Supplementary material to "SMAUG v1.0 – a user-friendly muon simulator for transmission tomography of geological objects in 3D"

2021 ◽  
Author(s):  
Alessandro Lechmann ◽  
David Mair ◽  
Akitaka Ariga ◽  
Tomoko Ariga ◽  
Antonio Ereditato ◽  
...  
Keyword(s):  
Transmission Tomography ◽  
Supplementary Material ◽  
User Friendly

scholarly journals PathScore: a web tool for identifying altered pathways in cancer data

2016 ◽  
Author(s):  
Stephen G. Gaffney ◽  
Jeffrey P. Townsend
Keyword(s):  
Web Application ◽  
Somatic Mutations ◽  
Supplementary Information ◽  
Web Tool ◽  
Cancer Data ◽  
Link Type ◽  
Novel Approach ◽  
Supplementary Material ◽  
User Friendly ◽  
Pathway Effect

ABSTRACTSummaryPathScore quantifies the level of enrichment of somatic mutations within curated pathways, applying a novel approach that identifies pathways enriched across patients. The application provides several user-friendly, interactive graphic interfaces for data exploration, including tools for comparing pathway effect sizes, significance, gene-set overlap and enrichment differences between projects.Availability and ImplementationWeb application available at pathscore.publichealth.yale.edu. Site implemented in Python and MySQL, with all major browsers supported. Source code available at github.com/sggaffney/pathscore with a GPLv3 [email protected] InformationAdditional documentation can be found at http://pathscore.publichealth.yale.edu/faq.

scholarly journals DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins

2021 ◽  
Author(s):  
Sarah Hall-Swan ◽  
Dinler A. Antunes ◽  
Didier Devaurs ◽  
Mauricio M. Rigo ◽  
Lydia E. Kavraki ◽  
...  
Keyword(s):  
Supplementary Information ◽  
Scoring Functions ◽  
Binding Modes ◽  
Computational Tool ◽  
Receptor Flexibility ◽  
Ensemble Docking ◽  
Main Protease ◽  
Docking Tool ◽  
Supplementary Material ◽  
User Friendly

AbstractMotivationRecent efforts to computationally identify inhibitors for SARS-CoV-2 proteins have largely ignored the issue of receptor flexibility. We have implemented a computational tool for ensemble docking with the SARS-CoV-2 proteins, including the main protease (Mpro), papain-like protease (PLpro) and RNA-dependent RNA polymerase (RdRp).ResultsEnsembles of other SARS-CoV-2 proteins are being prepared and made available through a user-friendly docking interface. Plausible binding modes between conformations of a selected ensemble and an uploaded ligand are generated by DINC, our parallelized meta-docking tool. Binding modes are scored with three scoring functions, and account for the flexibility of both the ligand and receptor. Additional details on our methods are provided in the supplementary material.Availabilitydinc-covid.kavrakilab.orgSupplementary informationDetails on methods for ensemble generation and docking are provided as supplementary data [email protected], [email protected]

scholarly journals RCGAToolbox: A real-coded genetic algorithm software for parameter estimation of kinetic models

2021 ◽  
Author(s):  
Kazuhiro Maeda ◽  
Fred C. Boogerd ◽  
Hiroyuki Kurata
Keyword(s):  
Parameter Estimation ◽  
User Interfaces ◽  
Kinetic Models ◽  
Biochemical Networks ◽  
Generation Gap ◽  
Supplementary Information ◽  
Real Coded Genetic Algorithm ◽  
Supplementary Material ◽  
Real Coded Genetic Algorithms ◽  
User Friendly

AbstractSummaryKinetic modeling is essential in understanding the dynamic behavior of biochemical networks, such as metabolic and signal transduction pathways. However, parameter estimation remains a major bottleneck in the development of kinetic models. We present RCGAToolbox, software for real-coded genetic algorithms (RCGAs), which accelerates the parameter estimation of kinetic models. RCGAToolbox provides two RCGAs: the unimodal normal distribution crossover with minimal generation gap (UNDX/MGG) and real-coded ensemble crossover star with just generation gap (REXstar/JGG), using the stochastic ranking method. The RCGAToolbox also provides user-friendly graphical user interfaces.Availability and implementationRCGAToolbox is available from https://github.com/kmaeda16/RCGAToolbox under GNU GPLv3, with application examples. The user guide is provided in the Supplementary Material. RCGAToolbox runs on MATLAB in Windows, Linux, and [email protected] informationSupplementary Material is available at Bioinformatics online.

