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1. Multigraph

Multigraph is a program for creating 2-dimensional scientific data graphs in web pages. It can read data in a variety of formats, and allows you to customize the appearance of the graph to your liking. Multigraph provides interactive pan and zoom capabilities, giving the viewer the ability to change the horizontal and/or vertical scales in the graph on the fly. Multigraph also has the ability to read data from a web service, which allows it to be used to surf through large datasets, downloading only those the parts of the data that are needed for display. Multigraph is written in pure JavaScript and will work in any reasonably modern web browser, including on mobile devices.

2. emgr - Empirical Gramian Framework

Empirical gramians can be computed for linear and nonlinear control systems for purposes of model order reduction or system identification. The emgr framework is a compact open source toolbox for gramian-based model reduction and compatible with OCTAVE and MATLAB.

3. relax

relax is a program designed for the study study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model or ensemble analysis and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, and the investigation of stereochemistry.

4. SimThyr, a numerical simulator of thyrotropic feedback control for education and research

SimThyr is a simulation program for the pituitary thyroid feedback control that is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients.

5. DuMuX

DuMuX, DUNE for multi-{phase, component, scale, physics, ...} flow and transport in porous media, is a free and open-source simulator for flow and transport processes in porous media. It is based on the Distributed and Unified Numerics Environment DUNE, dune-project.org. Its main intention is to provide a sustainable and consistent framework for the implementation and application of model concepts, constitutive relations, discretizations, and solvers. It has been successfully applied to CO2 storage scenarios, environmental remediation problems, transport of therapeutic agents through biological tissue, and subsurface-atmosphere coupling. DuMuX is part of the OPM (Open Porous Media) initiative, opm-project.org.

6. mMass - Open Source Mass Spectrometry Tool

mMass is designed to be feature rich, yet still easy to use. Stay focused on your data interpretation, not on the software. *Supports multiple formats (mZML, mzXML, mzData, MGF, ASCII and copy-Past from clipboard) *Various data processing tools avalaible (Proteomics, calibration, peak picking deconvolution, in-silico digestion and many more) *Platform Independent: No matter what operating system you are using, mMass works on MS Windows, Apple's Mac OS X and Linux platforms as well. Multiple Formats: mMass supports all of the modern open formats like mzML, mzXML, mzData, MGF, ASCII and even copy n' paste from clipboard.

7. OpenChrom

OpenChrom is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import binary and textual chromatographic data files, such as *.D chromatograms from Agilent Technologies or NetCDF. Moreover, it offers a nice graphical user interface and is available for various operating systems, e.g. Windows, Linux, Solaris and Mac OS X. A basis set of methods to detect baselines, peaks and to integrate peaks in a chromatogram are implemented. Preprocessing steps, e.g. to remove certain mass fragments (m/z) such as nitrogen (28) or water (18), are supported by applying filter on the chromatogram or mass spectrum. Extensions are welcome, as OpenChrom is open source and uses a flexible approach, which allows others to implement their own methods, algorithms, filters, detectors or integrators. Therefore, OpenChrom shall be an efficiently system to process chromatographic and mass spectrometric data using an extensible and flexible plugin approach. OpenChrom is distributed under the Eclipse Public License 1.0 (EPL). Third-party libraries are separated into single bundles and are released under various OSI compatible licenses.

8. pyofss - Python-based optical fibre system simulator

Pyofss allows optical component modules to be grouped together into a system. An optical field is propagated through the system and the evolution of the field viewed at each module. Fibre effects include attenuation, dispersion, self-phase modulation, self-steepening, and Raman scattering. There are many examples available demonstrating use of the program. A variety of ODE integration solvers are available along with a range of split-step methods, including the Runge-Kutta in the interaction picture method.

