scholarly journals BoardION: real-time monitoring of Oxford Nanopore sequencing instruments

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Aimeric Bruno ◽  
Jean-Marc Aury ◽  
Stefan Engelen
Keyword(s):  
Real Time ◽  
Web Application ◽  
Data Streaming ◽  
Access To Information ◽  
Library Preparation ◽  
Sequencing Data ◽  
Time Data ◽  
Interactive Interface ◽  
Oxford Nanopore

Abstract Background One of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of real-time sequencing. This gives access to information during the experiment and allows either to control the sequencing or to stop the sequencing once the results have been obtained. However, the ONT sequencing interface is not sufficient to explore the quality of sequencing data in depth and existing quality control tools do not take full advantage of real-time data streaming. Results Herein, we present BoardION, an interactive web application to analyze the efficiency of ONT sequencing runs. The interactive interface of BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the data generated during the experiment. It also enables the comparison of multiple flowcells to assess library preparation protocols or the quality of input samples. Conclusion BoardION is dedicated to people who manage ONT sequencing instruments and allows them to remotely and in real time monitor their experiments and compare multiple sequencing runs. Source code, a Docker image and a demo version are available at http://www.genoscope.cns.fr/boardion/.

scholarly journals BoardION: real-time monitoring of Oxford Nanopore Technologies devices

2020 ◽  
Author(s):  
Aimeric Bruno ◽  
Jean-Marc Aury ◽  
Stefan Engelen
Keyword(s):  
Real Time ◽  
Web Application ◽  
Data Streaming ◽  
Sequencing Data ◽  
Real Time Monitoring ◽  
Time Data ◽  
Oxford Nanopore ◽  
Sequencing Platforms ◽  
Oxford Nanopore Technologies

AbstractSummaryOne of the main advantages of the Oxford Nanopore Technology (ONT) is the possibility of sequencing in real time. However, the ONT sequencing interface is not sufficient to explore the quality of sequencing data in depth and existing tools do not take full advantage of real-time data streaming. We present BoardION, an interactive web application, dedicated to sequencing platforms, for real-time monitoring of all ONT sequencing devices (MinION, Mk1C, GridION and PromethION). BoardION allows users to easily explore sequencing metrics and optimize the quantity and the quality of the generated data during the experiment. It also enables the comparison of several flowcells to evaluate the library preparation protocols or the quality of input samples.AvailabilitySource code and a Docker image are available at http://www.genoscope.cns.fr/boardion/[email protected]

scholarly journals ASSESSMENT OF THE ACCURACY AND PRECISION OF MyRTKnet REAL-TIME SERVICES

2020 ◽  
Vol 83 (1) ◽  
pp. 93-103
Author(s):  
Muhammad Afiq Amirrudin ◽  
Ami Hassan Md Din ◽  
Nur Adilla Zulkifli ◽  
Muhammad Asyran Che Amat ◽  
Mohammad Hanif Hamden
Keyword(s):  
Real Time ◽  
Terrestrial Reference Frame ◽  
Data Streaming ◽  
Time Data ◽  
Real Time Kinematic ◽  
Accuracy And Precision ◽  
Streaming Service ◽  
Datum Transformation ◽  
Gnss Network

From a network of ninety-six (96) Continuously Operating Reference Stations (CORS), the Department of Survey and Mapping Malaysia (DSMM) has developed a reliable real-time data streaming service known as the Malaysia Real-Time Kinematic GNSS Network (MyRTKnet). MyRTKnet is now operating on Leica SpiderNet system that is configured to provide coordinate to users in Geocentric Datum of Malaysia 2000 (GDM2000). As the name implied, GDM2000 is a geocentric datum for Malaysia, developed based upon the International Terrestrial Reference Frame (ITRF) 2000 or ITRF2000. One could argue that the quality of coordinates provided by MyRTKnet are less optimal as the latest realisation of ITRF at present is ITRF2014. This study aims to investigate the accuracy and precision of the resultant coordinates from MyRTKnet real-time services through a comparison with the control-quality coordinates from a network of post-processed data at some independent points for positioning purpose. Meanwhile for mapping purpose, the coordinates from Network Real-Time Kinematic (NRTK) at selected Cadastral Reference Marks (CRM) points were compared with their known values. The results show that the observed points in ITRF2000 move approximately 37 cm away from the points in ITRF2014 due to the constant movement of Sundaland Block. Meanwhile for the assessment of NRTK technique, there is no significant displacement for coordinates in ITRF2000 but ITRF2014 with the values of 4.4 and 39.8 cm at KDOJ point, respectively. The discrepancy in ITRF2014 could be due to the improper datum transformation procedure. 

