Search Results for "synthetic"
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Showing 12 open source projects for "synthetic"
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Tellurium
Model, simulate, and analyze biochemical systems using one tool.
Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support. -
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GatcomSUMO
Automates the building of VANET simulations using SUMO and OMNeT++
GatcomSUMO is a multi-platform application that facilitates the building of VANET simulations using the SUMO traffic simulator and the OMNeT++ network simulator. The tasks related to the generation of abstract or synthetic scenarios, the download and conversion of network scenarios based on real maps (e.g. from OpenStreetMap), the route creation process, and the vehicles mobility modelling are integrated in a user-friendly graphical interface. This tool performs the necessary actions... -
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TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.
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MSP: a 3D flocking boids simulator
A highly flexible 3D flocking boids simulator, conceived as a tool for
.... The set of considered behaviors are inspired by the well-known approach introduced in 1987 by C. W. Reynolds. The simulator delivers a 3D visual interface and provides as an output file all the instantaneous microscopic information related to each boid (positions and velocities over time), allowing in this way subsequent analysis, such as searching for synthetic and higher-level descriptions of collective behaviors, relying for instance on global network and meta-structural properties. -
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RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.
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The TErminology for the Description of DYnamics (TEDDY) project aims to provide an ontology for dynamical behaviours, observable dynamical phenomena, and control elements of bio-models and biological systems in Systems Biology and Synthetic Biology.
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NoCTweak
a Parameterizable Simulator for Early Exploration of Networks On-Chip
A networks-on-chip (NoC) simulator allows designers to early estimate performance (latency and throughput), energy efficiency (average/peak power, average energy per packet) and area of several networks on-chip configurations at different CMOS nodes. This tool is a cycle-accurate simulator and is open-source using SystemC, a C++ plugin, which is used to quickly model complex systems at a higher level but less details than RTL. NoCTweak was developed by Dr. Anh Tran and Dr. Bevan Baas at UC... -
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Global Epidemic Simulator
A platform for modelling influenza-like epidemics and containment
The Global Epidemic Simulator is a platform for modelling directly transmissible human diseases such as influenza, and testing intervention policies that may reduce the duration or severity of an outbreak of such a disease. Building on previous work, this model is spatial and individual-based, using various geographical and demographic data sources to place households at absolute locations, populated with individuals of specific ages who each attend schools or workplaces situated in their... -
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Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
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Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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JRandO is a test data generator or better test object generator framework. It can be used in JUnit tests or in performance test (for e.g. using JMeter). It may also be useful in anonymization of data or in a simulation environment.
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Sample code for JRandO project. (testdata generator, test data generator, test object generator, simulation)
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