9. QuTiP: Quantum Toolbox in Python

QuTiP is open-source software for simulating the dynamics of open quantum systems. The QuTiP library depends on the excellent Numpy and Scipy numerical packages. In addition, graphical output is provided by Matplotlib. QuTiP aims to provide user-friendly and efficient numerical simulations of a wide variety of Hamiltonians, including those with arbitrary time-dependence, commonly found in a wide range of physics applications such as quantum optics, trapped ions, superconducting circuits, and quantum nanomechanical resonators. QuTiP is freely available for use and/or modification on all Unix based platforms such as Linux and Mac OSX. Being free of any licensing fees, QuTiP is ideal for exploring quantum mechanics and dynamics in the classroom.

10. Molekel

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

11. cuteNMR

NMR processing software using the Qt framework. Currently only 1D.

12. rNMR

rNMR is an open source software package for visualizing and interpreting one and two dimensional NMR data. In contrast to most existing 2D NMR software, rNMR is specifically designed for high-throughput assignment and quantification of small molecules. As a result, rNMR supports extensive batch manipulation of plotting parameters and has numerous tools for expediting repetitive resonance assignment and quantification tasks.

13. XDAT: A Tool to plot Parallel Coordinates

XDAT (x-dimensional data analysis tool) reads column-based data in text / csv format and plots it using parallel coordinates. It is written in Java and released under the GPL.

14. Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

15. Icy

Icy is an image analysis software primarily targeted at biological needs. It provides high-quality tools for biological image processing tasks, such as filtering (linear, nonlinear, morphological, etc.), cell segmentation, particles detection, tracking, multiple-class thresholding, measurements, microscope control, etc. It is designed to work on sequences from 2D to 5D (X, Y, Z, time, color channel), and runs on Windows, MacOS, Linux.

16. REDCRAFT

REDCRAFT is an open-source software tool for determining a protein's structure using residual dipolar couplings (RDCs). It allows simultaneous determination of a protein's structure and dynamics. Its effectiveness has been demonstrated on both synthetic and experimental data. REDCRAFT contains stages that allow the incorporation of user-specified dihedral angle constraints, such as those produced by TALOS or a restriction to specific regions of Ramachandran space. It is robust with respect to noise and missing data. The program is highly efficient and can produce a structure for an 80-residue protein within two hours.

17. cadnano

Cadnano simplifies and enhances the process of designing three-dimensional DNA origami nanostructures. Through its user-friendly 2D and 3D interfaces it accelerates the creation of arbitrary designs. The embedded rules within Cadnano paired with the finite element analysis performed by cando, provide relative certainty of the stability of the structures.

18. ns-3

ns-3 is a discrete-event network simulator for Internet systems, targeted primarily for research and educational use. ns-3 is free software, licensed under the GNU GPLv2 license, and is publicly available for research, development, and use.

19. Puma-EM

Puma-EM is a code that allows the computation of various electromagnetic quantities when a target is excited by an electromagnetic source. These quantities are the scattered fields and the currents on the surface of the target. It can compute: monostatic RCS for a variety of angles or positions (SAR) bistatic RCS for a variety of angles Antenna pattern electric and/or magnetic dipole excitation plane-wave excitation a combination of the above

20. Maxima

Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors. Maxima yields high precision numeric results by using exact fractions, arbitrary precision integers, and variable precision floating point numbers. Maxima can plot functions and data in two and three dimensions. Also has a graphical interface built in wxWidgets called wxMaxima (http://andrejv.github.com/wxmaxima/).

21. Finite Element Method Magnetics - FEMM

FEMMis a suite of programs for solving lowfrequency electromagnetic problems on two-dimensional planar and axisymmetric domains. The program currently addresses linear/nonlinear magnetostatic problems, linear/nonlinear time harmonic magnetic problems, linear electrostatic problems, and steady-state heat flow problems.

22. MPB

The MIT Photonic-Bands (MPB) package is a free program for computing the band structures (dispersion relations) and electromagnetic modes of periodic dielectric structures, on both serial and parallel computers. It was developed by Steven G. Johnson at MIT along with the Joannopoulos Ab Initio Physics group.

