Search results for "Object-oriented programming"
showing 10 items of 282 documents
Principal components analysis: theory and application to gene expression data analysis
2018
Advances in computational power have enabled research to generate significant amounts of data related to complex biological problems. Consequently, applying appropriate data analysis techniques has become paramount to tackle this complexity. However, theoretical understanding of statistical methods is necessary to ensure that the correct method is used and that sound inferences are made based on the analysis. In this article, we elaborate on the theory behind principal components analysis (PCA), which has become a favoured multivariate statistical tool in the field of omics-data analysis. We discuss the necessary prerequisites and steps to produce statistically valid results and provide gui…
Robust Analysis of Time Series in Virome Metagenomics
2018
Metagenomics is a powerful tool for assessing the functional and taxonomic contents in biological samples as it makes feasible to study, simultaneously, the whole living community related to a host organism or medium: all the microbes, including virus, bacteria, archaea, fungi, and protists. New DNA and RNA sequencing technologies are dramatically decreasing the cost per sequenced base, so metagenomic sequencing is becoming more and more widespread in biomedical and environmental research. This is opening the possibility of complete longitudinal metagenomic studies, which could unravel the dynamics of microbial communities including intra-microbiome and host-microbiome interactions through …
High-Throughput Mapping of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
2017
Detection of RNA modifications in native RNAs is a tedious and laborious task, since the global level of these residues is low and most of the suitable physico-chemical methods require purification of the RNA of interest almost to homogeneity. To overcome these limitations, methods based on RT-driven primer extension have been developed and successfully used, sometimes in combination with a specific chemical treatment. Nowadays, some of these approaches have been coupled to high-throughput sequencing technologies, allowing the access to transcriptome-wide data. RNA 2'-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from bacteria, archaea, and eukarya.…
Visualizing Human Protein‐Protein Interactions and Subcellular Localizations on Cell Images Through CellMap
2020
Visualizing protein data remains a challenging and stimulating task. Useful and intuitive visualization tools may help advance biomolecular and medical research; unintuitive tools may bar important breakthroughs. This protocol describes two use cases for the CellMap (http://cellmap.protein.properties) web tool. The tool allows researchers to visualize human protein-protein interaction data constrained by protein subcellular localizations. In the simplest form, proteins are visualized on cell images that also show protein-protein interactions (PPIs) through lines (edges) connecting the proteins across the compartments. At a glance, this simultaneously highlights spatial constraints that prot…
Generating Executable Code from High-Level Social or Socio-Ecological Model Descriptions
2019
Agent-Based Modelling has been used for social simulation because of the several benefits it entails. Social models are often constructed by inter-disciplinary teams that include subject-matter experts with no programming skills. These experts are typically involved in the creation of the conceptual model, but not the verification or validation of the simulation model. The Overview, Design concepts, and Details (ODD) protocol has emerged as a way of presenting a model at a high level of abstraction and as an effort towards improving the reproducibility of Agent-Based Models (ABMs) but it is typically written after a model has been completed. This paper reverses the process and provides non-…
Sensorial discourse and corpus in the digital humanities era: The example of the wine language
2019
International audience; This article intends to define sensorial discourses, to discuss the way they should be analyzed by stressing the importance of corpora. Putting these thoughts into the context of the digital revolution, it will show how corpora should evolve in the digital humanities. The association of digital and sensorial discourses needs to be clarified and this article proposes a way to find new approaches to better analyze them.
Retrieving Monitoring and Accounting Information from Constrained Devices in Internet-of-Things Applications
2013
Part 6: Monitoring Mechanisms; International audience; Internet-of-Things (IoT) is envisioned to provide connectivity to a vast number of sensing or actuating devices with limited computational and communication capabilities. For the organizations that manage these constrained devices, the monitoring of each device’s operational status and performance level as well as the accounting of their resource usage are of great importance. However, monitoring and accounting support is lacking in today’s IoT platforms. Hence, this paper studies the applicability of the Constrained Application Protocol (CoAP), a lightweight transfer protocol under development by IETF, for efficiently retrieving monito…