scholarly journals Target tracking accuracy and latency with different 4D ultrasound systems – a robotic phantom study

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Svenja Ipsen ◽  
Sven Böttger ◽  
Holger Schwegmann ◽  
Floris Ernst
Keyword(s):  
Target Tracking ◽  
Real Time ◽  
Template Matching ◽  
Image Data ◽  
Distinct Advantage ◽  
Reference Trajectory ◽  
Data Streaming ◽  
Tracking Accuracy ◽  
Time Data ◽  
4D Ultrasound

AbstractUltrasound (US) imaging, in contrast to other image guidance techniques, offers the distinct advantage of providing volumetric image data in real-time (4D) without using ionizing radiation. The goal of this study was to perform the first quantitative comparison of three different 4D US systems with fast matrix array probes and real-time data streaming regarding their target tracking accuracy and system latency. Sinusoidal motion of varying amplitudes and frequencies was used to simulate breathing motion with a robotic arm and a static US phantom. US volumes and robot positions were acquired online and stored for retrospective analysis. A template matching approach was used for target localization in the US data. Target motion measured in US was compared to the reference trajectory performed by the robot to determine localization accuracy and system latency. Using the robotic setup, all investigated 4D US systems could detect a moving target with sub-millimeter accuracy. However, especially high system latency increased tracking errors substantially and should be compensated with prediction algorithms for respiratory motion compensation.

Real-Time Data Streaming Architecture and Intelligent Workflow Management for Processing Massive Ecological Videos

2013 ◽  
Author(s):  
Gayathri Nadarajan ◽  
Cheng-Lin Yang ◽  
Yun-Heh Chen-Burger ◽  
Yu-Jung Cheng ◽  
Sun-In Lin ◽  
...  
Keyword(s):  
Real Time ◽  
Workflow Management ◽  
Data Streaming ◽  
Time Data ◽  
Real Time Data

scholarly journals Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Momchilo Vuyisich ◽  
Ayesha Arefin ◽  
Karen Davenport ◽  
Shihai Feng ◽  
Cheryl Gleasner ◽  
...  
Keyword(s):  
Genomic Dna ◽  
De Novo ◽  
Gc Content ◽  
Library Preparation ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Dna Amount ◽  
High Quality ◽  
Preparation Methods

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing andde novoassembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing andde novoassembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderiaspp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing andde novoassembly is not decreased when only 10 ng of input genomic DNA is used.

scholarly journals QoS Management for Embedded Databases in Multicore-Based Embedded Systems

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Woochul Kang ◽  
Jaeyong Chung
Keyword(s):  
Embedded Systems ◽  
Real Time ◽  
Control Method ◽  
Network Connectivity ◽  
Time Data ◽  
Quality Of Data ◽  
Multiple Control ◽  
Data Intensive ◽  
Real Time Data

With ubiquitous deployment of sensors and network connectivity, amounts of real-time data for embedded systems are increasing rapidly and database capability is required for many embedded systems for systematic management of real-time data. In such embedded systems, supporting the timeliness of tasks accessing databases is an important problem. However, recent multicore-based embedded architectures pose a significant challenge for such data-intensive real-time tasks since the response time of accessing data can be significantly affected by potential intercore interferences. In this paper, we propose a novel feedback control scheme that supports the timeliness of data-intensive tasks against unpredictable intercore interferences. In particular, we use multiple inputs/multiple outputs (MIMO) control method that exploits multiple control knobs, for example, CPU frequency and the Quality-of-Data (QoD) to handle highly unpredictable workloads in multicore systems. Experimental results, using actual implementation, show that the proposed approach achieves the target Quality-of-Service (QoS) goals, such as task timeliness and Quality-of-Data (QoD) while consuming less energy compared to baseline approaches.

scholarly journals On the Quality of Real-Time Altimeter Gridded Fields: Comparison with In Situ Data

2009 ◽  
Vol 26 (3) ◽  
pp. 556-569 ◽  
Author(s):  
Ananda Pascual ◽  
Christine Boone ◽  
Gilles Larnicol ◽  
Pierre-Yves Le Traon
Keyword(s):  
Real Time ◽  
Sea Level ◽  
Tide Gauge ◽  
Deep Ocean ◽  
Velocity Estimation ◽  
Time Data ◽  
In Situ Data ◽  
Delayed Time

