Search results for: bioinformatic workflow

Authors: Noha Nagy, Hoda Mokhtar, Mohamed El Sherkawi

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The popularity of workflow delegation models and the increasing number of workflow provenance-aware systems motivate the need for finding more strict delegation models. Such models combine different approaches for enhanced security and respecting workflow privacy. Although modern enterprises seek conformance to workflow constraints to ensure correctness of their work, these constraints pose a threat to security, because these constraints can be good seeds for attacking privacy even in secure models. This paper introduces a comprehensive Workflow Delegation Model (WFDM) that utilizes provenance and workflow constraints to prevent malicious delegate from attacking workflow privacy as well as extending the delegation functionalities. In addition, we argue the need for exploiting workflow constraints to improve workflow security models.

Keywords: workflow delegation models, secure workflow, workflow privacy, workflow provenance

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Authors: Zaide Montes Ortiz, Jorge Alberto Molina, Alejandro Reyes

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Insects are extremely successful organisms. A sophisticated olfactory system is in part responsible for their survival and reproduction. The detection of volatile organic compounds can positively or negatively affect many behaviors in insects. Compounds such as carbon dioxide (CO2), ammonium, indol, and lactic acid are essential for many species of mosquitoes like Anopheles gambiae in order to locate vertebrate hosts. For instance, in A. gambiae, the olfactory receptor AgOR2 is strongly activated by indol, which accounts for almost 30% of human sweat. On the other hand, in some insects of agricultural importance, the detection and identification of pheromone receptors (PRs) in lepidopteran species has become a promising field for integrated pest management. For example, with the disruption of the pheromone receptor, BmOR1, mediated by transcription activator-like effector nucleases (TALENs), the sensitivity to bombykol was completely removed affecting the pheromone-source searching behavior in male moths. Then, the detection and identification of olfactory receptors in the genomes of insects is fundamental to improve our understanding of the ecological interactions, and to provide alternatives in the integrated pests and vectors management. Hence, the objective of this study is to propose a bioinformatic workflow to enhance the detection and identification of potential olfactory receptors in genomes of relevant insects. Applying Hidden Markov models (Hmms) and different computational tools, potential candidates for pheromone receptors in Tuta absoluta were obtained, as well as potential carbon dioxide receptors in Rhodnius prolixus, the main vector of Chagas disease. This study showed the validity of a bioinformatic workflow with a potential to improve the identification of certain olfactory receptors in different orders of insects.

Keywords: bioinformatic workflow, insects, olfactory receptors, protein prediction

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Authors: Ahmed Alqaoud

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This paper describes Publish/Subscribe Scientific Workflow Interoperability Framework (PS-SWIF) architecture and its components that collectively provide interoperability between heterogeneous scientific workflow systems. Requirements to achieve interoperability are identified. This paper also provides a detailed investigation and design of models and solutions for system requirements, and considers how workflow interoperability models provided by Workflow Management Coalition (WfMC) can be achieved using the PS-SWIF system.

Keywords: publish/subscribe, scientific workflow, web services, workflow interoperability

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Authors: Fairouz Fakhfakh, Hatem Hadj Kacem, Ahmed Hadj Kacem

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Cloud computing offers a new model of service provisioning for workflow applications, thanks to its elasticity and its paying model. However, it presents various challenges that need to be addressed in order to be efficiently utilized. The resources provisioning problem for workflow applications has been widely studied. Nevertheless, the existing works did not consider the change in workflow instances while they are being executed. This functionality has become a major requirement to deal with unusual situations and evolution. This paper presents a first step towards the resources provisioning for a dynamic workflow. In fact, we propose a provisioning algorithm which minimizes the overall workflow execution cost, while meeting a deadline constraint. Then, we extend it to support the dynamic adding of tasks. Experimental results show that our proposed heuristic demonstrates a significant reduction in resources cost by using a consolidation process.

Keywords: cloud computing, resources provisioning, dynamic workflow, workflow applications

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Authors: Shuen-Tai Wang, Yu-Ching Lin

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With more and more workflow systems adopting cloud as their execution environment, it presents various challenges that need to be addressed in order to be utilized efficiently. This paper introduces a method for resource provisioning based on our previous research of dynamic allocation and its pipeline processes. We present an abstraction for workload scheduling in which independent tasks get scheduled among various available processors of distributed computing for optimization. We also propose an integrated web-based workflow designer by taking advantage of the HTML5 technology and chaining together multiple tools. In order to make the combination of multiple pipelines executing on the cloud in parallel, we develop a script translator and an execution engine for workflow management in the cloud. All information is known in advance by the workflow engine and tasks are allocated according to the prior knowledge in the repository. This proposed effort has the potential to provide support for process definition, workflow enactment and monitoring of workflow processes. Users would benefit from the web-based system that allows creation and execution of pipelines without scripting knowledge.

