Search Results for "data modeling"
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Showing 28 open source projects for "data modeling"
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DataPrep
Python-based data preprocessing tool
DataPrep v0.2 is a Tkinter-based GUI application/tool designed to assist users in data preprocessing, multicollinearity removal, and feature selection for a wide range of applications in Cheminformatics, Bioinformatics, Data Analysis, Feature Selection, Molecular Modeling, Machine Learning, and Quantitative-structure-property relationship (QSPR) studies. It includes functionality to load, process, and save datasets with support for different preprocessing & multicollinearity removal strategies with customizable parameter setting options. -
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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This project moved to GitHub in 2021 and is available at: https://cbrinkrolf.github.io/VANESA/ This tool is a platform-independent software to create individual pathways and to examine biological networks of distributed, heterogeneous data sources, e.g. KEGG, BRENDA. VANESA also offers Petri net modeling of extended hybrid Petri nets which can be also simulated using the OpenModelica framework.
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DBSolveOptimum
The software for systems biology/pharmacology modeling
...It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques, like quantitative systems pharmacology, to problems arising in drug research and development. By this time, DBSolveOptimum has been successfully tested and applied for the development and analysis of both systems pharmacology and conventional PK/PD models of drugs. ... -
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We are developing data standards and software tools that implement these standards to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
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PBTK Optimizer
Application for optimization of parameters in PBTK models
...Other parameters can be determined through in-vitro experiments or through extrapolation using published equations. When it is impractical to use these methods to estimate a parameter, techniques can be used to optimize parameters so that model results best fit validation data. This tool was designed to optimize a user-specified list of parameters to a user-specified PBTK model. The user also controls validation data and optimization algorithms. In addition to optimized parameters, the tool outputs statistical information about the fit of the optimized model. -
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PANTHER project: software for modeling of protein sequence and function evolution, and tools for applying these data to the analysis of genome data, expression data and coding SNPs. Details available at http://www.pantherdb.org.
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Phanto_maJ
build three dimensional structure
PhantomaJ is a software which aims to help users designing complexe three dimensional structures and building phantom banks. This software, implemented as an ImageJ plug-in, has been designed to be intuitive. PhantomaJ is thus "ready to use" for most users, but advanced users can choose to modify specific parameters such as intersection mode, intensity decrease function or virtual real three dimension. In addition, adding a new "basic form" consiste for advanced users to write two short... -
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R-gregmisc is a set of extension package for the open-source statistical environment/language "R''. It includes functions for plotting (gplots), data manupulation (gdata), modeling (gmodels), and programming tools (gtools), creation and management of sub-processes (fork), determing sample sizes for -omics experiments (ssize), and a variety of other packages.
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BiomeNet
BAYESIAN INFERENCE OF METABOLIC DIVERGENCE AMONG MICROBIAL COMMUNITIES
...The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). -
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budden2014predictive
Scripts and supplementary data for budden2014predictive manuscript
Scripts and supplementary data for the manuscript "Predictive modeling of gene expression from transcriptional regulatory elements" -
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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The Cell System Markup Language (CSML) is an XML format for modeling, visualizing and simulating biopathways. CSML supports to represent several pathway types including metabolic, signaling, genetic regulatory pathways, and cell-cell interactions.
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ELECANS
Electronic Computational Cancer Systems Biology Simulation Studio
A computational model development and simulation environment for cancer systems biology. ELECANS is the state of the art in the multi agent simulation tools available for computational modeling of tumorigenesis in a variety of tissues. -
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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.
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imDEV
Tools for multivariate data visualization, exploration and analysis.
You may also like some newer work: http://createdatasol.com/ Project imDEV is an application of RExcel, which seamlessly integrates Excel and R for tasks focused on multivariate data visualization, exploration, and analysis. Interactive modules for dimensional reduction (imPCA), prediction (imPLS), feature selection, analysis of correlation (imCorrelations) and generation of networked structures (imGraph) provide an integrated environment for systems level analysis of multivariate data. -
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MIDA
Mitochondiral Infectious Damage Adaptation (MIDA) model of aging
...Output is generated in terms of data files and the graphical visualization of readout parameters is automatically performed using the Graphical Layout Engine (GLE; see: http://glx.sourceforge.net/). Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code. -
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The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
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Software developed under MATLAB R14 environment. It's aim is to make the modeling of bacterial inactivation system and adjust a simulator to obtain new data of the experiment or validate the one that has been obtained at the laboratory.
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The VRML97-Import-Script is a Python-Script, that extends the capabilities of Blender to import VRML97-Files. It supports Blender since version 2.42.
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ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
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4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
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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.
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Experimental Lindenmayer System generator, in 3D using OpenGL. Used for modeling the fractal growth processes of plants.
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Vertex-vertex sytems: a modelling system for dynamical discrete 2-manifolds. For more information see http://vertex-vertex.blogspot.com.
