Search Results for "informatics"
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102 projects for "informatics" with 2 filters applied:
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PhysiCell
physics-based multicellular simulator
PhysiCell is a cross-platform C++ framework for large, physics-based multicellular simulations. -
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Nemo
Individual-based forward-time genetics simulation software
Nemo is an individual-based, forward-time, genetically explicit, and stochastic simulation software designed for the study of the evolution of life history and quantitative traits, and genetic markers under various types of selection, in a spatially explicit, metapopulation framework. -
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CyberUnits
Class library for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal. -
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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Fully Managed MySQL, PostgreSQL, and SQL ServerCloud SQL handles your database ops end to end, so you can focus on your app.
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SimThyr
A simulation program for thyroid homeostasis.
SimThyr is a continuous simulation program for the human pituitary-thyroid feedback control system. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses and patients. -
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ntx
Neutrality tests using the SNP site frequency spectrum
Tests on "neutrality" are designed to detect systematic deviations from chance patterns in genetic data. This tool computes for a given SNP site frequency spectrum some standard test statistics like Tajima's D, Fay & Wu's H, etc. Additionally, the user may adapt the tests to specific demographies by specifying non-standard first and secondary moments. These can be obtained e.g. from simulations. -
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Pysces
PySCeS is the Python Simulator of Cellular Systems
PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis. -
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Antimony
Antimony is a human-readable, human-writable model definition language
Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats. -
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CBMPy
PySCeS Constraint Based Modelling
PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently... -
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BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format
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APBS
Biomolecular electrostatics software
This software has moved to http://www.poissonboltzmann.org/. -
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Tissue Simulation Toolkit is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.
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PF_HP
Prediction of proteinfolding in 2D HP model
Even in the simplified two dimensional HP-model (hydrophob/polar) the prediction of proteinfolding is NP complete. We implement a brute force algorithm with serial and parallel execution to solve short inputs of HP sequences (0-1 bitstrings). Selbst im vereinfachten zweidimensionalen HP-Modell (hydrophob/polar) ist die Proteinfaltung bereits NP-vollständig. Hier implementieren wir einen brute-force Algorithmus zur Lösung kurzer Eingabesequenzen (0-1-Bitstrings) für die... -
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This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.
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RoadRunner represents a state-of-the-art simulation library for SBML models. It is fast, portable and accurate. This projects hosts the library and tools using the library.
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JBioFramework
Growing suite of proteomics simulations for educational purposes
JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please... -
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Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS
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Molecular Simulation Grid
Provides high performance computing power and state of the art tools
MoSGrid focuses on the configuration and provision of Grid services for molecular simulations and annotation of the results with metadata and their provision for data mining and knowledge generation. It is based on Liferay technology togethe with gUSE. -
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MGSyn
MGSyn - Automatic Synthesis for Industrial Automation
MGSyn (Model, Game, Synthesis) is an open-source tool which integrates game-based synthesis into model-driven development for industrial control and automation. It is served for research and educational purposes. MGSyn has been originally developed by Department of Informatics (Unit 6), TU München and fortiss GmbH and is now maintained by fortiss GmbH. The software is released under the GNU General Public License Version 3.0 (GPLv3). Please download the tutorial for step-by-step instructions on installing and using the tool. It is advised to use 32-bit version (Eclipse) associated in the "MGSyn supplementary files", as the 64-bit version will by default demand huge memory, which may lead to Java exceptions. -
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runjags
The 'runjags' R package and standalone JAGS extension module
This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A... -
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Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.
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Moose
Multiscale Neuroscience and Systems Biology Simulator
Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes. We have moved Github.com. This should be your source for the latest version of the code. -
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SFS_CODE (Selection on Finite Sites under COmplex Demographic Events) performs forward population genetic simulations under a general Wright-Fisher model with arbitrary demographic, selective, and mutational effects.