Search results for "TOOLBOX"
showing 10 items of 40 documents
A Global Sensitivity Analysis Toolbox to Quantify Drivers of Vegetation Radiative Transfer Models
2017
Abstract Global sensitivity analysis (GSA) enables to gain insight into the functioning of radiative transfer models (RTMs) by identifying the driving input variables of RTM spectral outputs such as reflectance, fluorescence, or radiance. This contribution introduces automated radiative transfer models operator's (ARTMO’s) new GSA toolbox. With the GSA toolbox the majority of ARTMO’s available RTMs can be decomposed into its driving variables. For a selected RTM output, a GSA identifies the most influential and noninfluential input variables according to Sobol' first-order and total-order indices. The toolbox can process RTM spectral outputs for any kind of optical sensor setting within the…
EFMviz
2020
Elementary Flux Modes (EFMs) are a tool for constraint-based modeling and metabolic network analysis. However, systematic and automated visualization of EFMs, capable of integrating various data types is still a challenge. In this study, we developed an extension for the widely adopted COBRA Toolbox, EFMviz, for analysis and graphical visualization of EFMs as networks of reactions, metabolites and genes. The analysis workflow offers a platform for EFM visualization to improve EFM interpretability by connecting COBRA toolbox with the network analysis and visualization software Cytoscape. The biological applicability of EFMviz is demonstrated in two use cases on medium (Escherichia coli, iAF1…
Expanding the toolbox for Synechocystis sp. PCC 6803 : validation of replicative vectors and characterization of a novel set of promoters
2018
Cyanobacteria are promising ‘low-cost’ cell factories since they have minimal nutritional requirements, high metabolic plasticity and can use sunlight and CO2 as energy and carbon sources. The unicellular Synechocystis sp. PCC 6803, already considered the ‘green’ Escherichia coli, is the best studied cyanobacterium but to be used as an efficient and robust photoautotrophic chassis it requires a customized and well-characterized toolbox. In this context, we evaluated the possibility of using three self-replicative vectors from the Standard European Vector Architecture (SEVA) repository to transform Synechocystis. Our results demonstrated that the presence of the plasmid does not lead to an e…
Resilience Patterns
2015
Resilience, or the capacity to be able to develop oneself successfully despite adverse circumstances, has become a concept of interest in recent years. There is a clear relationship between resilience, psychological well-being, and coping strategies. This study looked at 890 subjects with a mean age of 46.77 ( SD = 20.86) years, ranging from 18 and 95 years old. The participants were 40.6% men and 59.4% women. Using this sample, three clusters were developed by MATLAB R2010a and the Self-Organizing Maps toolbox. Two of these had high resilience, and the other one had low resilience; the psychological well-being variables and coping strategies were taken into account. Thereafter, multivaria…
Poor estimates of motor variability are associated with longer grooved pegboard times for middle-aged and older adults
2018
Goal-directed movements that involve greater motor variability are performed with an increased risk that the intended goal will not be achieved. The ability to estimate motor variability during such actions varies across individuals and influences how people decide to move about their environment. The purpose of our study was to identify the decision-making strategies used by middle-aged and older adults when performing two goal-directed motor tasks and to determine if these strategies were associated with the time to complete the grooved pegboard test. Twenty-one middle-aged (48 ± 6 yr; range 40–59 yr, 15 women) and 20 older adults (73 ± 4 yr; range 65–79 yr, 8 women) performed two target…
The Brain Electrophysiological recording & STimulation (BEST) toolbox
2021
Abstract Non-invasive brain stimulation (NIBS) experiments involve many recurring procedures that are not sufficiently standardized in the community. Given the diversity in experimental design and experience of the investigators, automated but yet flexible data collection and analysis tools are needed to increase objectivity, reliability, and reproducibility of NIBS experiments. The B rain E lectrophysiological recording and ST imulation (BEST) Toolbox is a MATLAB-based, open-source software with graphical user interface that allows users to design, run, and share freely configurable multi-protocol, multi-session NIBS studies, including transcranial magnetic, electric, and ultrasound stimul…
tbg - a new file format for genomic data
2021
AbstractMotivationThe question of determining whether a Single-Nucleotide Polymorphism (SNP) or a variant in general leads to a change in the amino acid sequence of a protein coding gene is often a laborious and time-consuming challenge. Here, we introduce the tbg file format for storing genomic data and tbg-tools, a user-friendly toolbox for the faster analysis of SNPs. The file format stores information for each nucleotide in each gene, allowing to predict which change in the amino acid sequence will be caused by a variant in the nucleotide sequence. Our new tool therefore has the potential to make biological sense of the unprecedented amount of genome-wide genetic variation that research…
Exploring Frequency-Dependent Brain Networks from Ongoing EEG Using Spatial ICA During Music Listening
2020
Recently, exploring brain activity based on functional networks during naturalistic stimuli especially music and video represents an attractive challenge because of the low signal-to-noise ratio in collected brain data. Although most efforts focusing on exploring the listening brain have been made through functional magnetic resonance imaging (fMRI), sensor-level electro- or magnetoencephalography (EEG/MEG) technique, little is known about how neural rhythms are involved in the brain network activity under naturalistic stimuli. This study exploited cortical oscillations through analysis of ongoing EEG and musical feature during freely listening to music. We used a data-driven method that co…
geomIO: An Open‐Source MATLAB Toolbox to Create the Initial Configuration of 2‐D/3‐D Thermo‐Mechanical Simulations From 2‐D Vector Drawings
2019
Creating the initial geometry and temperature configuration of 3D numerical simulations is a challenging task. Professional tools are expensive. They often have a steep learning curve and do mostly not interface with the numerical simulation software used by the geodynamics and tectonics academic community. There, we developed geomIO (geometry Input/Output), a MATLAB toolbox to create the initial configuration of geological models regarding model geometry and temperature structure. geomIO allows users to create a geo-referenced 3D volume by drawing multiple 2D cross-sections in a standard vector graphics editor. The volume is then used to assign material properties and set up initial temper…
Predictions concerning the use of health care services in Europe by migrants/refugees and the Mig-HealthCare Roadmap & Toolbox
2019
Abstract Based on the multiple levels of research conducted within the project the consortium developed a roadmap & toolbox which includes the following categories: Continuity of information, Language Culture & Communication, Mental Health, Vaccinations, Maternal/child health, Health promotion, Oral health/Dental Care and NCDs while the Toolbox contains tools on these categories in different languages. The roadmap & toolbox is accessible through the project website. In addition, different scenarios, giving a comprehensive picture of the foreseen situation and the evidence-based policies and actions needed to maximize the effective delivery and sensitivity in the service of care …