Augmented Reality-Systeme zur Unterstützung der Workflow-Ausführung – Entwicklung und praktische Anwendung einer Taxonomie

ZusammenfassungDie Ausführung von Workflows ist in vielen Anwendungsfeldern zunehmend mit einer Verarbeitung von Kontextinformationen verbunden. Dies ermöglicht es, den Nutzern die richtige Information zur richtigen Zeit zur Verfügung zu stellen, um die Workflow-Ausführung optimal zu unterstützen. Ein aktueller Ansatz, um eine kontextsensitive Unterstützung zu realisieren sind Augmented Reality-Systeme. Diese verarbeiten Kontextinformationen und liefern notwendige und hilfreiche Workflow-Informationen immersiv und intuitiv, um den Nutzer zu unterstützen und zu entlasten. Da sich die technischen Implementierungen in diesem Feld sehr unterschiedlich ausgestalten, wird in diesem Beitrag eine Taxonomie entwickelt, die es ermöglicht, Augmented Reality-Systeme einheitlich zu systematisieren. Mit dem resultierenden einheitlichen Vokabular bietet die Taxonomie eine praktisch nutzbare Grundlage, um state-of-the-art Augmented Reality-Systeme zu klassifizieren, Trends und Forschungslücken in der Literatur zu identifizieren sowie die Entwicklung neuer Augmented Reality-Systeme methodisch zu unterstützen. Für die Entwicklung der Taxonomie wurden insgesamt 142 Augmented Reality-Systeme analysiert, mit speziellem Hinblick auf die bereitgestellte Workflow-Unterstützung. Die wahrgenommene Nützlichkeit der Taxonomie wurde durch eine Befragung von Augmented Reality-System und Workflow-Management-Experten evaluiert. Zudem werden zwei neuartige Augmented Reality-Systeme, die innovative Ansätze für die Unterstützung der Workflow-Ausführung darstellen, als praktische Beispiele der Anwendung der Taxonomie vorgestellt.

ALiS: Entwicklung einer Designtheorie für Augmented Living Spaces zur erweiterten Autonomie älterer und kognitiv eingeschränkter Menschen

ZusammenfassungDer Alltag älterer und kognitiv eingeschränkter Menschen kann mithilfe von informationstechnologischen Lösungen erheblich unterstützt werden. In diesem Kontext ist, wie unterschiedliche Ansätze bereits zeigen, der Einsatz von Augmented Reality für viele Einsatzszenarien eine vielversprechende Lösung. Jedoch stellen die üblicherweise genutzten Head-Mounted-Displays eine technische Hürde dar und können nicht ausnahmslos von allen Personen getragen werden. Als alternativen Lösungsansatz entwickelt der vorliegende Beitrag einen Augmented Living Space (ALiS). Dieser nutzt anstatt Headsets oder anderen tragbaren Geräten Spatial Augmented Reality, welche bspw. durch Beamer und Lautsprecher implementiert wird. Damit können individuelle, bedürfnisorientierte Funktionen ergonomisch und dennoch immersiv bereitgestellt werden. Hierdurch sollen betroffene Menschen befähigt werden, länger autonom leben zu können, ohne dabei auf tragbare Technik angewiesen zu sein. Ein ALiS gewährt dabei insbesondere eine nutzerzentrierte Unterstützung in den Bereichen der Wahrnehmung, Mobilität, Organisation sowie Medizin und ermöglicht die Herausforderungen des Alltags leichter zu bewältigen. Spatial Augmented Reality ist aktuell ein nur wenig erforschter Ansatz und wird vornehmlich in der Produktion eingesetzt. Daher werden in diesem Beitrag Designanforderungen, Designprinzipien und Design-Features einer Designtheorie formuliert, anhand derer zukünftig ein ALiS für ältere und kognitiv eingeschränkte Menschen mithilfe von Spatial Augmented Reality zielführend gestaltet und eingesetzt werden kann. Zur Definition der nutzerspezifischen und technischen Anforderungen wurde eine zweistufige strukturierte Literaturanalyse sowie eine moderierte Fokusgruppe mit Expert*innen und Anwender*innen durchgeführt. Die entwickelte Designtheorie besteht aus 3 Designanforderungen, 8 Designprinzipien sowie 13 Design-Features und bildet die Grundlage für die Entwicklung eines ALiS-Prototypen. Die wahrgenommene Nützlichkeit der Designtheorie für die Entwicklung eines ALiS wurde durch eine Befragung von Augmented Reality- und Workflow-Management-Experten positiv evaluiert.

nf-rnaSeqCount: A Nextflow pipeline for obtaining raw read counts from RNA-seq data

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through ``multi-omics'' data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for differential gene expression analyses. The pipeline provides a quick and efficient way to obtain a matrix of read counts that can be used black with tools such as DESeq2 and edgeR for differential expression analysis. Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research.

