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Interdisciplinary Sciences→Resources: Software Links

Software Links for Interdisciplinary Science*
  • AFNI
    AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data. It is freely available (both in source code and in precompiled binaries) for research purposes. The software is made to run on virtually an Unix system with X11 and Motif displays. Binary Packages are provided for MacOS and Linux systems including Fedora, Ubuntu (including Ubuntu under the Windows Subsytem for Linux)

  • ANUGA
    ANUGA is a Free & Open Source Software (FOSS) package capable of modelling the impact of hydrological disasters such as dam breaks, riverine flooding, storm-surge or tsunamis. ANUGA is based on the Shallow Water Wave Equation discretised to unstructured triangular meshes using a finite-volumes numerical scheme. A major capability of ANUGA is that it can model the process of wetting and drying as water enters and leaves an area. This means that it is suitable for simulating water flow onto a beach or dry land and around structures such as buildings. ANUGA is also capable of modelling difficult flows involving shock waves and rapidly changing flow speed regimes (transitions from sub critical to super critical flows). ANUGA is developed by the Australian National University (ANU) and Geoscience Australia (GA) - hence the name.

  • Armadillo
    Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

  • Avogadro
    Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.

  • Bioconductor
    Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

  • BioModels Database
    BioModels Database is a repository of computational models of biological processes.

  • Blue Obelisk

  • BRP-PACU
    BRP-PACU is a dual channel FFT audio analysis tool. It is designed to aid in the equalization and time alignment of a sound system. It compares the output of the system to the input of the system to obtain the transfer function of the system.

  • Chemistry Development Kit (CDK)
    The Chemistry Development Kit (CDK) is a collection of modular Java libraries for processing chemical information (Cheminformatics). The modules are free and open-source and are easy to integrate with other open-source or in-house projects.

  • Chemtool
    Chemtool is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.

  • Elmer
    Elmer is an open source multiphysical simulation software mainly developed by CSC - IT Center for Science (CSC). Elmer includes physical models of fluid dynamics, structural mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by partial differential equations which Elmer solves by the Finite Element Method (FEM).

  • EXMARaLDA
    EXMARaLDA is a system for working with oral corpora on a computer. It consists of a transcription and annotation tool (Partitur-Editor), a tool for managing corpora (Corpus-Manager) and a query and analysis tool (EXAKT).

  • Experix
    Experix is a command-line driven environment for laboratory data acquisition and device control and graphical presentation and analysis of data.

  • FuncDesigner
    A python module for function design and automatic derivatives

  • GATE
    GATE is an open source software toolkit capable of solving almost any text processing problem It has a mature and extensive community of developers, users, educators, students and scientists

  • Gnaural
    naural is an opensource programmable auditory binaural-beat synthesizer, implementing the principle described in the October 1973 Scientific American article "Auditory Beats in the Brain" by Gerald Oster.

  • GTKWave
    GTKWave is a fully featured GTK+ based wave viewer for Unix, Win32, and Mac OSX which reads LXT, LXT2, VZT, FST, and GHW files as well as standard Verilog VCD/EVCD files and allows their viewing.

  • Impact Finite Element Program
    Impact has been designed to be easily extendible and modular to enable programmers a way to easy add features to the program without having to enter other parts of the code. Impact has been written in Java. This choice of language may seem strange at first, but with the recent development of Java engines, speed penalty is not that significant. On the other hand, the Object Oriented features and the high portability of Java is a clear advantage for the future.

  • Insight Segmentation and Registration Toolkit (ITK)
    ITK is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

  • InVesalius
    Open source software for reconstruction of computed tomography and magnetic ressonance images. Available for the Microsoft Windows, GNU/Linux and Apple Mac OS X platforms.

  • IT++
    IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.

  • JChemPaint
    JChemPaint (or JCP for short here) is the editor and viewer for 2D chemical structures developed using the Chemistry Development Kit (CDK). It is implemented in several forms: a Java application and two varieties of Java applet.

  • DataMelt
    DataMelt ("DMelt") is a free software for numeric computation, mathematics, statistics, symbolic calculations, data analysis and data visualization. This program combines the simplicity of scripting languages, such as Python, Ruby, Groovy (and others), with hundreds of Java numerical and graphical packages. Unlike other similar programs, DataMelt can be used for scientific computations using Java, word's most-popular enterprise programming language. The program runs on Windows/Mac OS/Linux and Android platform. DataMelt is a modern version of jHepWork (2005-2013) and SCaVis (2013-2015) programs.

