Search Results for "application"
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Showing 31 open source projects for "application"
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Build AI Apps with Gemini 3 on Vertex AIVertex AI gives developers access to Gemini 3—Google’s most advanced reasoning and coding model—plus 200+ foundation models including Claude, Llama, and Gemma. Build generative AI apps with Vertex AI Studio, customize with fine-tuning, and deploy to production with enterprise-grade MLOps. New customers get $300 in free credits.
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Easily Host LLMs and Web Apps on Cloud RunRun frontend and backend services, batch jobs, host LLMs, and queue processing workloads without the need to manage infrastructure. Cloud Run gives you on-demand GPU access for hosting LLMs and running real-time AI—with 5-second cold starts and automatic scale-to-zero so you only pay for actual usage. New customers get $300 in free credit to start.
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MolPrep
RDkit-based Molecule Optimization Tool (CLI) in python.
MolPrep is a powerful utility application designed to streamline the preparation and refinement of molecular geometries. With the help of RDKit, this tool enables users to load, clean, standardize, and optimize molecular structures effortlessly. Its robust design ensures scalability and efficiency, making it ideal for chemoinformatics workflows. -
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MAF
Bash Framework to combine many preprocessing and alignment tools
DNA and RNA nucleotide sequences are an ubiquitous element of all biological cells and are serving on one hand as a comprehensive library of capabilities for the cells and on the other as an impressive regulatory system to control cellular function. The presented multi-alignment framework (MAF) should give researchers a simple sequence alignment platform as a functional template, flexible enough to adjust all steps but also comprehensive enough to join many different tools and custom... -
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FAH-Web-Monitor
Web app to monitor Folding@Home
Une application WEB pour le monitoring des clients Folding@Home en sur-couche de HFM.net. Web app to monitor Folding@Home clients as a sub-layer to HFM.net. -
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding... -
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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HostDesigner
General purpose de novo molecular design software
Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library. ... -
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Toxmatch
Exploring chemical similarity
Toxmatch is a flexible and user-friendly open-source software application that encodes several chemical similarity indices to facilitate the grouping of chemicals into categories and read-across. The core functionalities include the ability to compare datasets based on various structural and descriptor-based similarity indices as well as the means to calculate pair wise similarity between compounds or aggregated similarity of a compound to a set. -
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ElemenTable - Periodic Table
Simple colored and interactive Periodic Table of Elements
ElemenTable is a colorful periodic table of elements application for Windows (requires .NET Framework v.4.5 or higher). It gives many important information, e.g. atomic mass or electronegativity, about all current chemical elements from Hydrogen [1] to Oganesson [118]. All elements are ordered in a colorful periodic table layout which can be changed in color to show either the element groups, the element states or the element types. -
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RElt
calculates overlap, kinetic integrals for numerical atomic orbitals.
...We prove that the integrand over the rectangular domain is continuous and does not have any slope singularities. For calculation of the integral over the rectangle any adaptive algorithm can be applied. The exemplary results were obtained by application of the adaptive Gauss quadrature. The implemented algorithm is described in my paper: "Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates", International Journal of Quantum Chemistry, Volume 108, Issue 2, Year 2008, Pages 249–256 http://onlinelibrary.wiley.com/doi/10.1002/qua.21485/full -
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RAtom
solves nonlinear Kohn-Sham equation for the neutral atom.
...The implemented algorithm is described in the following papers: 1. Z. Romanowski, "Adaptive solver of a Kohn-Sham equation for an atom", Modelling Simul. Mater. Sci. Eng. vol. 17, 045001 (2009) 2. Z. Romanowski, "Application of h-adaptive, high order finite element method to solve radial Schrödinger equation", Molecular Physics, vol. 107, pp. 1339-1348 (2009). Further questions: romz@wp.pl -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. -
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DNA patterns & application
A software for generating DNA patterns
The DNA pattern represents a new method of analysis for DNA sequences. In general it can easily detect relationships among species over the evolutionary landscape. Largely, in bioinformatics the DNA pattern method is unexplored and many discoveries can be made through it. One of the questions to which an answer was given is: How many types of promoters are out there regulating the genes ? It seems that there are 10 types of promoters. The project also contains 20,000 images (DNA... -
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Periodic Table of Elements
Periodic Table of Elements a quick reference tool
Periodic Table of Elements is a quick reference tool that allows you a quick glance to get general information about an element. The program is for educational purposes. -
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... * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular pipeline, called iMir, integrating multiple open source modules and resource in an automated workflow, devising different statistical approaches to analyze data rigorously. iMir comprises also a Graphical User Interface (GUI), so that the pipeline is particularly suited for biologist and early stage bioinformaticians and produces both graphics and text outputs. -
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OpenCFU
An application to count bacterial colonies and other circular objects
OpenCFU is a completely open source lightweight application designed to enumerate clustered circular objects such as bacterial colonies. It can handle digital pictures as well as live stream from a video device/webcam. OpenCFU is cross-platform, fast, reliable and allows the user to implement intuitive filters. Additional information is provided on the website: http://opencfu.sourceforge.net/ OpenCFU is published on PLoS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054072 -
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NanoCap
Carbon Fullerene and Capped Nanotube Generator
NanoCap is a generic application for the construction of low energy fullerene and capped nanotube structures. It provides an ideal tool to accompany the study of finite carbon molecules using computer simulation. The implementation involves a standalone application which includes a GUI and allows for dynamic visual inspection through 3D rendering. In addition, the NanoCap core libraries can be used in custom Python scripts that enabled the user to produce structures in bulk or to include the structure generation routines into pre-existing code. -
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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Quantum Chemistry Import Tool is a django application that parses the output file of quantum chemistry software as NWChem, Octopus, Gaussian, etc. The result can be saved in relational database.
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Chemistry Helper
A simple easy to use chemistry helper!
This application is intended to help students with the basics of chemistry. It can solve basic gas laws equations, and find the molar mass of a compound or element. These tasks allow students to cut the repetition out of basic chemistry. -
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SPiM2Eclipse
Eclipse plugin for Stochastic Pi Machine
Stochastic Pi Machine (SPiM), created by Microsoft, is a programming language for modeling biological processes. Two tools are available from Microsoft for simulation. A web application Visual SPiM, and a destkop application SPiM Player. Both simulation tools require to be run on a Windows platform. Fortunately Microsoft has also released a command line version for Linux and Mac OS based on OCAML however this version will only output a CSV file for the simulation results. SPiM2Eclipse provides a bridge for those running SPiM from the command-line by allowing simulations to be completed by a single click, displaying an embedded plot of the results. ... -
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HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
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Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.
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F@H League Web App is a simple ASP.Net Web application that allows you to create a League of Folding@Home Teams you are interested in and view a range of league tables, statistics and Graphs.
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QMGA is a Qt-based molecular graphics application for visualizing large ensembles of ellipsoids, spherocylinders or spheres. It is conceived for coarse-grained mesoscopic molecular simulation, but can be used for any kind of convex body systems.
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GOCART is a modular open-source application used to assemble biological sequences into Gene Ontology (GO) annotated contigs for Web GUI visualization based on their corresponding hierarchal GO structure, described by the Gene Ontology Consortium.
