Search Results for "chemical reaction software"
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Showing 31 open source projects for "chemical reaction software"
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The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io
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navmol-ch
A fork of the navmol (https://sourceforge.net/projects/navmol/)
NavMol with practical improvements, the addition of menus, the support of Mandarin, the addition of the text-to-speech, the implementation of the interrupt function of speech, and the full internationalization of text, easier and more convenient to be used. -
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Numerics for Chemical Engineering
Numerical models for chemical and process engineering
NCE Calculation Framework is a library of routines, models and data applicable to chemical and process engineering calculations, written in Java. -- NEW -- www.chesolver.com *ONLINE CALCULATORS*. A set of solvers to perform calculations consistently on any device, from smart-phone to desktop. The project includes the following ready to use software all based on the same core library: * Online Calculators at www.chesolver.com * Extensions for Libreoffice/Openoffice Calc spreadsheet: - NCE: https://extensions.libreoffice.org/extensions/nce - NCE-Units: https://extensions.libreoffice.org/extensions/nce-units Check out also our video channel: https://www.youtube.com/channel/UCt2EGdw33k2u19PnZAi8YJA -
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OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets.
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JSiteDescriptor
Binding site descriptor generation for SVM based classification.
A set of java programs that extract coordinate and chemical information from PDB files. The binding site regions are extracted using grid based scheme. For binding site, spatio-chemical descriptor is generated based on PocketMatch algorithm of Dr. Kalidas (author of this project too). -
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Rhea is a reaction database, where all reaction participants are linked to the ChEBI database (Chemical Entities of Biological Interest). Rhea provides built-in validations that ensure both mass and charge balance of the reactions.
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PixelFlow
A Processing/Java library for high performance GPU-Computing (GLSL)
PixelFlow is a Processing library focused on advanced graphics and visual effects, offering an extensive suite of GPU-based tools for visual artists, researchers, and creative coders. It enables real-time simulation and rendering of complex effects such as fluid dynamics, reaction-diffusion systems, soft shadows, and more, all powered by GLSL shaders. Its modular structure allows for chaining and composing various visual effects easily, making it ideal for installations, performances, and... -
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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. ... -
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...Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
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Systems Glycobiology
Glycosylation Network Analysis Toolbox (GNAT)
...The original GNAT package (file GNAT.zip) provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks (citation [1]). The second version of this software (GNATv2beta.zip) upgrades the original GNAT program with additional features that are geared towards incorporating glycan-structure experimental data into the simulation environment. For information about GNAT installation and usage, please see the GettingStarted.pdf file enclosed in the package. ... -
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Easily find and extract specific chemical reactions from the BioModels database.
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ezBioNet is a biological modeling and simulation tool of molecular interaction that occurred in a cell. We aim that this software can be used for collecting biological data and making biological models to simulate it by biological researchers. ezBioNet can build a detailed biological model including signal transduction, enzyme kinetics, expression network, etc. It also support number of numerical analysis method to simulate the biological reaction networks.
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Building controls often have a PID Loop (Proportional Integral Derivative). Adjust PI&D terms in realtime and visually see what the reaction to the system will be. This is a real-time simulator with speed adjustment. Software requires the old MS Java Machine to run. Interested in an updated desktop version? Please drop me a note in the forum or my blog: http://right-handed-monkey.blogspot.com/
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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jPeriodic
jPeriodic is a table of elements written in Java
jPeriodic is a simple table of elements coded in Java providing the user with the most common informations about each known chemical element. By clicking an element a popup will apear containing the selected elements attributes. Additionaly jPeriodic offers a small temperature converter which is able to convert between Celcius and Kelvin. Because jPeriodic is coded in Java the software is platform-independent, meaning you can run jPeriodic on Windows, Mac OS, Linux and many other operating systems which are able to run a Java Virtual Machine. -
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Khembalancer
Software to balance a chemical equation (redox too)
Balacing a chemical equation using the Laplace's rule to solve a system of linear equations or using the brute-force method. Khembalancer 2.5.5 received the "100% Free" award and that means Khembalancer does not contain any viruses, spyware, trojans and backdoors. For more information see: http://www.softpedia.com/progClean/Khembalancer-Clean-207422.html -
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iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l
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ActiveInsight provides real-time detection and reaction to events and patterns. It is a platform that enables the detection of meaningful events within multiple, high frequency, event streams.
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ReSpecT (Reaction Specification Tuples) is a logic-based language for distributed system coordination. ReSpecT is based on a coordination model exploiting tuple centres as first-class, general-purpose coordination media.
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OSCAR (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries.
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The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.
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GRaPe - a platform-independent software tool for building integrative gene-reaction-protein (GRP) networks. It generates the kinetic equations for each reaction and outputs a SBML document. It also implements two methods for parameter estimation.
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ScreeningAssistant is a software based on JOELib and dedicated to the management of chemical databases. It allows the user to select a set of compounds for screening tests (High Throughput Screening or Virtual Screening).
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Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