Online patológiai vizsgálatkérő felület létrehozása a Semmelweis Egyetemen

Összefoglaló. Bevezetés: Az I. Patológiai és Kísérleti Rákkutató Intézet – a Semmelweis Egyetemen belüli diagnosztikai szolgáltatásnyújtás mellett – kiterjedt külső partneri hálózattal (vizsgálatmegrendelővel) bír. Az Intézet a napi működése során párhuzamosan használja az egyetem központi informatikai rendszerét, valamint belső, folyamattámogató alkalmazását (workflow management). A külsős partnerek hozzáférése vizsgálatfeladásra az egyetemi központi informatikai rendszerhez nincs biztosítva. A vizsgálatok rendelése papíralapú, a minta érkeztetésekor a klinikai adatok rögzítése manuális, kifejezetten humánerőforrás-igényes. Célkitűzés: Célunk volt a patológiai minták regisztrációjának egyszerűsítése és felgyorsítása, az adminisztratív folyamatok hatékonyságának javítása. Módszer: A kitűzött célt a minőségfejlesztésből ismert Plan-Do-Check-Act (Tervezés-Cselekvés-Ellenőrzés-Beavatkozás) ciklus módszereit alkalmazva kívántuk elérni, online, a mintavétel helyén elérhető, a meglévő belső folyamattámogató alkalmazáshoz kapcsolódó, szakterület-specifikus vizsgálatkérő felület kifejlesztésével. Eredmények: A vizsgálati minták regisztrációjának átlagos ideje 65%-kal csökkent az online vizsgálatkérő rendszerhez csatlakozott klinikai partnerek körében. Megbeszélés: Az elmúlt években tapasztalható volt, hogy kisebb, nem hatékonyan működtethető patológiai osztályok megszűntek, részben vagy egészben beolvadtak nagyobb diagnosztikai egységekbe. A humánerőforrás-problémák (elöregedő szakma a patológia) a fenti folyamatot minden bizonnyal tovább erősítik. Várható, hogy a nagyobb patológiai osztályokon a következő években a mintaszám tovább növekszik, a vizsgálatkérések egyre nagyobb hányada érkezik majd intézményen kívülről. Következtetés: A patológiai informatika fejlesztésekor figyelembe kell venni, hogy szükséges már a mintavétel helyén biztosítani az informatikai támogatást a minta nyomon követéséhez, nem elégséges csak a laboron belüli folyamatok kiszolgálása. Orv Hetil. 2021; 162(49): 1962–1967. Summary. Introduction: The 1st Department of Pathology and Experimental Cancer Research, Semmelweis University (Budapest, Hungary) has a broad network of clinical partners, many of which are non-university hospitals. A separate hospital information system and a local laboratory workflow management system is used at the Department. University clinics use the hospital information system for electronic requesting of tests. Non-university partners have no access to the systems, requesting tests is paper-based, registration of the requests at the pathology lab is manual and laborious. Objective: Our main objective was to improve the efficiency of the sample registration step of the pathology workflow. Method: Applying the Plan-Do-Check-Act procedure, a quality improvement project has been carried out and an online, subspecialty-based requesting application tool, interfaced with the current laboratory information system, was developed. Results: The average sample registration time improved with 65% among the early user partners. Discussion: The past years have shown smaller, inefficient pathology labs decreasing in number and integrated into larger regional diagnostic centers. Both issues of efficiency and quality assurance and problems rooted in human resources are drivers of further centralisation. The numbers of test requests and samples from non in-house partners are expected to be increased in the pathology labs in the future. Conclusion: Efficient and safe sample tracking has to start at the site of sample acquisition. State of the art laboratory information systems should support this expansion of competence. Orv Hetil. 2021; 162(49): 1962–1967.

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 40000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year.