scholarly journals ATLAS: Analysis Tools for Low-depth and Ancient Samples

2017 ◽  
Author(s):  
Vivian Link ◽  
Athanasios Kousathanas ◽  
Krishna Veeramah ◽  
Christian Sell ◽  
Amelie Scheu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ancient Dna ◽  
State Of The Art ◽  
Supplementary Information ◽  
Post Mortem ◽  
Supplementary Data ◽  
Supplementary Material ◽  
C Program ◽  
User Friendly ◽  
Proper Analysis

AbstractSummaryPost-mortem damage (PMD) obstructs the proper analysis of ancient DNA samples and can currently only be addressed by removing or down-weighting potentially damaged data. Here we present ATLAS, a suite of methods to accurately genotype and estimate genetic diversity from ancient samples, while accounting for PMD. It works directly from raw BAM files and enables the building of complete and customized pipelines for the analysis of ancient and other low-depth samples in a very user-friendly way. Based on simulations we show that, in the presence of PMD, a dedicated pipeline of ATLAS calls genotypes more accurately than the state-of-the-art pipeline of GATK combined with mapDamage 2.0.AvailabilityATLAS is an open-source C++ program freely available at https://bitbucket.org/phaentu/[email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals MyelinJ: an ImageJ macro for high throughput analysis of myelinating cultures

2019 ◽  
Vol 35 (21) ◽  
pp. 4528-4530 ◽  
Author(s):  
Michael J Whitehead ◽  
George A McCanney ◽  
Hugh J Willison ◽  
Susan C Barnett
Keyword(s):  
Statistical Analysis ◽  
High Throughput ◽  
Supplementary Information ◽  
Local Contrast ◽  
High Throughput Analysis ◽  
Throughput Analysis ◽  
Neurite Density ◽  
Supplementary Material ◽  
User Friendly

Abstract Summary MyelinJ is a free user friendly ImageJ macro for high throughput analysis of fluorescent micrographs such as 2D-myelinating cultures and statistical analysis using R. MyelinJ can analyse single images or complex experiments with multiple conditions, where the ggpubr package in R is automatically used for statistical analysis and the production of publication quality graphs. The main outputs are percentage (%) neurite density and % myelination. % neurite density is calculated using the normalize local contrast algorithm, followed by thresholding, to adjust for differences in intensity. For % myelination the myelin sheaths are selected using the Frangi vesselness algorithm, in conjunction with a grey scale morphology filter and the removal of cell bodies using a high intensity mask. MyelinJ uses a simple graphical user interface and user name system for reproducibility and sharing that will be useful to the wider scientific community that study 2D-myelination in vitro. Availability and implementation MyelinJ is freely available at https://github.com/BarnettLab/MyelinJ. For statistical analysis the freely available R and the ggpubr package are also required. MyelinJ has a user guide (Supplementary Material) and has been tested on both Windows (Windows 10) and Mac (High Sierra) operating systems. Supplementary information Supplementary data are available at Bioinformatics online.

Supplementary material to "BUMPER v1.0: A Bayesian User-friendly Model for Palaeo-Environmental Reconstruction"

2016 ◽  
Author(s):  
Philip B. Holden ◽  
H. John B. Birks ◽  
Stephen J. Brooks ◽  
Mark B. Bush ◽  
Grace M. Hwang ◽  
...  
Keyword(s):  
Environmental Reconstruction ◽  
Supplementary Material ◽  
User Friendly

scholarly journals SMAUG v1.0 – a user-friendly muon simulator for transmission tomography of geological objects in 3D

2021 ◽  
Author(s):  
Alessandro Lechmann ◽  
David Mair ◽  
Akitaka Ariga ◽  
Tomoko Ariga ◽  
Antonio Ereditato ◽  
...  
Keyword(s):  
Inverse Problem ◽  
Data Analysis ◽  
Particle Physics ◽  
Transmission Tomography ◽  
Geophysical Model ◽  
Muon Tomography ◽  
Abstract Knowledge ◽  
Accuracy And Precision ◽  
Basic Physics ◽  
User Friendly

