Scientific research freeware / freeware voor
- I, Librarian
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.
- Regress Pro
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.
- DAE Tools
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.
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.
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.
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.
- Serial Cloner
a Molecular Biology software. It provides tools with an intuitive
interface that assists you in DNA cloning, sequence analysis and
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.
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
was designed to be a scientific software package for numerical
computations providing a powerful open computing environment for
engineering and scientific applications.
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
- The XL
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.
- Unipro UGENE
is a free visual software solution for DNA and protein sequence
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.
- SILAB -
Sistema de Imagens Laboratoriais
project eases the installation of computer lab systems with the usage
of preconfigured system images, specially considering the needs of
academic and research facilities.
- Bika is a combined LIMS
(laboratory information management system), workflow, and Web content
- jHepWork is a full-featured
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.
- Seismic Toolkit is a tool for
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.
- 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.
- Micro-Manager is a software
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.
- 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.
- 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
- ParaView is a scientific
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++.
- The Chemistry Development Kit (CDK)
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.
- DNALinux is a live Linux
distribution with bioinformatics software preloaded.
- VMD (Visual Molecular Dynamics)
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
- PhiloLogic is a full-text
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.
- VisIt is an interactive
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.
- Gwyddion is a modular SPM
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.
An astronomical images processing software.
- 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.
- 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.
- 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