Keywords: workflow systems, resources provisioning, workload scheduling, web-based, workflow engine

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Authors: Heejung Lee

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In a highly competitive environment, it becomes more important to shorten the whole business process while delivering or even enhancing the business value to the customers and suppliers. Although the workflow management systems receive much attention for its capacity to practically support the business process enactment, the effective workflow modeling method remain still challenging and the high degree of process complexity makes it more difficult to gain the short lead time. This paper presents a workflow structuring method in a holistic way that can reduce the process complexity using activity-needs and formal concept analysis, which eventually enhances the key performance such as quality, delivery, and cost in business process.

Keywords: workflow management, re-engineering, formal concept analysis, business process

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Authors: Xiaoping Qiu, Binci You, Yue Hu

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The executive time of the workflow network has an important effect on the efficiency of the business process. In this paper, the activity executive time is divided into the service time and the waiting time, then the lead time can be extracted from the waiting time. The executive time formulas of the three basic structures in the workflow network are deduced based on the activity lead time. Taken the process of e-commerce logistics as an example, insert appropriate lead time for key activities by using Petri net, and the executive time optimization model is built to minimize the waiting time with the time-cost constraints. Then the solution program-using VC++6.0 is compiled to get the optimal solution, which reduces the waiting time of key activities in the workflow, and verifies the role of lead time in the timeliness of e-commerce logistics.

Keywords: electronic business, execution time, lead time, optimization model, petri net, time workflow network

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Authors: Wang Shuen-Tai, Lin Yu-Ching, Chang Hsi-Ya

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Cloud computing is the innovative and leading information technology model for enabling convenient, on-demand network access to a shared pool of configurable computing resources that can be rapidly provisioned and released with minimal management effort. In this paper, we aim at the development of workflow management system for cloud computing platforms based on our previous research on the dynamic allocation of the cloud computing resources and its workflow process. We took advantage of the HTML 5 technology and developed web-based workflow interface. In order to enable the combination of many tasks running on the cloud platform in sequence, we designed a mechanism and developed an execution engine for workflow management on clouds. We also established a prediction model which was integrated with job queuing system to estimate the waiting time and cost of the individual tasks on different computing nodes, therefore helping users achieve maximum performance at lowest payment. This proposed effort has the potential to positively provide an efficient, resilience and elastic environment for cloud computing platform. This development also helps boost user productivity by promoting a flexible workflow interface that lets users design and control their tasks' flow from anywhere.

Keywords: web-based, workflow, HTML5, Cloud Computing, Queuing System

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Authors: A. A. AlRasheed, A. Atkins, R. Campion

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This paper focuses on using knowledge management and visualisation concepts to improve the patients and hospitals employee’s workflow. Hospitals workflow is a complex and complicated process and poor patient flow can put both patients and a hospital’s reputation at risk, and can threaten the facility’s financial sustainability. Healthcare leaders are under increased pressure to reduce costs while maintaining or increasing patient care standards. In this paper, a framework is proposed to help improving patient experience, staff satisfaction, and operational efficiency across hospitals by using knowledge management based visualisation concepts. This framework is using real-time visibility to track and monitor location and status of patients, staff, rooms, and medical equipment.

Keywords: knowledge management, improvements, visualisation, workflow

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Authors: Afiq Juazer Rizal, Siti Zaleha Misnan, M. Zairi M. Yusof

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Seismic data is the fundamental tool utilized by exploration companies to determine potential hydrocarbon. However, the importance of seismic trace data will be undermined unless the geo-spatial component of the data is understood. Deriving a proposed well to be drilled from data that has positional ambiguity will jeopardize business decision and millions of dollars’ investment that every oil and gas company would like to avoid. Spatial integrity QC workflow has been introduced in PETRONAS to ensure positional errors within the seismic data are recognized throughout the exploration’s lifecycle from acquisition, processing, and seismic interpretation. This includes, amongst other tests, quantifying that the data is referenced to the appropriate coordinate reference system, survey configuration validation, and geometry loading verification. The direct outcome of the workflow implementation helps improve reliability and integrity of sub-surface geological model produced by geoscientist and provide important input to potential hazard assessment where positional accuracy is crucial. This workflow’s development initiative is part of a bigger geospatial integrity management effort, whereby nearly eighty percent of the oil and gas data are location-dependent.

