Search Results for "dynamics"
Sort By:
Showing 35 open source projects for "dynamics"
View related business solutions-
Go From AI Idea to AI App FastAccess Gemini 3 and 200+ models. Build chatbots, agents, or custom models with built-in monitoring and scaling.
-
Fully Managed MySQL, PostgreSQL, and SQL ServerCloud SQL handles your database ops end to end, so you can focus on your app.
-
1
BioEmu
Inference code for scalable emulation of protein equilibrium ensembles
...To reconstruct the side-chains, several tools are available. As an example, we interface with HPacker to conduct side-chain reconstruction and also provide basic tooling for running a short molecular dynamics (MD) equilibration. -
2
relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data. -
3
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. -
4
UnityMol
Molecular viewer and prototyping framework
!!! New website is https://unity.mol3d.tech and new releases/source code are now on Github : https://github.com/LBT-CNRS/UnityMol-Releases !!!! Implementation of a visualization prototype for molecular structures and networks using the Unity3D game engine. Implementation of numerous graphical methods as spheres, particle systems, bond, etc.. as well as our recent HyperBalls methodology (see: www.hyperballs.sf.net). -
AI-powered service management for IT and enterprise teamsGive your IT, operations, and business teams the ability to deliver exceptional services—without the complexity. Maximize operational efficiency with refreshingly simple, AI-powered Freshservice.
-
5
Lipid Reporter
Modifies csv files with a range of user defined filters.
...The supplied filters are all about Lipids. Add the category names, reject Ids that our outside of your favourite retention time range and lots more! This program is not produced by Nonlinear Dynamics and is not supported by Nonlinear Dynamics . Put all support questions through the Tickets and Discussion pages. Happy reporting. -
6
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.
-
7
MDA
Molecular Dynamics Analyzer (MDA)
MDA is a 3D single-particle tracking software that explicitly addresses fluorescence microscopy experiments deep in living specimens. It is capable of minimizing the systematic error that occurs with astigmatism-based 3D techniques owing to the aberrations induced by the refractive index mismatch. In contrast to existing techniques, the method determines the aberration directly from the acquired 2D image stream by exploiting the inherent particle movement and the redundancy introduced by the... -
8
Stochastic Rule Builder (SRB)
Modeling framework for capturing positional and temporal dynamics
We present a modeling framework aimed at capturing both the positional and temporal behavior of transcriptional regulatory proteins. There is growing evidence that transcriptional regulation is the complex behavior that emerges not solely from the individual components, but rather from their collective behavior, including competition and cooperation. Our framework describes individual regulatory components using generic action oriented descriptions of their biochemical interactions with a... -
9
DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
...These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid in discerning differential gene expression across diverse conditions. Computational biology is in need of methods for integration of static networks and gene expression data, since it provides interesting insights into the dynamics of biological systems. DEN is an R/Bioconductor based package designed to assemble different types of human bio-molecular interactions as a complete interactome and contains functions to extract dynamic active networks by integration of gene expression data. -
Add Two Lines of Code. Get Full APM.Works out of the box for Rails, Django, Express, Phoenix, and more. Monitoring exceptions and performance in no time.
-
10
MDcons(Molecular Dynamics consensus)
Interpretation of Biomolecular MD simulations
MDcons is a tool to analyze conserved contacts during Molecular Dynamics (MD) simulations of Protein, Rna, Dna & Ligand based complexes. The input is either a Molecular Dynamics trajectory or a set of snapshots. The input can also be a single snapshot. The outputs are (1) map of most/less frequently conserved contacts during MD (2) a list of most/less frequently conserved contacts during MD. -
11
-
12
QUDeX-MS
Hydrogen/deuterium exchange estimation for isotopic fine structure MS
Hydrogen-deuterium exchange coupled to mass spectrometry permits analysis of structural dynamics, stability, and molecular interactions of proteins. Resolving isotopic fine structure during mass spectrometry has been recently demonstrated to allow direct detection and quantification of deuterium incorporation distinct from peaks corresponding to non-deuterium incorporated natural abundance heavy isotopomers. Here, we present a graphical tool that allows for a rapid and automated estimation of deuterium incorporation from a spectrum with isotopic fine structure resolved. ... -
13
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.
-
14
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. Torchala, P. Chelminiak, M. Kurzynski and P. A. Bates, 'RaTrav: a tool for calculating mean first-passage times on biochemical networks', BMC Syst. ... -
15
Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.
-
16
abc-sde
approximate Bayesian computation for stochastic differential equations
A MATLAB toolbox for approximate Bayesian computation (ABC) in stochastic differential equation models. It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. Variance components for the "measurement error" affecting the data/observations can be estimated. A 50-pages Reference Manual is provided with two case-studies implemented and discussed. ... -
17
-
18
cancer_dynamics
Cancer Dynamics web
Website that shows the dynamics of a tumor by solving a system of ordinary differential equations. The results are two kind of graph images, and a gif file, being all of them available for download as a compressed file. -
19
Arena is a computer simulation in which programs compete for CPU time and access to main memory. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density dependent natural selection are amenable to investigation.
-
20
ODD is a tool for optimal domain decomposition of atomic structure guided by the given molecular dynamics data.
-
21
birgHPC is a Linux Live CD distribution based on PelicanHPC and Debian Live. birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics. If you are looking for CUDA support, try birgHPCC (https://sourceforge.net/projects/birghpcc/) If you use birgHPC in your work, please cite us: Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir. birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics. Bioinformatics. ...
-
22
BioSpring is a molecular simulation software based on a spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics. It incorporates MyPal for locating ion binding sites and IMPALA for interactive placement of membrane proteins in a membrane environment.
-
23
Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.
-
24
jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.
-
25
ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