23. Meep

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package. Its features include: - Free software under the GNU GPL. - Simulation in 1d, 2d, 3d, and cylindrical coordinates. - Distributed memory parallelism on any system supporting the MPI standard. - Portable to any Unix-like system (GNU/Linux is fine). - Arbitrary anisotropic electric permittivity and magnetic permeability , along with dispersive () and () (including loss/gain) and nonlinear (Kerr & Pockels) dielectric and magnetic materials, and electric/magnetic conductivities . - PML absorbing boundaries and/or perfect conductor and/or Bloch-periodic boundary conditions. - Exploitation of symmetries to reduce the computation size even/odd mirror symmetries and 90/180 rotations. - Complete scriptability either via a Scheme scripting front-end (as in libctl and MPB), or callable as a C++ library; a Python interface is also available. - Field output in the HDF5 standard scientific data format, supported by many visualization tools. - Arbitrary material and source distributions. - Field analyses including flux spectra, frequency extraction, and energy integrals; completely programmable. - Multi-parameter optimization, root-finding, integration, etcetera (via libctl). Meep officially stands for MIT Electromagnetic Equation Propagation, but we also have several unofficial meanings of the acronym.

24. AcouSTO (Acoustics Simulation TOol)

AcouSTO (Acoustics Simulation TOol) is an open source Boundary Element Method (BEM) solver for the Kirchhoff-Helmholtz Integral Equation (KHIE). The code is released under GPL v3.0.

25. Eigen

Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. It provides high performance, arbitrary sized (and sparse) matricies, and excellent numerical stability. It is available under a LGPL3+/GPL2+ dual license.

26. Veusz

A publication-quality scientific plotting package built in Python, NumPy, and PyQt4.

27. BioBike

A platform for knowledge-based computational biology. Written in Lisp, downloadable or accessible through our web servers.

28. Open Source Seismic Interpretation System

OpendTect is an open source seismic interpretation software system for processing, visualizing and interpreting multi-volume seismic data, and for fast-track development of innovative interpretation tools. Optionally OpendTect can be extended with (closed source) commercial plugins.

29. Java Algebra System

The Java Algebra System (JAS) is an object oriented, type safe and multi-threaded approach to computer algebra. JAS provides a well designed software library using generic types for algebraic computations implemented in the Java programming language. The library can be used as any other Java software package or it can be used interactively or interpreted through an jython (Java Python) and jruby (Java Ruby) front end. The focus of JAS is at the moment on commutative and solvable polynomials, Gröbner bases and applications. By the use of Java as implementation language JAS is 64-bit and multi-core cpu ready.

30. Energy system modelling with ASCEND

ASCEND is a general-purpose equation-solving environment that has recently been used to model a range of gas turbine and steam turbine power cycles, approaching the complexity of commercial power stations. Collaborations are sought to deepen and broaden the library of models available for this purpose.

31. WebPlotDigitizer

WebPlotDigitizer is a based tool to extract data from plots in image form. This tool helps you retrieve data from scanned plots or plots from published papers quickly and easily. This is web based, so no installation is needed. The program generates data in .CSV format which can be easily imported by most data analysis programs like OpenOffice Spreadsheet, MS Excel etc.

32. OGSA-DAI

OGSA-DAI is an open source framework for executing complex data management scenarios (including data access, update, transformation, integration and delivery) involving distributed databases. It supports relational, XML and file resources. The supported functionality, data resources and presentation layers can all be customised or replaced. OGSA-DAI has been used to build applications in astronomy, medicine, geo-location, social sciences, environment, and transportation amongst others. OGSA-DAI, managed by EPCC, The University of Edinburgh, is 100% Java and is freely available under an Apache 2.0 licence from SourceForge (http://sourceforge.net/projects/ogsa-dai)

33. Sysmo db

SysMO-DB is a web-based platform for finding, sharing and exchanging Data, Models and Processes in Systems Biology. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects. The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that: * facilitates and maximises the potential for data exchange between SysMO research groups; * maximises the 'shelf life' and utility of data generated by SysMO; * provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community; and * facilitates standardisation of practices in Systems Biology for the interfacing of modelling and experimentation. We follow several key principles: * exploit what is already available, both within the consortium and outside it, and do not reinvent; * identify the least we can do to make a benefit and do this incrementally.