Keywords: oil and gas exploration, PETRONAS, seismic data, spatial integrity QC workflow

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Authors: Wang Mimi, Jiang Changjun, Liu Guanjun, Fang Xianwen

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Loop structure often appears in the business process modeling, analyzing the consistency of corresponding workflow net models containing loop structure is a problem, the existing behavior consistency methods cannot analyze effectively the process models with the loop structure. In the paper, by analyzing five kinds of behavior relations of transitions, a three-dimensional figure and two-dimensional behavior relation matrix are proposed. Based on this, analysis method of behavior consistency of business process based on Petri net branching processes is proposed. Finally, an example is given out, which shows the method is effective.

Keywords: workflow net, behavior consistency measures, loop, branching process

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Authors: María Fernanda Quiceno Vallejo, Patricia del Portillo, María Mercedes Zambrano, Jeisson Alejandro Triana, Dayana Calderon, Juan Manuel Anzola

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Microorganisms from tropical ecosystems can be novel in terms of adaptations and conservation. Given the macrodiversity of Colombian ecosystems, it is possible that this diversity is also present in Colombian soils. Tropical soil bacteria could offer a potentially novel source of bioactive compounds. In this study we analyzed a metagenomic fosmid library constructed with tropical bacterial DNAs with the aim of understanding its underlying diversity and functional potential. 8640 clones from the fosmid library were sequenced by NANOPORE MiniOn technology, then analyzed with bioinformatic tools such as Prokka, AntiSMASH and Bagel4 in order to identify functional biosynthetic pathways in the sequences. The strains showed ample difference when it comes to biosynthetic pathways. In total we identified 4 pathways related to aryl polyene synthesis, 12 related to terpenes, 22 related to NRPs (Non ribosomal peptides), 11 related PKs (Polyketide synthases) and 7 related to RiPPs (bacteriocins). We designed primers for the metagenomic clones with the most BGCs (sample 6 and sample 2). Results show the biotechnological / pharmacological potential of tropical ecosystems. Overall, this work provides an overview of the genomic and functional potential of Colombian soil and sets the groundwork for additional exploration of tropical metagenomic sequencing.

Keywords: bioactives, biosyntethic pathways, bioinformatic, bacterial gene clusters, secondary metabolites

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Authors: Nouf Alourfi

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This study examines the metabolism of amitriptyline (AMI) and verapamil (VER) using a KNIME-based method. KNIME improved workflow is an open-source data-analytics platform that integrates a number of open-source metabolomics tools such as CFMID and MetFrag to provide standard data visualisations, predict candidate metabolites, assess them against experimental data, and produce reports on identified metabolites. The use of this workflow is demonstrated by employing three types of liver microsomes (human, rat, and Guinea pig) to study the in vitro metabolism of the two drugs (AMI and VER). This workflow is used to create and treat UPLC-MS (Orbitrap) data. The formulas and structures of these drugs' metabolites can be assigned automatically. The key metabolic routes for amitriptyline are hydroxylation, N-dealkylation, N-oxidation, and conjugation, while N-demethylation, O-demethylation and N-dealkylation, and conjugation are the primary metabolic routes for verapamil. The identified metabolites are compatible to the published, clarifying the solidity of the workflow technique and the usage of computational tools like KNIME in supporting the integration and interoperability of emerging novel software packages in the metabolomics area.

Keywords: KNIME, CFMID, MetFrag, Data Analysis, Metabolomics

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Authors: Masoud Sheidai

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Biologists with a special field of population genetics and phylogeny have different research tasks such as populations’ genetic variability and divergence, species relatedness, the evolution of genetic and morphological characters, and identification of DNA SNPs with adaptive potential. To tackle these problems and reach a concise conclusion, they must use the proper and efficient statistical and bioinformatic methods as well as suitable genetic and morphological characteristics. In recent years application of different bioinformatic and statistical methods, which are based on various well-documented assumptions, are the proper analytical tools in the hands of researchers. The species delineation is usually carried out with the use of different clustering methods like K-means clustering based on proper distance measures according to the studied features of organisms. A well-defined species are assumed to be separated from the other taxa by molecular barcodes. The species relationships are studied by using molecular markers, which are analyzed by different analytical methods like multidimensional scaling (MDS) and principal coordinate analysis (PCoA). The species population structuring and genetic divergence are usually investigated by PCoA and PCA methods and a network diagram. These are based on bootstrapping of data. The Association of different genes and DNA sequences to ecological and geographical variables is determined by LFMM (Latent factor mixed model) and redundancy analysis (RDA), which are based on Bayesian and distance methods. Molecular and morphological differentiating characters in the studied species may be identified by linear discriminant analysis (DA) and discriminant analysis of principal components (DAPC). We shall illustrate these methods and related conclusions by giving examples from different edible and medicinal plant species.

