HLRnet.com: Freeware: Scientific research

Scientific research freeware / freeware voor wetenschappelijk onderzoek

I, Librarian is a PDF manager or PDF organizer that allows individual researchers or a group of researchers to create an annotated collection of PDF articles. Users may build the virtual library collaboratively, thus sharing the workload of literature mining. It enables smart browsing and fast searching in reference data and PDF files, and includes an advanced tool for mining scientific literature from PubMed, PubMed Central, NASA ADS, arXiv, JSTOR, and HighWire Press.

http://freecode.com/projects/i-librarian
Regress Pro is scientific and industrial software that can be used to study experimental data coming from spectroscopic ellipsometers or reflectometers. The program has been developed mainly looking to the application of thin film measurement in semiconductor industry. The software is suitable both to determine the thickness of the layers and to determine the optical properties of dielectric materials.

http://freecode.com/projects/regress-pro
DAE Tools is a collection of software tools for modelling, simulation, and optimization of real-world processes. DAE Tools was initially developed to model and simulate processes in chemical process industry (mass, heat, and momentum transfers, chemical reactions, separation processes, thermodynamics). However, DAE Tools can help you develop high-accuracy models of (in general) many different kind of processes and phenomena, simulate and optimize them, and visualize and analyse the results.

http://freecode.com/projects/dae-tools
yoshinoGRAPH is a scientific graph software for data analysis and presentation.
http://www3.ocn.ne.jp/~ygraph/
Strategico is an engine for running statistical analysis over groups of time series. It can manage one or more groups (projects) of time series: by default, you can get data from a database or CSV files, normalize them, and then save them inside the engine. The first statistical analysis implemented inside Strategico is the "Long Term Prediction": it automatically finds the best model that fits each time series. Some of the models implemented are mean, trend, linear, exponential smoothing, and Arima. Strategico is scalable: the statistical analysis over each time series (of a project) can be run separately and independently. It is suggested that you set up an HPC Cluster (High Performance Computing) and/or use a resource scheduler like slurm. It is developed with R, one of the most famous statistical languages.

http://freecode.com/projects/strategico
Gabedit is a graphical interface for the Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess, and Q-Chem computational chemistry packages. It includes a 3D molecule editor and viewer. Most major molecular file formats are supported, and graphics can be exported in many formats.

http://freecode.com/projects/gabedit
GriF is a collaborative grid framework to support computational chemistry applications. It is meant to be used as a tool to facilitate massive grid calculations and also to improve scientific collaboration. Accordingly, GriF facilitates profiling the users of grid virtual organizations in order to systematically evaluate the work carried out in a grid and to foster its sustainability.

http://freecode.com/projects/grif
Serial Cloner is a Molecular Biology software. It provides tools with an intuitive interface that assists you in DNA cloning, sequence analysis and visualization
http://serialbasics.free.fr/Serial_Cloner-Download.html
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.

http://freecode.com/projects/pathvisio
SciDAVis is an interactive application aimed at data analysis and publication-quality plotting. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility. It is similar in its field of application to proprietary Windows applications like Origin and SigmaPlot, as well as free applications like QtiPlot, Labplot, and Gnuplot. What sets SciDAVis apart from the above is its emphasis on providing a friendly and open environment (in the software as well as the project) for new and experienced users alike, and particularly in providing good documentation on all levels

http://freecode.com/projects/scidavis
Scilab was designed to be a scientific software package for numerical computations providing a powerful open computing environment for engineering and scientific applications.

http://www.freewarefiles.com/Scilab_program_49594.html
http://www.scilab.org/
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://freecode.com/projects/shared/
The XL Toolbox is an Excel 2003/2007 addin that provides important tools for the analysis and presentation of scientific data. It is intended for researchers in the life sciences.

http://sourceforge.net/projects/xltoolbox/
Unipro UGENE is a free visual software solution for DNA and protein sequence analysis.
http://ugene.unipro.ru
EPoS is a modular software framework for phylogenetic analysis and visualization. EPoS combines a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations, and data structures. EPoS currently supports distance based tree construction from multiple sequence alignments and distance matrices as well as different algorithms to create consensus trees and supertrees. EPoS also integrates a tree visualization module that can be used to compare two trees and export visualizations.

http://freecode.com/projects/epos/
SILAB - Sistema de Imagens Laboratoriais
This project eases the installation of computer lab systems with the usage of preconfigured system images, specially considering the needs of academic and research facilities.

http://www.codeplex.com/silab
Bika is a combined LIMS (laboratory information management system), workflow, and Web content management system.

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

http://freecode.com/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://freecode.com/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://freecode.com/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://freecode.com/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://freecode.com/projects/gwyddion/
IRIS
An astronomical images processing software.
http://www.freewarefiles.com/IRIS_program_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://freecode.com/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://freecode.com/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://freecode.com/projects/clcfreeworkbench