Search Results for "optimization" - Page 3

postgresqltuner is a Perl script designed to analyze PostgreSQL database configurations and provide tuning advice. It assists database administrators in optimizing performance by offering recommendations based on the current setup.​

ATLAS mPBPK is a MATLAb-based tool for modeling and Simulation of minimal Physiology Based Pharmacokinetic (mPBPK) models of small and large molecules. The tool enables the users to perform: i) PK data visualization, ii) simulation, iii) parameter optimization, and iv) local sensitivity analysis (SA) of mPBPK models in a simple and efficient manner.

ComplexHeatmap is an R/Bioconductor package by Zuguang Gu et al. designed to create highly flexible, complex, richly annotated heatmaps and related visualizations. It allows arranging multiple heatmaps, adding annotations, combining heatmaps, customizing colors, layouts, and integrating other plots. Often used in genomics/bioinformatics to show expression, methylation, etc., with sidebars, annotations, clustering, etc. Highly customizable layout: combining different heatmaps, arranging and...

MoCalc2012 is a simple, efficient Graphical User Interface for MOPAC, DFTB+, GAMESS(US), Firefly, NWChem, ORCA and PSI4.

Linear Program Solver (Solvexo) is an optimization package intended for solving linear programming problems. The main features of the Solvexo are: · Solvexo solver is based on the efficient implementation of the simplex method (one or two phases); · Solvexo provides not only an answer, but a detailed solution process as a sequence of simplex matrices, so you can use it in studying (teaching) linear programming

The goal of this project is to implement a graph layout / network visualization algorithm as a Java plugin for Cytoscape (http://cytoscape.org/), using a recently published relative entropy optimization based method, called Unified Data Representation (Kovács IA et al. Sci Rep. 2015). If you are using the plugin, please cite: Ágg B, Császár A, Szalay-Bekő M, Veres DV, Mizsei R, Ferdinandy P, Csermely P and Kovács IA (2019) The EntOptLayout Cytoscape plug-in for the efficient visualization of major protein complexes in protein-protein interaction and signalling networks, Bioinformatics 35(21):4490-4492 https://academic.oup.com/bioinformatics/article/35/21/4490/5475596 Our detailed Tutorial on the use of the plugin: https://suopte.com/entopt_2_1_tutorial_20200518.pdf A video about the version 2.1: http://suopte.com/entopt_2_1_tutorial_video.mp4 Don't hesitate to send any questions, comments or bug reports also to agg.bence {at} med.semmelweis-univ.hu.

This Java software includes algorithms of combinatorical optimization for the NP-hard offline ship lock scheduling problem. Solutions and performed computations can be displayed graphically. Besides, there is a framework for generating test instances and running these in parallel, as well as R/JGR code for statistical evaluation. Some tools for estimating the quality of calculated solutions will be further improved.

We introduce optPBN, a Matlab-based toolbox for the optimization of probabilistic Boolean networks (PBN) which operates under the framework of the BN/PBN toolbox from Shmulevich et al. optPBN offers an easy generation of probabilistic Boolean networks from Boolean rule-based modeling and allows for flexible measurement data integration from multiple experiments and a subsequent integrated optimization problem generation which then can be solved with different optimizers. ...

PROPER is a package for visual evaluation of ranking classifiers for biological big data mining studies in the mathematical language MATLAB. It is an efficient tool for optimization and comparison of the state-of-the-art ranking classifiers by generating over 20 different high quality two- and three-dimensional performance curves.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

PROPER is a package for visual evaluation of ranking classifiers for biological big data mining studies in the mathematical language MATLAB. It is an efficient tool for optimization and comparison of the state-of-the-art ranking classifiers by generating over 20 different high quality two- and three-dimensional performance curves.

...At the same time, our model can incorporate some user control by ranking of relative importance of the criteria. [...] decision makers only rank the relative importance of criteria, rather than specifying the degree of relativity. [...] [our model] does not require users with any optimization background."

...Inheriting the use of Hoeffding bound in VFDT algorithm for node-splitting check, it contains four optional strategies of functional tree leaf, which improve the classifying accuracy. In addition, a multi-objective incremental optimization mechanism investigates a balance among accuracy, mode size and learning speed...

Linear Program Solver (LiPS) is an optimization package oriented on solving linear, integer and goal programming problems. The main features of LiPS are: ● LiPS is based on the efficient implementation of the modified simplex method that solves large scale problems. ● LiPS provides not just an answer, but a detailed solution process as a sequence of simplex tables, so you can use it for studying/teaching linear programming

The FAKE GAME tool uses natural evolution to evolve Data Mining models. It incorporates several preprocessing, optimization and visualization methods aimed to streamline the Knowledge Discovery process. Knowledge Extraction from data is being automated!

ProteinShop is an interactive protein manipulation tool. Users apply their knowledge and intuition to quickly create a set of protein configurations that can be subjected to local or global optimization. More information at http://proteinshop.org

A library including the whole bunch of standard algorithms in graph optimization and drawing. On top of this, a GUI for manipulating and editing of graphs.

PAIDA is pure Python scientific analysis package and supports AIDA (Abstract Interfaces for Data Analysis). PAIDA can create/plot histograms and functions etc. The parameter optimization and its error evaluation are also supported. Can use with Jython!

Vistools is a set of tools to easily visualize some scientific data, without need to learn difficult API, so you can see your 3d results very quickly. Also some sci tools for which we made it, including vector field tracing and simple optimization.

QRay is an interactive 3D modelling system in Java. It's built-in real-time raytracing engine implements the Quadric-CSG representation model and the Seed-Fill optimization method, which empower QRay to provide cool WYSIWYG 3D modelling functionalities.

pySPACE is a modular software for processing of large data streams that has been specifically designed to enable distributed execution and empirical evaluation of signal processing chains. Various signal processing algorithms (so called nodes) are available within the software, from finite impulse response filters over data-dependent spatial filters (e.g. CSP, xDAWN) to established classifiers (e.g. SVM, LDA). pySPACE incorporates the concept of node and node chains of the MDP framework. Due...