scholarly journals Practical aspects of implementing the IRIDA system as a solution for One Health bioinformatics analyses

2021 ◽  
Vol 4 ◽  
Author(s):  
Jeevan Karloss Antony-Samy ◽  
Georgios Marselis ◽  
Eve Fiskebeck ◽  
Taran Skjerdal ◽  
Camilla Sekse ◽  
...  
Keyword(s):  
User Interface ◽  
One Health ◽  
Virtual Machines ◽  
Web Server ◽  
Data Access ◽  
Dynamic Scaling ◽  
Bioinformatics Analyses ◽  
Data Access Control ◽  
Visualization Tools ◽  
Set Up

Managing sequence data, associated metadata, bioinformatics analyses and results can be challenging. In a One Health context, the challenge is even larger as there are many actors involved, many diverse types of results need to be produced, and the ensuing process data, such as software versions and options have to be tracked for auditing purposes. In addition, results must often be produced rapidly to be actionable, and non-bioinformaticians should be able to perform the the analyses. Therefore, a graphical user interface (preferably web system) with pipelines and visualization tools are needed to do these analyses. The Public Health Agency of Canada has together with other actors developed the web based system IRIDA (https://www.irida.ca) which uses Galaxy for analyses. IRIDA comes with a set of pipelines, visualization tools and a project based data management system that allows for fine grained data access control, which satisfies many of the requirements that a One Health bioinformatics platform dictates. However, as is often the case with a system meant to satisfy high demands, the platform is not trivial to set up and adapt for local use. In our setup, we are using two web servers, two database servers and one file server. The IRIDA web server provides the user interface. The Galaxy web server receives commands from IRIDA, executes the commands and returns results. Each web server has a database that keeps their respective metadata: user information, file locations and results. The actual files are stored on the fileserver. This spoke-and-wheel infrastructure was implemented to ensure minimum disruption of service if a component should go down. To get the necessary compute resources for this system, we are contracting with the Norwegian Research and Education Cloud (NREC), which offers Infrastructure as a Service (IaaS) services for Norwegian institutions and universities. NREC utilizes template VM images which can be instantiated according to need. The automated configuration and orchestration of images ensure that we can have dynamic access to resources according to need. This dynamic scaling is accomplished through collaboration with Elixir Norway. They have implemented the Pulse software which can check usage and instantiate and take down virtual machines as needed. At the Institute, we have spent close to two years on exploring and setting up this system. We have learned that it is important to not underestimate the amount compute resources needed to get a solid setup. However, having enough compute is irrelevant without knowledgeable staff. IRIDA comes with many features, which require considerable prior knowledge to adapt and set up in a local infrastructure. This includes knowledge on webservers, database systems, linux administration and Galaxy systems administration. The complexity dictates that these systems need to be set up and managed by in-house IT trained staff that will be able to tend the system along the way. It is also very important to maintain interactions with the users of the system, to ensure that the setup produces results that are useful to the users. To accomplish this, bioinformaticians are needed to develop pipelines and visualizations that give results that will on their own be easy for users to interpret in a biologically correct manner. Last but not least - such systems require a significant investment from the institution, thus it is important to showcase the benefits that the system will provide.

scholarly journals A Lightweight Blockchain-Based IoT Identity Management Approach

2021 ◽  
Vol 13 (2) ◽  
pp. 24
Author(s):  
Mohammed Amine Bouras ◽  
Qinghua Lu ◽  
Sahraoui Dhelim ◽  
Huansheng Ning
Keyword(s):  
Identity Management ◽  
Single Point ◽  
Data Access ◽  
Emerging Technology ◽  
Management Approach ◽  
Proof Of Concept ◽  
Data Access Control ◽  
And Storage ◽  
Privacy Issues ◽  
Centralized System

Identity management is a fundamental feature of Internet of Things (IoT) ecosystem, particularly for IoT data access control. However, most of the actual works adopt centralized approaches, which could lead to a single point of failure and privacy issues that are tied to the use of a trusted third parties. A consortium blockchain is an emerging technology that provides a neutral and trustable computation and storage platform that is suitable for building identity management solutions for IoT. This paper proposes a lightweight architecture and the associated protocols for consortium blockchain-based identity management to address privacy, security, and scalability issues in a centralized system for IoT. Besides, we implement a proof-of-concept prototype and evaluate our approach. We evaluate our work by measuring the latency and throughput of the transactions while using different query actions and payload sizes, and we compared it to other similar works. The results show that the approach is suitable for business adoption.

scholarly journals The impact of translation modality on user experience: an eye-tracking study of the Microsoft Word user interface

2021 ◽  
Author(s):  
Ana Guerberof Arenas ◽  
Joss Moorkens ◽  
Sharon O’Brien
Keyword(s):  
User Interface ◽  
Eye Tracking ◽  
Cognitive Load ◽  
Task Completion ◽  
Eye Tracker ◽  
Software Products ◽  
Microsoft Word ◽  
Set Up ◽  
The Impact ◽  
The Given

