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python tools for enhanced native structure-based modeling
eSBMTools: python tools that assist the setup and evaluation of native structure-based simulations of proteins and nucleic acids, both at the Cα and all-atom level. The tools interface with GROMACS and support its standard output formats. Information from other sources like bioinformatics or experimental data can be added to the standard native structure-based model (SBM).
Publication to be cited:
Benjamin Lutz, Claude Sinner, Geertje Heuermann, Abhinav Verma, and Alexander Schug. eSBMTools 1.0: enhanced native structure-based modeling tools. Bioinformatics 29(21):2795-6, November 2013
Attention :
This project is currently being migrated, some services are no longer supported.
NifTools aims to provide users with Tools to View, Edit, Create and Visualise 3D Models stored in the NetImmerse File Format.
The NIF format is used by many popular games based on the NetImmerse/Gamebryo Game Engine such as Morrowind, Oblivion, Fallout 3, Fallout: New Vegas and Skyrim.
We are creating a unified description of the NIF file format allowing our contributors to build...
Importer library to import assets from different common 3D file formats such as Collada, Blend, Obj, X, 3DS, LWO, MD5, MD2, MD3, MDL, MS3D and a lot of other formats. The data is stored in an own in-memory data-format, which can be easily processed.
www.open3mod.com/ is a 3D model viewer and exporter based on Assimp that is also Open Source.
...A few of its main features are:
- A full-featured 2D display library for rapid development
- Full control of computer I/O (display, mouse, keyboard, gamepad, joystick, audio)
- Advanced library of data collection techniques
- Data export to NumPy/SciPy, R, MATLAB, and Microsoft Excel
- Compatibility with PyACT-R for cognitive modeling
If you are interested in contributing to the CogPy project, contact the lead developer, Jasper Danielson, at jrd4@rice.edu.
Math tools in Python to tackle down problems in Operational Research fields. Comes with a Django based web interface to allow remote access to complex simulation means.
A library to compute the electron and chemical kinetics on plasmas
PLASMAKIN is a package to handle physical and chemical data used in plasma physics modeling and to compute gas-phase and gas-surface kinetics data: particle production and loss rates, photon emission spectra and energy exchange rates.
PROJECT MOVED: see http://www.vmtk.org for up-to-date information.
Libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis in image-based blood vessel modeling.
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aim is to provide support for monitoring system behaviour through dynamic analysis, and for analysing and modeling this data for a better understanding of system behaviour and for test automation
The neuroimaging in python (NIPY) project is an environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).
EnSuite is a network management plateform prototype based on NetConf. It aims at providing to the network management community an open source environment using NetConf configuration protocol and the Yang datamodeling language.
This project examines techniques to model three-dimensional rigid body motion using the geometric algebra of Dual Quaternions and how such models compare to more traditional models when used in underconstrained filtering applications.
Gaphor is a UML modeling environment written in Python. Gaphor is small and very extensible.
The repository is located at http://github.com/gaphor/gaphor.
The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
The purpose of this projects is to define, design and code a models-sharing system for the RepRap replication machines, so that end-users and designers can easily find, create, modify or build objects models.
This program generates customizable hyper-surfaces (multi-dimensional input and output) and samples data from them to be used further as benchmark for response surface modeling tasks or optimization algorithms.
PyGTS is a python package used to construct, manipulate, and perform computations on triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. THIS PROJECT IS NOT BEING MAINTAINED.
This project provides Blender Python scripts that will allow users to work with the propriatory mesh format used by the Orbiter space flight simulator.
Armagetron Advanced modding tools! Armagetron is a Tron-clone in 3D that provides a unique gameplay experience. AATools allows you to edit the visual data for Armagetron Advanced from within Blender, a comprehensive, open-source 3d graphics program.
This project simulates a multi-agent system (swarm) behavior both graphically and not. The purpose of this project is to research the properties suggested in "stability analysis of swarms" V.Gazi & K.M.Passino. Using the vpython library for 3D modeling