Comprehensive Analysis of Large-Scale Transcriptomes from Multiple Cancer Types

Various abnormalities of transcriptional regulation revealed by RNA sequencing (RNA-seq) have been reported in cancers. However, strategies to integrate multi-modal information from RNA-seq, which would help uncover more disease mechanisms, are still limited. Here, we present PipeOne, a cross-platform one-stop analysis workflow for large-scale transcriptome data. It was developed based on Nextflow, a reproducible workflow management system. PipeOne is composed of three modules, data processing and feature matrices construction, disease feature prioritization, and disease subtyping. It first integrates eight different tools to extract different information from RNA-seq data, and then used random forest algorithm to study and stratify patients according to evidences from multiple-modal information. Its application in five cancers (colon, liver, kidney, stomach, or thyroid; total samples n = 2024) identified various dysregulated key features (such as PVT1 expression and ABI3BP alternative splicing) and pathways (especially liver and kidney dysfunction) shared by multiple cancers. Furthermore, we demonstrated clinically-relevant patient subtypes in four of five cancers, with most subtypes characterized by distinct driver somatic mutations, such as TP53, TTN, BRAF, HRAS, MET, KMT2D, and KMT2C mutations. Importantly, these subtyping results were frequently contributed by dysregulated biological processes, such as ribosome biogenesis, RNA binding, and mitochondria functions. PipeOne is efficient and accurate in studying different cancer types to reveal the specificity and cross-cancer contributing factors of each cancer.It could be easily applied to other diseases and is available at GitHub.

Developing Efficient Workflows for Contemporary Design Processes and Robotics

<p>This Master’s thesis forms a section of a team based research project with the aim to understand how contemporary tools can inform a contemporary design workflow. This workflow is primarily focused on utilizing a robotic arm to incrementally form sheet aluminium into architectural components. Specifically, my role within this team is from the Project Management point of view trying to understand how Project Management can improve team focused contemporary design. The goal of the thesis is to establish a workflow outlining an efficient process for designing and fabricating prototype architectural systems. Research Questions: Team: How can contemporary tools inform a contemporary digital workflow? Individual: How can Project Management improve the performance and efficiency of team focused contemporary design workflows? The aims of the research are to first establish an understanding of the digital fabrication workflow and establish what management tools best fit within the workflow. This aligns with the team goal to create and establish how digital fabrication and robotics could be applied to New Zealand construction practice. The goal is not to suggest a replacement for current methods, but to understand and integrate a methodology using a parametric design process and, to aid the introduction of complexity in design not currently available through traditional construction and joinery methods. Understanding the function Project Management has for workflow management and development is a primary research goal which can be broken down into parts. - How can activities be efficiently designed? - What procedures need to be implemented? - What are the best process management techniques? The knowledge gained through an iterative work study shows that project managers have a unique perspective within the development of digital fabrication workflows. A project manager integrated into this process is able to influence and define the key performance indicators of projects undertaken within this contemporary environment. The method used to establish and develop a workflow for digital fabrication processes, is a work study. This involves developing a workflow based on similar cases and then redevelop it based on performance indicators from literature. Identifying key areas of failure is a part of this process and is a common method within industry for improving organisation efficiency and productivity. A limiting factor of this research is the fact the team was learning the process overtime. Therefore, people are subject to unequal levels of understanding of what needs to be considered as part of workflow development gaining new perspective with hindsight. This is not, and cannot be accounted for, however is noted as part of lessons learnt during the reflection process of the work-study.</p>

Developing Efficient Workflows for Contemporary Design Processes and Robotics

<p>This Master’s thesis forms a section of a team based research project with the aim to understand how contemporary tools can inform a contemporary design workflow. This workflow is primarily focused on utilizing a robotic arm to incrementally form sheet aluminium into architectural components. Specifically, my role within this team is from the Project Management point of view trying to understand how Project Management can improve team focused contemporary design. The goal of the thesis is to establish a workflow outlining an efficient process for designing and fabricating prototype architectural systems. Research Questions: Team: How can contemporary tools inform a contemporary digital workflow? Individual: How can Project Management improve the performance and efficiency of team focused contemporary design workflows? The aims of the research are to first establish an understanding of the digital fabrication workflow and establish what management tools best fit within the workflow. This aligns with the team goal to create and establish how digital fabrication and robotics could be applied to New Zealand construction practice. The goal is not to suggest a replacement for current methods, but to understand and integrate a methodology using a parametric design process and, to aid the introduction of complexity in design not currently available through traditional construction and joinery methods. Understanding the function Project Management has for workflow management and development is a primary research goal which can be broken down into parts. - How can activities be efficiently designed? - What procedures need to be implemented? - What are the best process management techniques? The knowledge gained through an iterative work study shows that project managers have a unique perspective within the development of digital fabrication workflows. A project manager integrated into this process is able to influence and define the key performance indicators of projects undertaken within this contemporary environment. The method used to establish and develop a workflow for digital fabrication processes, is a work study. This involves developing a workflow based on similar cases and then redevelop it based on performance indicators from literature. Identifying key areas of failure is a part of this process and is a common method within industry for improving organisation efficiency and productivity. A limiting factor of this research is the fact the team was learning the process overtime. Therefore, people are subject to unequal levels of understanding of what needs to be considered as part of workflow development gaining new perspective with hindsight. This is not, and cannot be accounted for, however is noted as part of lessons learnt during the reflection process of the work-study.</p>