Keywords: GWAS analysis, K-Means clustering, LFMM, multidimensional scaling, redundancy analysis

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Authors: Imen Amari, Kaouther Gasmi, Asma Rebaya, Salem Hasnaoui

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The problem of scheduling and mapping data flow applications on multi-core architectures is notoriously difficult. This difficulty is related to the rapid evaluation of Telecommunication and multimedia systems accompanied by a rapid increase of user requirements in terms of latency, execution time, consumption, energy, etc. Having an optimal scheduling on multi-cores DSP (Digital signal Processors) platforms is a challenging task. In this context, we present a novel technic and algorithm in order to find a valid schedule that optimizes the key performance metrics particularly the Latency. Our contribution is based on Satisfiability Modulo Theories (SMT) solving technologies which is strongly driven by the industrial applications and needs. This paper, describe a scheduling module integrated in our proposed Workflow which is advised to be a successful approach for programming the applications based on NoC-DSP platforms. This workflow transform automatically a Simulink model to a synchronous dataflow (SDF) model. The automatic transformation followed by SMT solver scheduling aim to minimize the final latency and other software/hardware metrics in terms of an optimal schedule. Also, finding the optimal numbers of cores to be used. In fact, our proposed workflow taking as entry point a Simulink file (.mdl or .slx) derived from embedded Matlab functions. We use an approach which is based on the synchronous and hierarchical behavior of both Simulink and SDF. Whence, results of running the scheduler which exist in the Workflow mentioned above using our proposed SMT solver algorithm refinements produce the best possible scheduling in terms of latency and numbers of cores.

Keywords: multi-cores DSP, scheduling, SMT solver, workflow

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Authors: Mohamed Elshal, Hazim El-Mounayri, Omar El-Mounayri

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Emergency department (ED) is considered as a complex system of interacting entities: patients, human resources, software and hardware systems, interfaces, and other systems. This paper represents a research for implementing a detailed Systems Engineering (SE) approach in a mid-size hospital in central Indiana. This methodology will be applied by “The Initiative for Product Lifecycle Innovation (IPLI)” institution at Indiana University to study and solve the crowding problem with the aim of increasing throughput of patients and enhance their treatment experience; therefore, the nature of crowding problem needs to be investigated with all other problems that leads to it. The presented SE methods are workflow analysis and systems modeling where SE tools such as Microsoft Visio are used to construct a group of system-level diagrams that demonstrate: patient’s workflow, documentation and communication flow, data systems, human resources workflow and requirements, leadership involved, and integration between ER different systems. Finally, the ultimate goal will be managing the process through implementation of an executable model using commercialized software tools, which will identify bottlenecks, improve documentation flow, and help make the process faster.

Keywords: systems modeling, ED operation, workflow modeling, systems analysis

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Authors: Keaghan Brown

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The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Katalina Grigorova, Kaloyan Mironov

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The paper focuses on the benefits of business process modeling. Although this discipline is developing for many years, there is still necessity of creating new opportunities to meet the ever-increasing users’ needs. Because one of these needs is related to the conversion of business process models from one standard to another, the authors have developed a converter between BPMN and EPC standards using workflow patterns as intermediate tool. Nowadays there are too many systems for business process modeling. The variety of output formats is almost the same as the systems themselves. This diversity additionally hampers the conversion of the models. The presented study is aimed at discussing problems due to differences in the output formats of various modeling environments.

Keywords: business process modeling, business process modeling standards, workflow patterns, converting models

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Authors: Qianjia Cheng, Hongquan Jiang

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Crowdsourcing solves the problems that computers can't handle by integrating computers and the Internet. Its extensive knowledge sources, high efficiency and high quality, make crowdsourcing attract wide attention in industry and academia in recent years. The development of online crowdsourcing platforms such as Clickworker and Amazon Mechanical Turk(Mturk) tend to mature gradually. This paper sorts out the concept of crowdsourcing, sorts out the workflow of competitive crowdsourcing, summarizes the related technologies of crowdsourcing based on the workflow, quality control, cost control and delay control, introduces the typical crowdsourcing platform. Finally, we highlight some open problems of the current crowdsourcing and present some future research direction in this area.