AbstractThis paper presents results of the effect of different translation modalities on users when working with the Microsoft Word user interface. An experimental study was set up with 84 Japanese, German, Spanish, and English native speakers working with Microsoft Word in three modalities: the published translated version, a machine translated (MT) version (with unedited MT strings incorporated into the MS Word interface) and the published English version. An eye-tracker measured the cognitive load and usability according to the ISO/TR 16982 guidelines: i.e., effectiveness, efficiency, and satisfaction followed by retrospective think-aloud protocol. The results show that the users’ effectiveness (number of tasks completed) does not significantly differ due to the translation modality. However, their efficiency (time for task completion) and self-reported satisfaction are significantly higher when working with the released product as opposed to the unedited MT version, especially when participants are less experienced. The eye-tracking results show that users experience a higher cognitive load when working with MT and with the human-translated versions as opposed to the English original. The results suggest that language and translation modality play a significant role in the usability of software products whether users complete the given tasks or not and even if they are unaware that MT was used to translate the interface.

scholarly journals European Union One Health Country Visits as Driver to Combat on Antimicrobial Resistance

2020 ◽  
Vol 41 (S1) ◽  
pp. s222-s222
Author(s):  
Pita Spruijt ◽  
Paul Bergervoet ◽  
Robbin Westerhof ◽  
Merel Langelaar ◽  
Marie-Cécile Ploy
Keyword(s):  
European Union ◽  
Antimicrobial Resistance ◽  
Peer Review ◽  
Infection Prevention ◽  
One Health ◽  
Competent Authority ◽  
Political Agenda ◽  
The European Union ◽  
Review System ◽  
Set Up

Background: In 2016, the European Union adopted unanimously Council Conclusions on the next steps to combat antimicrobial resistance under a One Health approach. To implement some of the provisions laid down in the Council Conclusions, a European Joint Action on Antimicrobial Resistance (AMR) and Healthcare-Associated Infections (HCAI) or EU-JAMRAI was set up, gathering 44 partners. Methods: As part of EU-JAMRAI, 13 participating European countries set up a country-to-country peer review system to evaluate each other’s national action plans (NAPs). This review system entailed a self-assessment, strengths–weaknesses–opportunities–threats (SWOT) analysis, and country visits. All steps were executed with representatives from both the human and the veterinary domains (One Health approach). Special attention was given to supervision and the way supervision can enhance the implementation of guidelines on AMR, both at the policy level and within healthcare institutions. Results: Despite differences in the stage of developing and implementing NAPs, all 13 countries are working on NAPs. In this process, country visits function as a moment to exchange best practices and to provide an outsider’s point of view. At the end of 2019, 13 country-to-country visits had taken place, resulting in tailor-made recommendations for each country. These recommendations were shared with the competent authority. An example is a country that used the recommendation to improve infection prevention as an immediate reason to get the topic on the agenda of the Ministry of Health. During the country visits, intersectoral participation was perceived as desirable, but in some cases it was challenging to arrange. For some highly relevant topics, it has been recognized that discussion should take place on a European level. Examples of such topics include supervision, infection prevention guidelines, funding, surveillance, and regular audits of antibiotic prescriptions for physicians including feedback loops. Conclusions: Peer review is a cooperative and friendly working method compared to common audits. The country visits function as an agenda setting tool to get or to keep AMR on the political agenda and presenting the most relevant topic(s) to address for each country.Funding: NoneDisclosures: None

STM3: a chemistry visualization platform

2005 ◽  
Vol 220 (5/6) ◽  
Author(s):  
Mario Valle
Keyword(s):  
User Interface ◽  
New Technologies ◽  
Software Platform ◽  
Visualization Tools ◽  
Visualization Techniques

AbstractTo support CSCS research users we built STM3, a software platform on which advanced chemistry visualization techniques can be integrated. Its main goal is not to replace existing tools, but to provide functionalities not covered by them. STM3’s unusual characteristic among chemistry visualization tools is its ability to combine chemistry and general visualization techniques in the same view. STM3 is built on top of a proven visualization environment (AVS/Express) that lets CSCS’s visualization staff concentrate its efforts on developing new technologies rather than investing time on graphical and user interface implementation issues.

Virtual Machines Scheduling Algorithm Based on Multi-Objective Optimization in Cloud Computing

2014 ◽  
Vol 1046 ◽  
pp. 508-511
Author(s):  
Jian Rong Zhu ◽  
Yi Zhuang ◽  
Jing Li ◽  
Wei Zhu
Keyword(s):  
Cloud Computing ◽  
Energy Consumption ◽  
Virtual Machine ◽  
Virtual Machines ◽  
Scheduling Algorithm ◽  
Machine Scheduling ◽  
Multi Objective Optimization ◽  
Multi Objective ◽  
Virtual Machine Scheduling ◽  
Set Up

How to reduce energy consumption while improving utility of datacenter is one of the key technologies in the cloud computing environment. In this paper, we use energy consumption and utility of data center as objective functions to set up a virtual machine scheduling model based on multi-objective optimization VMSA-MOP, and design a virtual machine scheduling algorithm based on NSGA-2 to solve the model. Experimental results show that compared with other virtual machine scheduling algorithms, our algorithm can obtain relatively optimal scheduling results.

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