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Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.
Download Gwyddion

XParallax viu
XParallax viu is a free software tool for automated astrometric data reduction of astronomic CCD images. It helps astronomers to perform an accurate astrometric reduction of dozens ore even hundreds of images which can be used in subsequent data analysis process. Fit headers generated by this software are fully compatible with other commonly used image utilities like SAO DS9 or Aladin Sky Atlas.
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Mass-Up is an open-source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. Mass-Up includes the following analyses: Quality Control, Biomarker discovery, Principal Component Analysis, Hierarchical clustering, Biclustering, and Classification analysis.
Download Mass-Up

Rapid Sequence Analysis Toolkit (RSAT) facilitates the fast and easy generation and analysis of protein-coding sequence datasets. RSAT saves researches of all bioinformatics experience levels considerable time by automating the numerous tasks required for the generation and analysis of protein-coding sequence datasets using a straightforward graphical interface. The application uses a portable database framework to manage and organize sequences along with a graphical user interface (GUI) that makes the application extremely easy to use, even for those with little bioinformatics experience.
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A collection of cheminformatics and machine-learning software written in C++ and Python. The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
Download RDKit

XFLR5 includes the xfoil program for foil analysis, and several 3d analysis methods for planes:
- a non-linear lifting line method for standalone wings,
- two vortex-lattice and a 3d panel method for the analysis of aerodynamic performance of wings and plane operating at low Reynolds numbers.
The latest v6 version introduces stability analysis of planes.
Download XFLR5

Combination of reverse transcription (RT) and deep sequencing has emerged as a powerful instrument for detection of RNA modifications, a field that has seen a recent surge in activity because of its importance in gene regulation. Recent studies yielded high-resolution RT signatures relying on both, sequence dependent mismatch patterns and RT arrests. Common alignment viewers lack in specialized functionality, such as filtering, tailored visualization, differential analysis and export.
Download CoverageAnalyzer

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. Cantera provides types (or classes) of objects representing phases of matter, interfaces between these phases, reaction managers, time-dependent reactor networks, and steady one-dimensional reacting flows. Cantera is currently used for applications including combustion, detonations, electrochemical energy conversion and storage, fuel cells, batteries, aqueous electrolyte solutions, plasmas, and thin film deposition.
Download Cantera

E-foto software possess photogrammetric functionalities that allow the development of professional topographic tridimensional mapping projects, by using as data sources aerial photogrammetric images obtained by both analog cameras and digital sensors.
Download E-FOTO

A computer code for simulation of electron-hydrogen scattering. Contains three (more or less) finished sub-programs:
- 'hex-ecs' which solves the Schrödinger equation in the B-spline basis,
- 'hex-dwba' which computes scattering variables for high energies using the distorted wave Born approximation of the first order and finally,
- 'hex-db' which is a user interface to a plain SQLite database, where the intermediate results are being stored, and which is used to extract derived quantities like a cross section from it.
Download Hex

AltAnalyze is an easy-to-use application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, ...).
Download AltAnalyze

GridLAB-D is a new power system simulation tool that provides valuable information to users who design and operate electric power transmission and distribution systems, and to utilities that wish to take advantage of the latest smart grid technology. It incorporates advanced modeling techniques with high-performance algorithms to deliver the latest in end-use load modeling technology integrated with three-phase unbalanced power flow, and retail market systems.
Download GridLAB-D

OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets. The application allows the user to load a genome-scale model of a given organism. This will serve as the basis to simulate the wild type and mutants (original strain with a set of selected gene deletions).
Download OptFlux

Toolbox for handling X-ray transmission image data collected using the Xradia TXM system. Features: Xradia file format support; FBP and ART tomo reconstruction; Command script generation for different experimental designs; TXM XANES imaging data analysis; PCA and k-means clustering of TXM XANES data.
Download TXM-Wizard

Kalypso is an open source application for geospatial modelling and simulation. It is primarily developed to be a user friendly tool for GIS-based modelling and simulation of hydrological and hydraulic numerical models. Features: Hydrological model; Water surface profile model; Unsteady coupled 1D/2D finite element model; Module for flood depth determination; Module for flood risk determination.
Download Kalypso

Finite Element Method Magnetics (FEMM) is a finite element package for solving 2D planar and axisymmetric problems in low frequency magnetics and electrostatics. The package is composed of an interactive shell encompassing graphical pre- and postprocessing; a mesh generator; and various solvers. A powerful scripting language, Lua, is integrated with the program. Lua allows users to create batch runs, describe geometries parametrically, perform optimizations, etc.
Download FEMM

TexGen is a geometric textile modelling software package to be used for obtaining engineering properties of woven textiles and textile composites. Features: 2D Weave Wizard; 3D Weave Wizard; Variable yarn cross sections; Export in various formats including ABAQUS, IGES and STEP.
Download TexGen

PCRaster is a collection of tools and software libraries tailored to the construction of spatio-temporal environmental models. Application domains are amongst others hydrology (rainfall-runoff, global water balance, groundwater), ecology, or land use change. Two scripting languages (PCRcalc and Python) include a rich set of spatial operations for manipulating and analysing raster maps. A Python framework supports Monte Carlo simulations and data assimilation (Ensemble Kalman Filter and Particle Filter).
Download PCRaster

VisTrails is an open-source scientific workflow and provenance management system that provides support for simulations, data exploration and visualization. Whereas workflows have been traditionally used to automate repetitive tasks, for applications that are exploratory in nature, such as simulations, data analysis and visualization, very little is repeated - change is the norm. As an engineer or scientist generates and evaluates hypotheses about data under study, a series of different, albeit related, workflows are created while a workflow is adjusted in an interactive process. VisTrails was designed to manage these rapidly-evolving workflows.
Download VisTrails

ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results.
Download ChelomEx

IDP is a knowledge Base System (KB-system) for the FO(·) language. Using IDP, it is possible to model systems and problems, both from the real world as several artificial intelligence research problems. Solutions to these problems can then be found using one or more inference techniques. One class of real world problems that serves as a nice introduction to IDP is a scheduling problem.
Download IDP

Toast++ is a software suite for image reconstruction in diffuse optical tomography (DOT). It contains a forward solver module using the finite element method for simulating the propagation of light in highly scattering, inhomogeneous biological tissues, such as the brain. The inverse solver module uses an iterative, model-based approach to reconstruct the unknown distributions of absorption and scattering coefficients in the volume of interest from boundary measurements of light transmission.
Download Toast++

Arabidopsis Motif Scanner
The major mechanism driving cellular differentiation and organism development is the regulation of gene expression. Cis-acting en-hancers and silencers appear to have key roles in regulating gene expression. Arabidopsis Motif Scanner was design to build gene networks by identifying the cis-regulatory elements position in the model plant Arabidopsis thaliana and by providing an easy interface to evaluate gene relations.
Download Arabidopsis Motif Scanner

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.
Download Gimias

CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Previously known as PIVOT (Protein Interaction Visualization and Observation Tool).
Download CIG-P

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