Search Results for "informatics"
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Showing 141 open source projects for "informatics"
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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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MzDOCK - Multiple Ligand Docking Tool
MzDOCK is A Virtual Screening Tool For Drug Discovery Research
- Molecular Docking Virtual Screening Tool To Aid In Drug Discovery Research. - Published in Wiley, Journal of Computational Chemistry . Link: https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.27390 - Developed with Synchronized functioning of Python and Batch scripts -Integerated With Pymol-open-source for visualizing interaction (PSE file) generated from MzDOCK - Integrated with Molecule Drawing Tool - JSME Editor - If you are facing any issues or for queries . Contact us -... -
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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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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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GromacsProSuite
Graphical User Interface for Gromacs
This tool is an integrated graphical interface that simplifies molecular dynamics simulations using Gromacs. It provides a structured, tab-based environment to set up, execute, and analyze simulations data without complex command-line operations. The software automates tasks such as topology generation, solvation, ion addition, minimization, equilibration, and production runs while executing GROMACS commands in the background. Built-in monitoring tracks CPU, RAM, and disk usage to ensure... -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters...
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Mendel’s Accountant is a biologically realistic, forward-time, parallel, numerical simulation program which models genetic change within a population, as affected by mutation and selection.
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the... -
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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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GFtbox is a Matlab package for simulating biological growth of leaves, petals, and similar organs.
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DBSolveOptimum
The software for systems biology/pharmacology modeling
DBSolveOptimum is a stand-alone software tool for the construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling... -
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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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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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N2A
Neurons to Algorithms - A neural modeling and simulation workbench
"Neurons to Algorithms" (N2A) is a language for modeling neural systems, along with a software tool for editing models and simulating them. N2A is currently "alpha" software. The download provided on SF is for convenience to those who wish to preview the software. Please see our site on github for development status. -
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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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GenCodeGenerator
C++ class to generate biologically plausible genetic codes
The "GeneticCode" C++ class is designed to generate versions of the genetic code subject to the requirements of the three major models of the genetic code origin and evolution (about these models see, e.g., Koonin & Novozhilov, 2009, IUBMB Life). This class was written specifically to perform statistical test for the paper Makukov & shCherbak (2017), but it might be used for a wider class of studies related to the genetic code. By default, the class "GeneticCode" generates... -
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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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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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pybrn is a Python package for the analysis of biochemical reaction networks. It provides basic model handling capabilities, import from SBML, analysis of conservation relations, steady state computation and model simulation.
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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.