Search Results for "topology" - Page 4
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Showing 205 open source projects for "topology"
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DART
DART: Denoising Algorithm using Relevance network Topology
The DART-CLQ R-script is an add-on to the Bioconductor DART package (www.bioconductor.org). In due course, both will be merged. DART/DART-CLQ aims to denoise gene expression perturbation signatures in order to obtain more reliable estimates of perturbation activity in primary cancers. It is thus aimed for Personalized Medicine. Licence: MIT -
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codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, codonPhyML will return the phylogenetic tree that best describes their evolutionary relationship. Our paper describing codonPhyML has been published in the journal "Molecular Biology and Evolution" (MBE). For more details, follow the link: http://mbe.oxfordjournals.org/content/30/6/1270. codonPhyML is on the cover of MBE! Check this out...
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dep-trace
gdeptrace dependancy solver correct for pkg or make deps
gdeptrace sorts an input dependancy list or table and prints it, and can do other actions. It's default operation is to act like tsort (1) except that it sorts by pure pkg / make dependancy (tsort sorts by grapical topology: see notes about differences). EXAMPLE: $ echo -e "b e\ne\nc b" | sort -k1,1 | gdeptrace [opts] e b c (b depends on e, c depends on b, e has no depends) (also: e has more items depending on it and is below anything it depends on; in this case... -
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Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.
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Bio.B-Gen
Initial system (box) generator for biological molecular simulations
"Bio.B-Gen" is a command line tool to generate initial systems for biological molecular simulations. "Bio.B-Gen" was mainly designed to be used with the GROMACS molecular dynamics simulation package (http://www.gromacs.org). "Bio.B-Gen" depends on the GROMACS topology and force field information (.top and .itp data files) during the generation stage. "Bio.B-Gen" adds specified number of copies of a molecule to an existing configuration to a specified spacial domain inside the system... -
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wireless_data_acquisitionTICC430
wireless data acquisition system using TI CC430 family
Project of wireless data acquisition system using TI CC430 family microcontroles. Project aims: - design RF modules base on CC430F5137 868MHz - design END_DEVICE and RECIVER module - develop simple protocol - apply network configuration interface and supporting star/tree topology -
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LDNI-based Solid Modeling
Solid Modeling Framework in GPU
This project provides a set of solid modeling tools which aims to help processing 3D objects with complex topology and geometry that are widely used in many industrial applications (e.g., microstructure design and manufacturing, biomedical products and applications, jewelry products, reverse engineering). The system is completely GPU-based and heavily based on an implicit representation named LDNI. -
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FractalNeuroComputer
Artificial Neural Network
This is version 2 of a simulation that I wrote over a decade ago and never released. It is intended for research purposes. The FNC uses a fractal topology for the interconnect matrix and a "literal" neuron model inspired from biological neurons. The original source is long gone and I'm re-coding from scratch. -
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GoIFISH
for the semi-automated analysis of IFISH images
GoIFISH has been developed for the analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection. Users can manually edit segmentation results, perform background adjustments, construct heatmaps, topology maps, and perform cell classification. All results can be exported for further analysis. GoIFISH has been developed in MATLAB, however binaries are provided to run the program outside of the MATLAB environment. Source... -
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evotopo
Evolving Realistic Topologies for Wireless Network Simulation
There is a need for realistic node topologies for simulating and testing wireless network protocols. The softare evoTopo is able to generate multiple different topologies based on a given reference example, typically from a real-world setup. Based on this an evolutionary algorithm evolves new topology files with equal parameters regarding node density, distribution homogeneity and network properties such as node degree distrbution. evoTopo can be used with any wireless network simulator... -
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GraphDruid
Graphs sorting in 2D
Graph Druid program provides topological sorting of mathematical graphs in 2D space. Graph druid uses ranking and clustering methods to sort graph topology. Result of sorting is visualized and can be stored. -
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MILPFlow: An Open Source Project to Simulate VM Placement of Data Centers. Data center network topology simulator with Lingo and network simulator 2 (ns-2)
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ViennaGrid is a generic mesh handling library that provides the traversal of structured and unstructured grids in arbitrary spatial dimensions, in particular 1d, 2d and 3d. Quantities can be conveniently stored on mesh elements using ViennaData.