  • Jmol
    an open-source Java viewer for chemical structures in 3D Jmol icon with features for chemicals, crystals, materials and biomolecules. Jmol is a free, open source viewer of molecular structures useful for students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

  • JOELib
    JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

  • Kalyspo
    Kalypso combines all state-of-the-art functions of hydrological and hydraulic simulation. The modules Hydrology, WSPM, 1D / 2D, Flood and Risk belong to the free open source version. For the operation of numerical forecast models or the centrally controlled processing and management of water profiles, we offer the stand-alone "Forecast" and "Profile database", which dock seamlessly with Kalypso. Hydro_As-2D, D-Flow and Telemac-2D are add-ons that expand the functionality of the 1D / 2D module with additional 2D computing cores.

  • Kalzium
    Kalzium 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.

  • KEEL
    KEEL (Knowledge Extraction based on Evolutionary Learning) is an open source (GPLv3) Java software tool that can be used for a large number of different knowledge data discovery tasks. KEEL provides a simple GUI based on data flow to design experiments with different datasets and computational intelligence algorithms (paying special attention to evolutionary algorithms) in order to assess the behavior of the algorithms. It contains a wide variety of classical knowledge extraction algorithms, preprocessing techniques (training set selection, feature selection, discretization, imputation methods for missing values, among others), computational intelligence based learning algorithms, hybrid models, statistical methodologies for contrasting experiments and so forth. It allows to perform a complete analysis of new computational intelligence proposals in comparison to existing ones. Moreover, KEEL has been designed with a two-fold goal: research and education.

  • LabKey Server
    LabKey Server is an open-source software platform designed to help research organizations integrate, analyze, and share complex biomedical data. Adaptable to varying research protocols, analysis tools, and data sharing requirements, LabKey Server couples the flexibility of a custom solution with enterprise-level scalability to support scientific workflows.

  • LAMMPS
    LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Many of its models have versions that provide accelerated performance on CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to modify or extend with new functionality. LAMMPS is distributed as an open source code under the terms of the GPL. LAMMPS is distributed by Sandia National Laboratories, a US Department of Energy laboratory.

  • lumi
    The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

  • Madagascar
    Madagascar is an open-source software package for multidimensional data analysis and reproducible computational experiments. Its mission is to provide: a convenient and powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.

  • MDynaMix
    This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell. Rigid bonds are constrained by the SHAKE algorithm. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT and NPT (including anizotropic NPT) statistical ensembles are implemented. Ewald summation is used for treatment of the electrostatic interactions. Computations of solvation free energies can be done by the expanded emsembles method with Wang-Landau optimization.

  • MicroDicom
    MicroDicom is application for primary processing and preservation of medical images in DICOM format MicroDicom DICOM viewer is equipped with most common tools for manipulation of DICOM images and it has an intuitive user interface. MicroDicom DICOM viewer also has the advantage of being free for use and accessible to everyone for non-commercial use.

  • Molekel
    Molekel is an open-source multi-platform molecular visualization program.

  • OpenMS
    As part of the deNBI Center for integrative Bioinformatics, OpenMS offers an open-source software C++ library (+ python bindings) for LC/MS data management and analyses. It provides an infrastructure for the rapid development of mass spectrometry related software as well as a rich toolset built on top of it. OpenMS is free software available under the three clause BSD license and runs under Windows, macOS and Linux.

  • OpenOpt
    OpenOpt is a free MATLAB Toolbox, which is also run in Octave.

  • OsiriX
    With high performance and an intuitive interactive user interface, OsiriX is the most widely used DICOM viewer in the world. It is the result of more than 15 years of research and development in digital imaging. It fully supports the DICOM standard for an easy integration in your workflow environment and an open platform for development of processing tools. It offers advanced post-processing techniques in 2D and 3D, exclusive innovative technique for 3D and 4D navigation and a complete integration with any PACS. OsiriX supports 64-bit computing and multithreading for the best performances on the most modern processors. OsiriX MD, the commercial version, is certified for medical use (FDA cleared and CE II labeled).

  • PDL ("Perl Data Language")
    PDL ("Perl Data Language") gives standard Perl the ability to compactly store and speedily manipulate the large N-dimensional data arrays which are the bread and butter of scientific computing.

  • PyEphem
    PyEphem provides basic astronomical computations for the Python programming language. Given a date and location on the Earth’s surface, it can compute the positions of the Sun and Moon, of the planets and their moons, and of any asteroids, comets, or earth satellites whose orbital elements the user can provide. Additional functions are provided to compute the angular separation between two objects in the sky, to determine the constellation in which an object lies, and to find the times at which an object rises, transits, and sets on a particular day.

  • PyMOL
    PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.