Abstract. Knowledge about muon tomography has spread in recent years in the geoscientific community and several collaborations between geologists and physicists have been founded. As the data analysis is still mostly done by particle physicists, we address the need of the geoscientific community to participate in the data analysis, while not having to worry too much about the particle physics equations in the background. The result hereof is SMAUG, a toolbox consisting of several modules that cover the various aspects of data analysis in a muon tomographic experiment. In this study we show how a comprehensive geophysical model can be built from basic physics equations. The emerging uncertainties are dealt with by a probabilistic formulation of the inverse problem, which is finally solved by a Monte Carlo Markov Chain algorithm. Finally, we benchmark the SMAUG results against those of a recent study, which however, have been established with an approach that is not easily accessible to the geoscientific community. We show that they reach identical results with the same level of accuracy and precision.

scholarly journals AFCMHeatMap: A shiny web tool for heatmap generation of genetic expression datasets using R packages

2017 ◽  
Author(s):  
Mohammad Tarek ◽  
Ayman S Shafei ◽  
Mahmoud A Ali
Keyword(s):  
Expression Data ◽  
Rna Seq ◽  
Web Tool ◽  
Graphical Visualization ◽  
Supplementary Material ◽  
R Packages ◽  
Web App ◽  
Visualization Of Data ◽  
The Individual ◽  
User Friendly

Generating heatmaps of genetic datasets is a 2D graphical visualization of data where the individual expression values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction of genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a *.CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for interactive expression data visualization that can be easily deployed without any restrictions to any operating system used by any online user.

scholarly journals mirtronDB: a mirtron knowledge base

2018 ◽  
Author(s):  
Bruno Henrique Ribeiro Da Fonseca ◽  
Douglas Silva Domingues ◽  
Alexandre Rossi Paschoal
Keyword(s):  
Knowledge Base ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Knowledge Database ◽  
Group Type ◽  
Link Type ◽  
Supplementary Material ◽  
Access To Knowledge ◽  
User Friendly ◽  
Organism Group

AbstractMotivationMirtrons are originated from short introns with atypical cleavage from the miRNA canonical pathway by using the splicing mechanism. Several studies describe mirtrons in chordates, invertebrates and plants but in the current literature there is no repository that centralizes and organizes these public and available data. To fill this gap, we created the first knowledge database dedicated to mirtron, called mirtronDB, available at http://mirtrondb.cp.utfpr.edu.br/. MirtronDB has a total of 1,407 mirtron precursors and 2,426 mirtron mature sequences in 18 species.ResultsThrough a user-friendly interface, users can browse and search mirtrons by organism, organism group, type and name. MirtronDB is a specialized resource to explore mirtrons and their regulations, providing free, user-friendly access to knowledge on mirtron data.AvailabilityMirtronDB is available at http://mirtrondb.cp.utfpr.edu.br/[email protected] informationSupplementary data are available.

scholarly journals AFCMHeatMap: A shiny web tool for HeatMap generation of genetic expression datasets using R packages

2017 ◽  
Author(s):  
Mohammad Tarek ◽  
Ayman S Shafei ◽  
Mahmoud A Ali
Keyword(s):  
Graphical Representation ◽  
Rna Seq ◽  
Input File ◽  
Web Tool ◽  
Individual Values ◽  
Supplementary Material ◽  
R Packages ◽  
Web App ◽  
The Individual ◽  
User Friendly

Generating heatmaps of genes datasets have been known to be a graphical representation of data where the individual values contained in a matrix are represented as colors. Herein, we describe AFCMHeatMap a shiny web App that integrates quantitative interaction genomics data and results from microarrays or RNA-Seq to highlight expression levels of various genetic datasets with a .CSV input file. The application also facilitates downloading heatmaps as a supplementary material for user's publications. Written in R using Shiny framework, it is a user-friendly framework for integrative genetic analyses that can be easily deployed across various operating systems distributions.

Sign in / Sign up

Export Citation Format

Share Document