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Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
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This software is designed to help users visualize and analyze 3D point clouds with an associated real value, in a fast and flexible fashion. The primary use is in Atom Probe Tomography, which is an atomic imaging technique. However the program may also be useful in other areas, such as geospatial data, lidar, etc. Features: Load and view large point clouds; Slice, query and perform complex computations on points; Integration with external programs; ...
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Cytoscape is an open source software platform for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms.
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The Chromatography Analysis and Design Toolkit (CADET) is developed at the Institute of Bio- and Geosciences 1 (IBG-1) of Forschungszentrum Jülich (FZJ) under supervision of Dr. Eric von Lieres. The core of the CADET software is a fast and accurate solver for the General Rate Model (GRM) of packed bed liquid chromatography. The CADET solver covers a wide range of GRM variants, combining different transport and binding models with state-of-the-art mathematical algorithms and scientific computing techniques.
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The Tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Tinker has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98, ff99, ff99SB), CHARMM (19, 22, 22/CMAP), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA), Merck Molecular Force Field (MMFF), Liam Dang's polarizable model, and the AMOEBA polarizable atomic multipole force field.
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The Mantid project provides a framework that supports high-performance computing and visualisation of materials science data. Mantid has been created to manipulate and analyse neutron scattering and muon spectroscopy data, but could be applied to many other techniques.
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OpenChrom Community Edition
OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS and GC/FID systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP. Features: baseline detection; peak detection, integration and identification; mass spectrometric data filter (remove m/z, smooth data, ...); extensibility, modularity; native data file import converter; advanced GUI.
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ITK-SNAP is a software application used to segment structures in 3D medical images. ITK-SNAP provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. In addition to these core functions, ITK-SNAP offers many supporting utilities. Compared to other, larger open-source image analysis tools, ITK-SNAP design focuses specifically on the problem of image segmentation, and extraneous or unrelated features are kept to a minimum.
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The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
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OVITO is a freely available visualization software. Being a single integrated application it covers both the analysis and the visualization of large-scale atomistic datasets produced by molecular dynamics/statics and Monte-Carlo simulation codes. The name OVITO is an acronym for Open Visualization Tool, emphasizing that this software has been designed with flexibility and extensibility in mind.
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BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc.
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Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Combenefit only requires the user to save replicate data in the predefined .xls template files. It is based on an interactive platform which collects all experimental replicates and generates surface analyses for selected models. A wealth of outputs can be obtained and the software populates the project folder with the results.
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QBlade is a Blade Element Momentum Method (BEM), Double Multiple Streamtube (DMS) and nonlinear Lifting Line Theory (LLT) Design and Simulation Software for Vertical and Horizontal Axis Wind Turbines. It also includes tools to setup and simulate the internal blade structure and perform an aeroelastic analysis of a wind turbine rotor in turbulent inflow conditions through a coupling with FAST from NREL.
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itom is an open source software suite for operating measurement systems, laboratory automation and data evaluation. One main application of itom is the development and operation of sensor and measurement system for instance in a laboratory environment. Therefore, the software has to be able to communicate with a wide range of different hardware systems, such as cameras or actuators and should provide a diversified and as complete as possible set of evaluation and data processing methods.
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CueMol is a computer program for the macromolecular structure visualization (CueMol was formerly called 'Que'). CueMol's aims are to visualize and create the publication-quality images of the macromolecular structures with user-friendly interfaces. Currently supported files are molecular coordinates (PDB format), electron density (CCP4, CNS , and MTZ formats), MSMS surface data, and APBS electrostatic potential map (OpenDX format).
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The Tonatiuh project aims to create an open source, cutting-edge, accurate, and easy to use Monte Carlo ray tracer for the optical simulation of solar concentrating systems. It intends to advance the state-of-the-art of the simulation tools available for the design and analysis of solar concentrating systems, and to make those tools freely available to anyone interested in using and improving them.
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Morpheus is a database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast-up to nearly 5 times faster than OMSSA for large human datasets.
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AtomicJ is a Java application for processing of force curves that allows for fast and reliable estimation of mechanical properties of the sample. AtomicJ supports a wide range of contact mechanics models, including the models for blunt tips, the corrections for the effect of finite sample thickness, models of adhesive contact and models of spherical indentation of hyperelastic material. It implements novel procedures for analysis of force curves which allow for greater resistance to model deviations.
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catool is an open source command line tool that enables the loading, analysis and export of in-cylinder pressure data. It supports the industry standard AVL IFile file format and can convert this to CSV or MATLAB file formats. catool has been developed over the past 15 years and has proven robustness in both industy and academia.
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xfemm is a refactoring of the core algorithms of the popular Windows-only FEMM (Finite Element Method Magnetics) to use only the standard template library and therefore be cross-platform. The codes can be used as a library, standalone executables, or through the advanced Matlab/Octave interface, which uses direct data exchange at the memory level rather than the original FEMM ActiveX of file-based interface, for much improved communication speed.
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MSqBAT is a freely-available all-platform software application for label-free quantification of proteins from LS-MS data.
- label-free protein quantification
- MS1-based quantification
- MALDI ADA (Advanced Data Aquisition).
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UnityMol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). UnityMol can currently read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX potential maps and Wavefront OBJ meshes.
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LithoGraphX is an open source software for scientists, by scientists. It aims at providing the plant science community with a solid, open, community developed, software for 3D data analysis and visualization. LithoGraphX is a fork of the MorphoGraphX project. Features: volumetric rendering; 3D visualization; 3D recontruction; image processing; scientific application.
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SWAN is a third-generation wave model that computes random, short-crested wind-generated waves in coastal regions and inland waters.
SWAN accounts for the following physics:
- Wave propagation in time and space, shoaling, refraction due to current and depth, frequency shifting due to currents and non-stationary depth.
- Wave generation by wind.
- Three- and four-wave interactions.
- Whitecapping, bottom friction and depth-induced breaking. ...
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