. It intends to advance the state-of-the-art of the simulation tools available for the design and analysis of solar concentrating systems, and to make those tools freely available to anyone interested in using and improving them.
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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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.
BTK (Biomechanical ToolKit) is an open-source and cross-platform library for biomechanical analysis. BTK read and write acquisition files and can modify them. All these operations can be done by the use of the C++ API or by the wrappers included (Matlab, Octave, and Python). The core of BTK is primary based on a pipeline design and on shared pointers. Each process can be linked (the output of previous is the input of the next) and scheduled together. The use of shared pointers permits to avoid the need of memory allocation/deletion, the choice of object's owner and the possibilities of memory leaks.
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.
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.
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.
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.
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.
Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. It is intended for analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM), and it can be generally used for any other height field and image analysis, for instance for analysis of profilometry data. It features fractal dimension analysis, removal of data under arbitrary mask using Laplace or fractal interpolation, automatic xy plane rotation correction, arbitrary polynomial deformation on xy plane, and 1D and 2D FFT filtering.
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.
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.
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.
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.
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.
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.
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.
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.
GAMA is a platform that provides a complete modeling and simulation development environment for building spatially explicit agent-based simulations.
The most important requirements of spatially explicit multi-agent simulations that GAMA fulfils are:
- The ability to use complex GIS data as an environment for the agents.
- The ability to handle a vast number of (possibly heterogeneous) agents.
- The ability to offer a platform for automated controlled experiments (by automatically varying parameters, recording statistics, etc.).
- The possibility to let non-computer scientists design models and interact with the agents during simulations.
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.
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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GlycoWorkbench is a suite of software tools designed for rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. The graphical interface of GlycoWorkbench provides an environment in which structure models can be rapidly assembled, their mass computed, their fragments automatically matched with MSn data, and the results compared to assess the best candidate. GlycoWorkbench can reduce the time needed for the interpretation and annotation of mass spectra of glycans.
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.