  • QuteMol
    QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

  • RasMol
    RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.bThe program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

  • Rmetrics
    Rmetrics is a free, open source and open development software project for teaching computational finance.

  • Root
    ROOT is a modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.

  • RDQA
    RDQA is a R package for Qualitative Data Analysis, a free (free as freedom) qualitative analysis software application (BSD license). It works on Windows, Linux/FreeBSD and Mac OSX platforms. RQDA is an easy to use tool to assist in the analysis of textual data. At the moment it only supports plain text formatted data. All the information is stored in a SQLite database via the R package of RSQLite.

  • Visualization Library
    Visualization Library is a C++ middleware for high-performance 2D and 3D graphics applications based on the industry standard OpenGL 1.x-4.x, designed to develop portable applications for the Windows, Linux and Mac OS X operating systems.

  • Visualization Toolkit (VTK)
    The Visualization Toolkit (VTK) is open source software for manipulating and displaying scientific data. It comes with state-of-the-art tools for 3D rendering, a suite of widgets for 3D interaction, and extensive 2D plotting capability.

  • Weka
    Weka is tried and tested open source machine learning software that can be accessed through a graphical user interface, standard terminal applications, or a Java API. It is widely used for teaching, research, and industrial applications, contains a plethora of built-in tools for standard machine learning tasks, and additionally gives transparent access to well-known toolboxes such as scikit-learn, R, and Deeplearning4j.

  • XDrawChem
    XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.

  • XMD
    XMD is a computer program for performing molecular dynamics simulations. It is designed for the simulation of metals and ceramics.

  • NAMD
    NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

  • Biskit
    Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. For efficient number crunching, Biskit objects tightly integrate with numpy (Numeric Python). Biskit also offers a platform for the rapid integration of external programs and new algorithms into complex workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, DSSP, Fold-X, T-Coffee, TMAlign and Modeller; interfaces to further software can be added easily. Biskit also simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine).

  • Cn3D
    Cn3D ("see in 3D") is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez Structure database. Cn3D is provided for Windows and Macintosh, and can be compiled on Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. (For those who prefer to view 3D structures on the web, without the need to install a separate application, iCn3D ("I see in 3D") is available as of April 2016.)

  • Coot (Crystallographic Object-Oriented Toolkit)
    Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots, skeletonization, non-crystallographic symmetry and more.

  • Emergent

  • EXCITING
    exciting is a full-potential all-electron density-functional-theory package implementing the families of linearized augmented planewave methods. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for exploring the physics of core electrons. A particular focus are excited states within many-body perturbation theory.

  • Fityk
    Fityk [fi:tik] is a program for data processing and nonlinear curve fitting. Primarily used 1)by scientists who analyse data from powder diffraction, chromatography, photoluminescence and photoelectron spectroscopy, infrared and Raman spectroscopy, and other experimental techniques, 2) to fit peaks – bell-shaped functions (Gaussian, Lorentzian, Voigt, Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic, etc.), but it is suitable for fitting any curve to 2D (x,y) data.

  • GarlicSim

  • Geant4
    Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

  • GIMIAS
    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.

  • Image SXM
    Image SXM is a version of the public domain image analysis software NIH Image that has been extended to handle the loading, display and analysis of scanning microscope images.

  • ImageJ
    ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

  • Montage Image Mosaic Software
    Montage is a toolkit for assembling Flexible Image Transport System (FITS) images into custom mosaics.

  • NumPy
    NumPy is the fundamental package for scientific computing with Python. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.

  • SimPy
    SimPy is a process-based discrete-event simulation framework based on standard Python. Processes in SimPy are defined by Python generator functions and may, for example, be used to model active components like customers, vehicles or agents. SimPy also provides various types of shared resources to model limited capacity congestion points (like servers, checkout counters and tunnels).

  • Spatiotemporal Epidemiological Modeler (STEM)
    The Spatiotemporal Epidemiological Modeler (STEM) tool is designed to help scientists and public health officials create and use spatial and temporal models of emerging infectious diseases. These models can aid in understanding and potentially preventing the spread of such diseases.

  • VMD
    VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.


*Disclaimer: The software listed above are for information purpose only and csfreelist has nothing to do with these software and their respective organizations. We DO NOT guarantee about the correctness, perfectness, flawlessness, etc. of the information provided on this webpage and on other information-purpose webpages of this website. For the contents of Third party websites / resources, we take absolutely no responsibility. The software which are free are conditionally free and available with terms & conditions established by their developers and other concerned persons / organizations. For exact terms & conditions, please visit their websites and /or contact them.

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