Search Results for "the linux command line" - Page 2
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Showing 83 open source projects for "the linux command line"
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**(9 march 2016) this project is continued on github : http://jaapkroe.github.io/polypy ** Python script to analyze (shortest-path) rings in structures read from xyz-files. It can be useful for example to identify defects in crystal structures or molecules.
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KEMP
A FDTD solver for electromagnetic wave simulations on a GPU cluster
KEMP is a fast FDTD solver on a GPU-based cluster. The FDTD (Finite-Difference Time-Domain) method is a popular numerical method for electromagnetic field simulations. KEMP enables hardware accelerations suitable for multi-GPU, multi-core CPU and GPU cluster. KEMP also provide easy configuration by using Python scripting language. -
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LipidWrapper
Create lipid-bilayer models of arbitrary geometry.
LATEST VERSION NOW LOCATED AT http://git.durrantlab.com/jdurrant/lipidwrapper As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. When building large-scale models of whole subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature are essential. LipidWrapper, written by Jacob Durrant in the lab of Rommie E. Amaro,... -
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ReorJS
Distributed Computing with JavaScript
Create your own distributed computer that can distributed javascript based applications to any computer with a web browser, headless browser or node.js installation. For more information and updates please see our website - http://reorjs.com. -
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That project aims at studying and comparing typical airline IT methods, for instance RM-related algorithms. It works from a Unix/Linux/Mac command-line, and exposes basic APIs. It is being developed in C++, with Python wrappers for some components.
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path... -
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Autonomous Robot Simulator
Physically-accurate robotics simulator written in Python
ARS is a physically-accurate robotics simulator written in Python. It's main purpose is to help researchers with to develop mobile manipulators and, in general, any multi-body system. It is open-source, modular, easy to learn and use, and can be a valuable tool in the process of robot design, in the development of control and reasoning algorithms, as well as in teaching and educational activities. -
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SunlightDPD
Open source codes related to dissipative particle dynamics
SunlightDPD provides a home for open source codes related to the dissipative particle dynamics (DPD) simulation method. Currently the file release contains the HNC integral equation code. -
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BETR-Research (BETRS) is a modelling framework to create spatially resolved multimedia models for the environmental fate- and transport of chemical contaminants. It is intended to serve the research community and can be used as a teaching tool.
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ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid
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QtoNum
python calculus library with imprecise and precise representations
...QtoNum also handles infinitesimals and infinites. All these types can be mixed in expressions and conversions are performed automatically. QtoNum can be used as an interactive calculator (command line) and as a calculus library. -
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CAPLET
GDS visualization and parallelized capacitance extraction
Project CAPLET is a capacitance extraction toolkit that extract capacitance at field-solver accuracy. CAPLET can directly handle GDS2 layout files into capacitance matrices in both GUI and command line interfaces. The internal extraction algorithm is specialized for VLSI interconnect structures but not exclusively, as long as the structure is of Manhattan geometry and embedded in a uniform dielectric material. -
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PyMbs has moved to Bitbucket: https://bitbucket.org/pymbs/pymbs PyMbs is a Python library for modelling holonomic multibody systems. It is able to generate simulation code for Python, Modelica and Matlab.
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That project aims at providing a clean API and a simple implementation (C++ library) of an Airline-related Seat Inventory Availability Calculation system. That library uses the Standard Airline IT C++ object model (http://sf.net/projects/stdair).
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Topographica
Simulation software for brain modelling
Topographica is a neural modeling package developed in a Human Brain Project grant from NIH. Topographica helps neuroscientists and computational scientists simulate and understand how topographic maps contribute to brain function. Topographica is now primarily maintained at github.com; see https://github.com/ioam/topographica for recent updates and releases. -
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That project aims at studying and comparing typical airline IT methods, for instance RM-related algorithms. It works from a Unix/Linux/Mac command-line, and exposes basic APIs. It is being developed in C++, with Python wrappers for some components.
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SunlightLB is an open-source 3d lattice Boltzmann code which can be used to solve a variety of hydrodynamics problems, including passive scalar transport problems.
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ProSym
Software package that facilitates traffic simulation
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GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.
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QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.
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VERTIS Virtual Scanner
A virtual scanner for 3D models.
A virtual scanner that converts 3D models (in Wavefront .obj format) into pointcloud files (in PCL .pcd format). Useful for simulating robotic input. NOTE: This project has been merged into the project at https://github.com/canderegg/cfg_obj -
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Differential-algebraic simulator in python. Process and control systems are modelled w/ bloc diagrams. It allows algebraic loops, has an automatic steady-state computation, detects singular systems, and uses variable time-step transient integration.
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HPC cloud computing for OpenFOAM (R) users
