Search Results for "data modeling"

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

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.

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.

...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.

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.

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...

...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).

Scripts and supplementary data for the manuscript "Predictive modeling of gene expression from transcriptional regulatory elements"

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...

...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.

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.

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.

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.

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.

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.

Experimental Lindenmayer System generator, in 3D using OpenGL. Used for modeling the fractal growth processes of plants.

Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.