Abstract The timeliness of satellite altimeter measurements has a significant effect on their value for operational oceanography. In this paper, an Observing System Experiment (OSE) approach is used to assess the quality of real-time altimeter products, a key issue for robust monitoring and forecasting of the ocean state. In addition, the effect of two improved geophysical corrections and the number of missions that are combined in the altimeter products are also analyzed. The improved tidal and atmospheric corrections have a significant effect in coastal areas (0–100 km from the shore), and a comparison with tide gauge observations shows a slightly better agreement with the gridded delayed-time sea level anomalies (SLAs) with two altimeters [Jason-1 and European Remote Sensing Satellite-2 (ERS-2)/Envisat] using the new geophysical corrections (mean square differences in percent of tide gauge variance of 35.3%) than those with four missions [Jason-1, ERS/Envisat, Ocean Topography Experiment (TOPEX)/Poseidoninterlaced, and Geosat Follow-On] but using the old corrections (36.7%). In the deep ocean, however, the correction improvements have little influence. The performance of fast delivery products versus delayed-time data is compared using independent in situ data (tide gauge and drifter data). It clearly highlights the degradation of real-time SLA maps versus the delayed-time SLA maps: four altimeters are needed in real time to get the similar quality performance as two altimeters in delayed time (sea level error misfit around 36%, and zonal and meridional velocity estimation errors of 27% and 33%, respectively). This study proves that the continuous improvement of geophysical corrections is very important, and that it is essential to stay above a minimum threshold of four available altimetric missions to capture the main space and time oceanic scales in fast delivery products.

PSXIV-24 Real-time, on-site whole genome sequencing with oxford nanopore technologies’ MinION

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 257-258
Author(s):  
Hanna Ostrovski ◽  
Rodrigo Pelicioni Savegnago ◽  
Wen Huang ◽  
Cedric Gondro
Keyword(s):  
Real Time ◽  
Ease Of Use ◽  
Whole Genome Sequence ◽  
Genomic Sequencing ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Base Calling ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

Abstract Most quantitative geneticists are traditionally trained for data analysis in genetic evaluation and genomic prediction, but rarely have extensive knowledge of molecular genetics or experience in experimental labs. Recent products, such as those launched by Oxford Nanopore Technologies (ONT), give those quantitative geneticists a comprehensible and hands-on toolkit to explore DNA sequencing. The ‘MinION’, a small DNA sequencer, is of interest for quantitative geneticists due to both the minimal learning curve and the non-proprietary USB connectivity. This device is small enough to be portable, allowing for potential real-time, on-farm sequencing. The objective of this project is to compare the whole genome sequence (WGS) output of the MinION sequencer to that of the Illumina HiSeq 4000. Blood was collected from a 6-month-old Akaushi calf born on a Michigan State University farm. DNA was extracted from the sample using the QIAamp DNA Blood Kit from Qiagen, and library DNA ligation preparation (SQK-LSK109) from ONT was used. After base-calling with guppy software (provided by ONT), the data were preprocessed and experimental runs with the MinION were compared using quality control. Finally, the data were aligned with guppy software, and was compared to the aligned WGS obtained with Illumina HiSeq. Quality results from each MinION indicate that, despite the low amount of sequence collected in each run (~225,303 reads per run), the quality of bases sequenced was high (Q≥7). The aligned data from the Illumina sequencer provided 40x coverage of the genome, with a total of 739,339,742 reads. Although the amount of data obtained with MinION is much smaller than that of Illumina HiSeq, the high quality of MinION’s data combined with its ease of use give an opportunity of genomic sequencing for users who are either inexperienced or do not have access to large genomic sequencing devices.

Traffic Controller for Handling Service Quality in Multimedia Network

2010 ◽  
pp. 96-112
Author(s):  
Manjunath Ramachandra ◽  
Vikas Jain
Keyword(s):  
Real Time ◽  
Long Range ◽  
Multimedia Data ◽  
Time Data ◽  
Self Similarity ◽  
Real Time Data ◽  
Data Transfers ◽  
Multimedia Network ◽  
Different Origin

The present day Internet traffic largely caters for the multimedia traffic throwing open new and unthinkable applications such as tele-surgery. The complexity of data transactions increases with a demand for in time and real time data transfers, demanding the limited resources of the network beyond their capabilities. It requires a prioritization of data transfers, controlled dumping of data over the network etc. To make the matter worse, the data from different origin combine together imparting long lasting detrimental features such as self similarity and long range dependency in to the traffic. The multimedia data fortunately is associated with redundancies that may be removed through efficient compression techniques. There exists a provision to control the compression or bitrates based on the availability of resources in the network. The traffic controller or shaper has to optimize the quality of the transferred multimedia data depending up on the state of the network. In this chapter, a novel traffic shaper is introduced considering the adverse properties of the network and counteract with the same.

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