Search results for "Workflow"
showing 10 items of 133 documents
Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite
2023
The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of each application (scripts, databases, and command line interface software). Implementation of the Serv…
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms
2020
The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomic…
Adalimumab efficacy in enteropathic spondyloarthritis: A 12-mo observational multidisciplinary study
2017
AIM To report adalimumab (Ada) efficacy on articular-gastrointestinal disease and health-related quality of life (HRQoL) in patients with enteropathic spondyloarthritis (ES). METHODS A cohort of 52 patients with ES was evaluated in the departments of gastroenterology and internal medicine. At baseline, all patients underwent assessment by an integrated gastro-rheumatologic evaluation of articular and gastrointestinal activity, as well patient reported outcomes (PROs) of the HRQoL questionnaires. After this integrated evaluation and following a specific working flowchart, the Ada anti-tumor necrosis factor (TNF)-inhibitor was assigned to a cohort of 30 patients and its clinical efficacy was …
Earth system data cubes unravel global multivariate dynamics
2020
Understanding Earth system dynamics in light of ongoing human intervention and dependency remains a major scientific challenge. The unprecedented availability of data streams describing different facets of the Earth now offers fundamentally new avenues to address this quest. However, several practical hurdles, especially the lack of data interoperability, limit the joint potential of these data streams. Today, many initiatives within and beyond the Earth system sciences are exploring new approaches to overcome these hurdles and meet the growing interdisciplinary need for data-intensive research; using data cubes is one promising avenue. Here, we introduce the concept of Earth system data cu…
Documenting carved stones by 3D modelling – Example of Mongolian deer stones
2018
Rock art studies are facing major technical challenges for extensive documentation. Nowadays, recording is essentially obtained from time-consuming tracing and rubbing, techniques that also require a high level of expertise. Recent advances in 3D modelling of natural objects and computational treatment of the modelled surfaces may provide an alternative, and reduce the current documentation bottleneck. The aim of this study is to examine the extent to which such treatments can be applied. The case study presented here concerns the famous deer stones erected by ancient Mongolian nomad populations. The 3D acquisition workflow is based on structure-from-motion, a versatile photogrammetric tech…
Deep learning to detect built cultural heritage from satellite imagery. - Spatial distribution and size of vernacular houses in Sumba, Indonesia -
2021
Abstract In Sumba Island – Indonesia, the implantation of vernacular houses, inside and outside traditional villages, is considered to be an efficient proxy for the on-going complex cultural transformations resulting from globalization. This study presents an easily reproducible workflow allowing buildings to be automatically detected from satellite imagery, demonstrating how modern computer vision methods based on deep learning can help in this task, which would be far too time-consuming when undertaken by hand. Eight deep learning architectures based on convolutional neural networks were compared in terms of ability to identify and locate precisely traditional houses from satellite images…
The effects of vegetation on indoor thermal comfort: the application of a multi-scale simulation methodology on a residential neighborhood renovation…
2017
Abstract Despite the acknowledged positive effects of vegetation at urban, neighborhood and building scales, there are still only limited comprehensive design tools for multi-scale evaluation of the microclimate and thermal benefits of plants and building-integrated vegetation (BIV) systems. The paper describes a case study in the city of Palermo (Italy) that applied simulation methodology to quantitatively assess the microclimate effects of different neighborhood and building retrofit scenarios where vegetation plays a main role. The simulation workflow moves from a micro-urban to a building scale assessment by linking the ENVI-met software to the building energy simulation program EnergyP…
Development of Applications for Interactive and Reproducible Research: a Case Study
2016
For a proper understanding of the organization and regulation of gene expression, the computational analysis is an essential component of the scientific workflow, and this is particularly true in the fields of biostatistics and bioinformatics. Interactivity and reproducibility are two highly relevant features to consider when adopting or designing a tool, and often they can not be provided simultaneously.In this work, we address the issue of developing a framework that can provide interactive analysis, in order to allow experimentalists to fully exploit advanced software tools, as well as reproducibility as an internal validation of the analysis steps, by providing the underlying code and d…
TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of Shewanella putrefaciens…
2019
Probiotic microorganisms are of great interest in clinical, livestock and aquaculture. Knowledge of the genomic basis of probiotic characteristics can be a useful tool to understand why some strains can be pathogenic while others are probiotic in the same species. An automatized workflow called TarSynFlow (Targeted Synteny Workflow) has been then developed to compare finished or draft bacterial genomes based on a set of proteins. When used to analyze the finished genome of the probiotic strain Pdp11 ofShewanella putrefaciensand genome drafts from seven known non-probiotic strains of the same species obtained in this work, 15 genes were found exclusive of Pdp11. Their presence was confirmed …
Protein Interaction Networks and Disease: Highlights of the 3rd Challenges in Computational Biology Meeting
2017
Cellular functions are managed by a complex network of protein interactions, the malfunction of which may derive in disease phenotypes. In spite of the incompleteness and noise present in our current protein interaction maps, computational biologists are making strenuous efforts to extract knowledge from these intricate networks and, through their integration with other types of biological data, expedite the development of novel and more effective treatments against human disorders. The 3rd Challenges in Computational Biology meeting revolved around the Protein Interaction Networks and Disease subject, bringing expert network biologists to the city of Mainz, Germany to debate the current st…