Open Source Chemistry Software - Page 10
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Analytical Information Markup Language
Open XML format for analytical chemistry and biology data.
This project supports ASTM E13.15 "Analytical Data Magement" in its work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry and biology data. -
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Animp is an OpenGL program to display movies of particles in motion where the movies are produced by adding calls to animp library routines to simulation code written in either C++ or Fortran. Animp can also display molecules read from PDB files.
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Arduino Temperature Controller
Arduino Temperature Controller
This code allows an Arduino to work like a PID controller. It uses a MAX6675 with K type thermocouple to turn a heat source (hotplate), to maintain a constant temperature. This version uses a Adafruit SSD1306 OLED for visual output. 3 inputs are used, temp scale (C/F/K), target temperature up, and target temperature down. Those are simple momentary contact buttons to ground, on 3 analog pins. -
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3D modeling of chemical elements atoms
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This software searches the potential energy surface of small to medium size atomic systems for global minima using quantum ab initio techniques. It performs bond rotations and molecule translations and rotations on a Linux cluster with MPI.
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Software developed for the analysis of Neutron Reflectivity data.
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We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.
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Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
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AutoMap
AutoMap is a tool for structural biology and drug design.
AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes. -
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Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
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ALC (Automated Layer Construction) is a computer program that highly simplifies the building of reduced modular models of signaling systems, according to the layer-based approach.
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BETR-Research (BETRS) is a modelling framework to create spatially resolved multimedia models for the environmental fate- and transport of chemical contaminants. It is intended to serve the research community and can be used as a teaching tool.
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BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environ
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Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells
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Beer Wizard is the possibly temporary title for a piece of software being developed for members of the Craft Beer community.
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Beryllium¹º is a program designed to facilitate the creation of group safety data sheets (GSDSs) for hazardous substances and processes. The created GSDSs fulfill the conditions of EG Nr. 1272/2008 (Globally Harmonized System of Classification and Labelling of Chemicals, GHS) and §20 Gefahrenstoffverordnung (German regulation and version of European Union Directive 67/548/EEC: Safety advice concerning dangerous substances and preparations).
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BiMS
BiMS (biclustering for mass spectrometry data) is a Java application d
BiMS (biclustering for mass spectrometry data) is a Java application designed to allow the application of biclustering algorithms to mass spectrometry datasets. Users can load their MS datasets and apply different clustering and biclustering algorithms (current version includes Bimax and BiBit). In adition, users can load raw datasets (in mzML or mzXML formats) and preprocess them using MALDIquant package and MassSpecWavelet. -
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Bika Open Source LIMS/LIS
Web based laboratory information management system
A web-based LIMS (Laboratory Information Management System) · Built in Plone · Professionally supported · Making waves · bi:ka (Zulu): tell it as it is More information and links to manuals, user forums, support and translations are available at https://www.bikalims.org/support-and-service-provision Bika community: www.bikalims.org Main project sponsor, Bika Lab Systems: www.bikalabs.com Inquiries: lemoene@bikalabs.com -
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BinBase
BinBase is a software for the automatic analysis of Massspec data from
BinBase is a software for the automatic analysis of Massspec data from LECO GC-Tofs. All code and documentation has been moved to the google code site of this project: https://code.google.com/p/binbase/ And support is provided by the company coding and more, which can be reached under: contact@codingandmore.org -
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BioNLP-Corpora is a repository of biomedically and linguistically annotated corpora and biomedical data sources. There are many resources available in separate packages in this project.
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Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
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BlochLib is an expression template library of generic data structures and algorithms to perform large scale nuclear magnetic resonance classical and quantum mechanical spin simulations, with many I/O capabilities,and integrated numerical routines.
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Brabosphere is a multiplatform application with two main uses: a 3D molecular visualisation tool and a graphical frontend for the quantum chemical program BRABO.
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BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.