Search results for "pipeline"
showing 10 items of 157 documents
Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq
2020
International audience; A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing. Multiple protocols have been described for several important RNA modifications, such as 5-methylcytosine (m5C), pseudouridine (ψ), 1-methyladenosine (m1A), and 2'-O-methylation (Nm). One commonly used method is the alkaline cleavage-based RiboMethSeq protocol, where positions of reads' 5'-ends are used to distinguish nucleotides protected by ribose methylation. This method was successfully applied to detect and quantify Nm residues in vari…
Numerical Study on the Heading Misalignment and Current Velocity Reduction of a Vessel-Shaped Offshore Fish Farm
2019
Recently, the concept of a vessel-shaped fish farm was proposed for open sea applications. The fish farm comprises a vessel-shaped floater, five fish cages, and a single-point mooring system. Such a system weathervanes, and this feature increases the spread area of fish waste. Still, the downstream cages may experience decreased exchange of water flow when the vessel heading is aligned with the current direction, and fish welfare may be jeopardized. To ameliorate the flow conditions, a dynamic positioning (DP) system may be required, and its power consumption should relate to the heading misalignment. This paper proposes an integrated method for predicting the heading misalignment between t…
Using UAV Based 3D Modelling to Provide Smart Monitoring of Road Pavement Conditions
2020
Road pavements need adequate maintenance to ensure that their conditions are kept in a good state throughout their lifespans. For this to be possible, authorities need efficient and effective databases in place, which have up to date and relevant road condition information. However, obtaining this information can be very difficult and costly and for smart city applications, it is vital. Currently, many authorities make maintenance decisions by assuming road conditions, which leads to poor maintenance plans and strategies. This study explores a pathway to obtain key information on a roadway utilizing drone imagery to replicate the roadway as a 3D model. The study validates this by using stru…
Semi-automated annotation of page-based documents within the Genre and Multimodality framework
2016
This paper describes ongoing work on a tool developed for annotating document images for their multimodal features and compiling this information into a corpus. The tool leverages open source computer vision and natural language processing libraries to describe the content and structure of multimodal documents and to generate multiple layers of XML annotation. The paper introduces the annotation schema, describes the document processing pipeline and concludes with a brief description of future work.
3D production pipeline in game development
2012
3D-tuotanto on merkittävä osa esimerkiksi peli- ja elokuvateollisuutta, jotka ovat itsessään suuria teollisuudenaloja. Näillä aloilla työprosesseja voidaan kuvata tuotantolinjastoina. 3D-tuotantolinjastot rakentuvat sillä työskentelevistä tekijöistä, näiden työnkuluista ja tässä työssä käytettävistä työkaluista. Tuotantolinjastoillaon tehostettu ja järkeistetty toimintaa. Tämän tutkielman tavoitteena on selvittää 3D-tuotantolinjojen merkitys pelikehitykselle ja tarkastella siihen kuuluvaa tuotantoprosessia. Asiaa tarkastellaan tässä tutkielmassa tekemällä katsaus alan kirjallisuuteen sekä kuvaamalla yksinkertainen malli tuotantolinjastoille. 3D production has grown to be major part of the d…
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…
A Digital Twin for Lift Planning With Offshore Heave Compensated Cranes
2020
Abstract This paper presents a state-of-the-art digital twin of a hydraulic actuated winch that is used for heave compensation in offshore applications. The digital twin is used as part of a larger simulation model that involves all necessary components to perform lift planning and, subsequently, determine the corresponding weather window. The winch simulation model is described and verified by means of full-scale measurements. In addition, a set of acceptance criteria are presented that should be used whenever verifying digital twins of heave compensating winches that are to be used for lift planning.
pBrain: A novel pipeline for Parkinson related brain structure segmentation
2020
[EN] Parkinson is a very prevalent neurodegenerative disease impacting the life of millions of people worldwide. Although its cause remains unknown, its functional and structural analysis is fundamental to advance in the search of a cure or symptomatic treatment. The automatic segmentation of deep brain structures related to Parkinson's disease could be beneficial for the follow up and treatment planning. Unfortunately, there is not broadly available segmentation software to automatically measure Parkinson related structures. In this paper, we present a novel pipeline to segment three deep brain structures related to Parkinson's disease (substantia nigra, subthalamic nucleus and red nucleus…
The Mediterranean Sea and the Gulf of Cadiz as a natural laboratory for paleotsunami research: Recent advancements
2021
International audience; After the 2004 Indian Ocean (IOT) and the 2011 Tohoku-oki tsunamis, new research in tsunami-related fields was strongly stimulated worldwide and also in the Mediterranean. This research growth yields substantial advancements in tsunami knowledge.Among these advancements is the “Paleotsunami” research that has marked particular progress on the reconstruction of the tsunami history of a region. As an integration of the historical documentation available in the Mediterranean and the Gulf of Cadiz areas, geological and geoarchaeological records provide the insights to define the occurrence, characteristics, and impact of tsunamis of the past. Here, we present the recent …