34. myExperiment

myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.

35. MethodBox

Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. A deployed version of the methodbox code can be found at http://www.methodbox.org

36. Biocatalogue

The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring. Our Goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Provide a curated catalogue of life science web services * Providers, Expert curators and Users will provide oversight, monitor the catalogue and provide high quality annotations for services. * BioCatalogue as a place where the community can find, contact and meet the experts and maintainers of these services.

37. myExperiment

The myExperiment Virtual Research Environment enables you and your colleagues to share digital items associated with your research in particular it enables you to share and execute scientific workflows. You can use www.myexperiment.org to find publicly shared workflows. If you want further access, and the ability to upload and share workflows, you will need to sign up.

38. BioCatalogue - the Life Sciences Web Service Registry

The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring.

39. Taverna Workbench and Server

Taverna is an open source domain independent Workflow Management System a suite of tools used to design and execute scientific workflows. Taverna has been created by the myGrid project and funded through the OMII-UK. Taverna has a guaranteed funding till 2014. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool that for a quick execution of workflows from a terminal without the overheads of the GUI. Taverna allows for the automation of experimental methods through the use of a number of different (local or remote) services from a very diverse set of domains biology, chemistry and medicine to music, meteorology and social sciences. Effectively, Taverna allows a scientist with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources, all from a standard PC, UNIX box or Apple computer.

40. SciDAVis

SciDAVis is a free application for Scientific Data Analysis and Visualization. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility. SciDAVis runs on GNU/Linux, Windows and MacOS X; possibly also on other platforms like *BSD, although this is untested.

41. LiveGraph: Real-Time Plotter and Exploratory Data Analysis Tool

Plots data live - while it's being produced by any application. * Very simple point-and-click interface. * Fully automatic intelligent graph layout. * Single click graph transformations: Linear, Logarithm, Unit Interval, etc. * Time axes support. * APIs for integration into 3rd party software and for data logging. * Open standard data file format.

42. PyBLAW

PyBLAW is a lightweight Python framework for solving one-dimensional systems of hyperbolic balance laws of the form q_t + f(q)_x = s(q).

43. PyWENO (Python WENO)

PyWENO is a Python implementation of one-dimensional Weighted Essentially Non-oscillatory (WENO) approximations over unstructured (non-uniform) grids.

44. jHepWork

Data analysis framework

45. Debellor

Debellor is an open source Java framework for scalable data mining and machine learning. You may implement your own algorithms in Debellor's architecture and combine them with pre-existing ones to create complex data processing networks and experimental setups. The unique feature of Debellor is data streaming, which enables efficient processing of massive data and is essential for scalability of algorithms.

46. Science Laboratory Inventory

Science Laboratory Inventory Control Management System and Orders: Web-based system that is useful for managing chemical and equipment inventory management and handling science labs orders from teachers to technicians for their practical sessions.

47. Webolab

A web-based platform for collaborative research and high-performance computing interface, a tool for implementation of virtual labs. Supports Condor cluster management engine.

48. OpenOpt

Universal cross-platform (Win, Linux, Mac OS) Python-written numerical optimization toolbox. License: new BSD. Problems: NLP, LP, QP, SDP, SOCP, DFP(Non-linear Data Fit), NSP(nonsmooth), MILP, LSP, LLSP, MMP, GLP, MINLP etc. Connects to dozens of solvers (some are C- or Fortran-written). Provides graphic output of convergence and some more numerical optimization "MUST HAVE" features. Can involve automatic differentiation of FuncDesigner (http://openopt.org/FuncDesigner) models.

49. Adevs

Adevs (A Discrete EVent System simulator) is a C++ library for constructing discrete event simulations based on the Parallel DEVS and Dynamic DEVS (dynDEVS) formalisms.

50. Saros

Saros is a research project to enable distributed pair programming (also called remote pair programming) in the Java IDE Eclipse. Saros supports real-time collaboration by two and more peers and adds many features to increase awareness and presence regarding the whereabouts of each peer.