HLRnet.com: Freeware: Scientific research

Scientific research freeware / freeware voor wetenschappelijk onderzoek

Shared Scientific Toolbox in Java is a library of quality lightweight components for scientific/distributed computing that includes the first true multidimensional array package in Java, a parallel data flow engine, an asynchronous sockets layer, an annotation-driven class loader, and more.

http://freshmeat.net/projects/shared/
Bika is a combined LIMS (laboratory information management system), workflow, and Web content management system.

http://freshmeat.net/projects/bika/
jHepWork is a full-featured object-oriented data analysis framework for scientists. Jython macros are used to plot data, 1D and 2D histograms, perform fit, etc. The program includes many tools for interactive scientific plots in 2D and 3D. Data structures and data manipulation methods integrated with Java and JAIDA classes combines remarkable power with a very clear syntax. Programs written with jHepWork are usually very short due to high-level constructs.

http://freshmeat.net/projects/jhepwork/
Seismic Toolkit is a tool for processing and displaying seismic signal data in a graphical interface. It reads seismic signals in SAC format, and provides a variety of signal processing, such as filtering, spectral analysis, polarisation analysis, time-frequency representation, Hilbert transform, and singular value decomposition. Some utilities are included for useful seismological applications, like computation of Seismic Moment Mo, Mantle magnitude Mm and Moment magnitude Mw, MTPA spectral analysis, plotting focal mechanisms, computation (and plotting) of instrumental response from poles and zeros, and some usefull GMT (Generic Mapping Tool) scripts for plotting signals, responses, and time-frequency in Postscript files for high quality prints.

http://freshmeat.net/projects/seismictoolkit-stk/
The massXpert software package is a mass spectrometry environment for linear (bio-) polymers. It inherits all the innovations of GNU polyxmass, as it is a port of that project to a cross-platform development environment.

http://freshmeat.net/projects/massxpert
Micro-Manager is a software package for microscope image acquisition. It controls a number of scientific grade cameras, shutters, filter wheels, stages, and other devices. It enables the acquisition of time-lapses, z-stacks, and multi-channel images.

http://freshmeat.net/projects/micro-manager/
http://micro-manager.org/
Happydigger is a program which can be used for cataloging archaeological finds. It is intended both for semi-professional use and by amateurs (e.g. metal detector users) who want to keep track of their finds. Data is stored in a database with extensive find and findspot details. If images are available, they will be displayed together with the find information.
http://freshmeat.net/projects/happydigger/
jHepWork is a full-featured object-oriented data analysis framework for scientists. Jython macros are used to plot data, 1D and 2D histograms, perform fit, etc. The program includes many tools for interactive scientific plots in 2D and 3D. Data structures and data manipulation methods integrated with Java and JAIDA classes combines remarkable power with a very clear syntax. Programs written with jHepWork are usually very short due to high-level constructs.

http://freshmeat.net/projects/jhepwork/
The Virtual Microsocope
Provides interactive viewing of high-resolution, multi-dimensional image datasets from various microscopes.
http://www.freewarefiles.com/program_16_233_27584.html
ParaView is a scientific visualization application designed with the need to visualize large data sets in mind. The goals of the ParaView project are to develop an open source, multi-platform visualization application, support distributed computation models to process large data sets, create an open, flexible, and intuitive user interface, and develop an extensible architecture based on open standards. ParaView runs on distributed and shared memory parallel as well as single processor systems and has been succesfully tested on Windows, Linux, and various Unix workstations and clusters. It uses the Visualization Toolkit (VTK) as the data processing and rendering engine and has a user interface written in Tcl/Tk and C++.

http://freshmeat.net/projects/paraview/
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

http://freshmeat.net/projects/cdk/
DNALinux is a live Linux distribution with bioinformatics software preloaded.

http://freshmeat.net/projects/dnalinux
VMD (Visual Molecular Dynamics) is designed for the 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. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.

http://freshmeat.net/projects/visualmoleculardynamics/
PhiloLogic is a full-text database engine developed for humanities computing text analysis by the ARTFL Project and the Digital Library Development Center at the University of Chicago. It is optimized for fast searching across very large collections of documents. It currently supports TEI-Lite, TEI XML, and TEI SGML documents.

http://freshmeat.net/projects/philologic/
VisIt is an interactive parallel visualization and graphical analysis tool for viewing scientific data. Users can quickly generate visualizations from their data, animate them through time, manipulate them, and save the resulting images for presentations. VisIt contains a rich set of visualization features so that you can view your data in a variety of ways. It can be used to visualize scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured and unstructured meshes. It was designed to interactively handle very large data set sizes in the terascale range, and works well down to small data sets in the kilobyte range.

http://freshmeat.net/projects/visit/
Gwyddion is a modular SPM (Scanning Probe Microsope) data visualization and analysis tool. It can be used for all most frequently used data processing operations including: leveling, false color plotting, shading, filtering, denoising, data editing, integral transforms, grain analysis, profile extraction, fractal analysis, and many more. The program is primarily focused on SPM data analysis (e.g. data obtained from AFM, STM, NSOM, and similar microscopes). However, it can also be used for analyzing SEM (scaning electron microscopy) data or any other 2D data.

http://freshmeat.net/projects/gwyddion/
IRIS
An astronomical images processing software.
http://www.freewarefiles.com/program_3_34_18168.html
Cell Electrophysiology Simulation Environment is a framework to perform electrophysiological simulations. It can, for example, simulate cardiac myocyte electrical activity. It is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.

http://freshmeat.net/projects/cese/
Statist is a statistics program with an interactive menu that makes it very easy to use. It can also be run in scripts, and large data sets are handled reasonably well even on small machines. In spite of its low overhead, it can do quite a few regression functions and tests. It can produce colorized output, and uses gnuplot to create graphics.

http://freshmeat.net/projects/statist/
CLC Free Workbench enables users to perform bioinformatics analyses and smooth data management, combined with excellent graphical viewing and output options. Some of the features are GenBank searching, including download facilities and full graphical overview; user-friendly graphical tools for viewing DNA, RNA, and protein sequences; full integration of data input, data management, calculations results, and data export; DNA, RNA, and protein alignment tools; reverse translation; restriction site analysis; and phylogenetic analyses.

http://freshmeat.net/projects/clcfreeworkbench