Search Results for "model-builder"
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Showing 26 open source projects for "model-builder"
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Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
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JRC QSAR Model Database
(Q)SAR Model Reporting Format Inventory
...This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. The information is structured according to the OECD validation principles. ... -
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Avogadro
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture. -
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relax
Molecular dynamics by NMR data analysis
...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. -
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GenX
X-Ray and Neutron Reflectivity Modeling
GenX is a scientific program to refine x-ray refelcetivity, neutron reflectivity and surface x-ray diffraction data using the differential evolution algorithm. GenX is very modular and highly extensible and can be used as a general fitting program. -
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Chemical Trajectory Analyzer
A software package for processing and analyzing chemical trajectories
...Theory Comput. 13 (2017), 3955-3960 M.Döntgen, F.Schmalz, W.A.Kopp, L.C.Kröger, K.Leonhard, "Automated Chemical Kinetic Modeling via Hybrid Reactive Molecular Dynamics and Quantum Chemistry Simulations", J. Chem. Inf. Model. 58 (2018), 1343-1355 Check the Wiki for bug reports and fixes. -
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MESMER is designed to analyze and simulate reactions in the gas phase that take place on a potential energy surface that is characterized by having one or more potential wells, and which are typically described by rate coefficients that depend on pressure (or concentration) as well as temperature. MESMER allows you to simulate systems over a wide range of pressures and temperatures, extract rate coefficients, analyze experimental data, fit model parameters and represent rate coefficients in formats that can be used directly in large scale simulations (e.g. Cantera or Chemkin).
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Aestel
Applications for data management
...DataLoader and AEREA, respectively. The data loader application applies user-defined instructions to validate, process and load data. The reporting application provides a query builder and spreadsheet template designer. Both applications work with any relational data model. (Postgres and Oracle have been tested). The two applications have been initially developed for small molecule drug discovery research. However, they can be extended for use in other data domains. -
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CoolingPower
Print Steam Tables; Plot diagrams and cycles from equations of state
...Unix-based operating systems also require the Boost program options library. The repository is structured as described in https://nvie.com/posts/a-successful-git-branching-model/ . -
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TheoDORE
Theoretical Density, Orbital Relaxation and Exciton analysis
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole, ...) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities. Code development moved to github: https://github.com/felixplasser/theodore-qc -
Build Agents and Models on One PlatformGemini Enterprise Agent Platform is Google Cloud's comprehensive platform for developers to build, scale, govern, and optimize agents and models. Choose from Google's most advanced models and third-party models like Anthropic's Claude Model Family.
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Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
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Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.
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nmr-nessy
NMR relaxation dispersion spectroscopy analysis software
...The graphical interface enables simple management of large experimental data sets and simple and automated analysis. NESSY automatically calculates effective transverse relaxation rate (R2eff) and performs model selection between different relaxation dispersion models. -
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In silico fragmentation evaluation
Comparative analysis of open source in silico fragmentation tools
We compared the performance of four publicly available in silico fragmentation tools that help in structure elucidation of metabolites (MetFrag, CFM-ID, MAGMa+ and MS-FINDER). Using the output of these tools we developed a voting/consensus model which is combining, re-ordering and re-ranking the candidates file and increases the correct hit percentage. We used 520 compounds from the 2016 CASMI challenge with 312 compounds for training and 208 compounds for validation purposes. -
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µic is a modelling engine for simulations of microstructural development. It takes localied behaviours as input from the user and integrates the global behaviour, with the calculation of all interactions as required by the application.
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ThermV
Comprehensive thermal analysis software package
...It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project is currently in alpha stage, where individual modules will be provided for data analysis. The modules for peak deconvolution, peak profile analysis and determination of Ea and lnA will be provided first. ... -
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WISP
Weighted Implementation of Suboptimal Paths (WISP)
UPDATE: LATEST VERSION AT http://git.durrantlab.com//jdurrant/wisp Allostery can occur by way of subtle cooperation among protein residues (e.g., amino acids) even in the absence of large conformational shifts. Dynamical network analysis has been used to model this cooperation, helping to computationally explain how binding to an allosteric site can impact the behavior of a primary site often many angstroms away. Traditionally, computational efforts have focused on the most optimal path of correlated motions leading from the allosteric to the primary active site. We present a program called Weighted Implementation of Suboptimal Paths (WISP) capable of rapidly identifying additional suboptimal pathways that may also play important roles in the transmission of allosteric signals. ... -
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Starch CLD fit
Least-squares fit of amylopectin chain-length distribution
This FORTRAN program package finds the parameters involved in amylopectin chain-length distribution (CLD) biosynthesis by fitting experimental CLD data to a model which incorporates the underlying starch biosynthesis. The amylopectin CLD biosynthesis model used by this program is explained in the article “A Parameterized Model of Amylopectin Synthesis provides key insights into the Synthesis of Granular Starch”, by Alex Chi Wu, Matthew K. Morell and Robert G. Gilbert. The downloadable .zip file contain the main code readily usable after compiling. ... -
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LibreAquarium
An aquarium management software with a Simulation Model System
...With all the records, the Simulation Model predicts the algae risk too (low,medium,high) and the algae type(green,cyanotic.) using the Redfield coefficient. Appart from that, the program tries to bring another modest contribution to Open Source Software and the World of Aquariums. SME LibreAquarium helps to daily maintenace of the aquarium with habitants control(fishes,plants, invertebrates), expenses, statistics, alarms, etc. -
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MolEd
Molecular builder
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Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.
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A reactor solver which uses stochastic particle methods to model particle population balances. This code is developed by the CoMo group in the chemical engineering department at the university of Cambridge (como.cheng.cam.ac.uk).
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A matlab/octave based reaction transport model describing microbially mediated isotope fractionation processes in porous media.
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This application transcribes basic codons and tells you the amino acid it codes for, the tRNA anti-Codon, and give you a 3D structural model of the amino acid and 2D picture of its chemical structure. Analysis reports can then be printed by the user.
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Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.
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JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.