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A Software Laboratory for studying the properties of different types of Random Boolean Networks. It can calculate attractor statistics, graphic representation of dynamics, topology graph, etc. In Java, more at http://turing.iimas.unam.mx/~cgg/rbn
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Dynamic Ad Hoc Simulator (DARS) is a platform-independent simulator of mobile, ad hoc network (MANET) protocols. It is expandable and already comes with Ad hoc On Demand Distance Vector (AODV) and Destination-Sequenced Distance-Vector Routing (DSDV).
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Toponet is a framework and a set of tools for network topology discovery and hardware inventory. Currently IS-IS topology discovery for Cisco and Juniper routers is supported. Toponet uses Jifty application server (http://jifty.org).
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NetGames
MATLAB tool for network formation games modeling and visualization
A toolbox for network formation games researches. Currently focused on game theoretic topology formation in wireless ad hoc networks. Additionally includes functions for Granovetter threshold model of social activity. The project still under development -
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S-BITE
S-BITE is an AS level topology generator for the Internet
The Structure-Based Internet Topology gEnerator (S-BITE) is an Autonomous System (AS) level topology generator for the Internet. The generator exploits a technique that partitions the network topology into two distinct blocks: the Core, which captures the underlying community structure of the Internet, and the Periphery, representing the “tendrils” of the topology. Thanks to this layering, S-BITE is able to accurately reproduce Internet topology at the statistical level,matching classical... -
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COQ Theorems, Abstractions and Implementations (bachelor Level) Coqtail is a library of mathematical proofs using the Coq proof assistant.
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SAWU104 textile / knot diagram editor
Generic textile / knot diagram / thread topology editor
A linked data structure for modelling generic weaving patterns, more like a topological representation than a grid type one, for the non-weavers. This editor is capable to represent all the weaveable patterns and more. In other terms, it is up to you to check if the patterns drawn can be physically created, without endless loops of threads etc. Its original use is to document an artifact (parts of which may be missing) in a museum, without damage to it. The curator, while trying to... -
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GEMS IoT
IoT Device, Gateway, Server platform
Bi-directional Wireless Sensor Line Protocol(Bi-WSLP) is a sensor network communication protocol based on a line topology, which is common in outdoor monitoring cases for IoT(Internet of Things). Bi-WSLP runs fast and provides a response rapidly, yet it takes a small code size occupies small memory. Bi-WSLP can be easily ported to various hardware platforms because it is coded in C, which is the most popular programming language for embedded systems. In addition, Bi-WSLP allows transmission... -
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RaTrav
mean first passage times and node occupancies calculations
RaTrav tool was designed to support computational biology studies where mean first-passage times (MFPTs) between initial and single or multiple final states in network-like systems are used. The tool approves arbitrary networks (graphs) where a dynamics of the Markovian type takes place. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method. References: M... -
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TSIF
Topology Security and Inventory Files
Simplified Files designed to share ICTO data across systems and/or teams in a World. Also Here you should find a way how to collect usefull data about your network and do not spend too much effort. Such data are mostly used for daily network troubleshooting, customers charging, capacity planning etc. These tools provides you a benefit when you need to collect data about hundred and more network devices, such as switches, routers or firewalls. Tens of thousands of them should not be a... -
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CASMR Advisor
Source Code content for Open Source packages used by the CASMR Advisor
Source code content for Open Source packages used by the CASMR Advisor, Server, which is a stand alone CASMR product that provides notifications to registered users based on the status of firebird based products (CASMR, CAST, CSS, DKS) connectivity as well as of CASMR installed plugins and topology status. A CASMR Advisor Client (iOS and Android) registers with the Advisor Server and is granted visibility to the notifications from a subset of the AS (advisor server) firebird platforms.