Keywords: application, crowdsourcing, crowdsourcing platform, system architecture

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Authors: Qianjia Cheng, Hongquan Jiang

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Crowdsourcing solves the problems that computers can't handle by integrating computers and the Internet. Its extensive knowledge sources, high efficiency, and high quality have made crowdsourcing attract wide attention in industry and academia in recent years. The development of online crowdsourcing platforms such as Clickworker, Amazon Mechanical Turk(Mturk) tends to mature gradually. This paper sorts out the concept of crowdsourcing, sorts out the workflow of competitive crowdsourcing, summarizes the related technologies of crowdsourcing based on workflow, quality control, cost control, and delay control, and introduces the typical crowdsourcing platform. Finally, we highlight some open problems of the current crowdsourcing and present some future research directions in this area.

Keywords: application, crowdsourcing, crowdsourcing platform, system architecture

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Authors: Asma Rebaya, Kaouther Gasmi, Imen Amari, Salem Hasnaoui

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Over these last years, applications such as telecommunications, signal processing, digital communication with advanced features (Multi-antenna, equalization..) witness a rapid evaluation accompanied with an increase of user exigencies in terms of latency, the power of computation… To satisfy these requirements, the use of hardware/software systems is a common solution; where hardware is composed of multi-cores and software is represented by models of computation, synchronous data flow (SDF) graph for instance. Otherwise, the most of the embedded system designers utilize Simulink for modeling. The issue is how to simplify the c code generation, for a multi-cores platform, of an application modeled by Simulink. To overcome this problem, we propose a workflow allowing an automatic transformation from the Simulink model to the SDF graph and providing an efficient schedule permitting to optimize the number of cores and to minimize latency. This workflow goes from a Simulink application and a hardware architecture described by IP.XACT language. Based on the synchronous and hierarchical behavior of both models, the Simulink block diagram is automatically transformed into an SDF graph. Once this process is successfully achieved, the scheduler calculates the optimal cores’ number needful by minimizing the maximum density of the whole application. Then, a core is chosen to execute a specific graph task in a specific order and, subsequently, a compatible C code is generated. In order to perform this proposal, we extend Preesm, a rapid prototyping tool, to take the Simulink model as entry input and to support the optimal schedule. Afterward, we compared our results to this tool results, using a simple illustrative application. The comparison shows that our results strictly dominate the Preesm results in terms of number of cores and latency. In fact, if Preesm needs m processors and latency L, our workflow need processors and latency L'< L.

Keywords: hardware/software system, latency, modeling, multi-cores platform, scheduler, SDF graph, Simulink model, workflow

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Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Gionata Carmignani, Mario G. C. A. Cimino, Franco Failli

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Business Processes (BPs) are the key instrument to understand how companies operate at an organizational level, taking an as-is view of the workflow, and how to address their issues by identifying a to-be model. In last year’s, the BP Model and Notation (BPMN) has become a de-facto standard for modeling processes. However, this standard does not incorporate explicitly the Problem-Solving (PS) knowledge in the Process Modeling (PM) results. Thus, such knowledge cannot be shared or reused. To narrow this gap is today a challenging research area. In this paper we present a framework able to capture the PS knowledge and to improve a workflow. This framework extends the BPMN specification by incorporating new general-purpose elements. A pilot scenario is also presented and discussed.

Keywords: business process management, BPMN, problem solving, process mapping

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Authors: Sofiane Bendoukha, Daniel Moldt, Hayat Bendoukha

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Workflow concepts are essential for the development of remote sensing applications. They can help users to manage and process satellite data and execute scientific experiments on distributed resources. The objective of this paper is to introduce an approach for the specification and the execution of complex scientific workflows in Cloud-like environments. The approach strives to support scientists during the modeling, the deployment and the monitoring of their workflows. This work takes advantage from Petri nets and more pointedly the so-called reference nets formalism, which provides a robust modeling/implementation technique. RENEWGRASS is a tool that we implemented and integrated into the Petri nets editor and simulator RENEW. It provides an easy way to support not experienced scientists during the specification of their workflows. It allows both modeling and enactment of image processing workflows from the remote sensing domain. Our case study is related to the implementation of vegetation indecies. We have implemented the Normalized Differences Vegetation Index (NDVI) workflow. Additionally, we explore the integration possibilities of the Cloud technology as a supplementary layer for the deployment of the current implementation. For this purpose, we discuss migration patterns of data and applications and propose an architecture.

Keywords: cloud computing, scientific workflows, petri nets, RENEWGRASS

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Authors: Tim Nikolsky

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This paper seeks to explore the different ways in which music producers choose to embrace various levels of technology based on musical values, objectives, affordability, access and workflow benefits. Current digital audio production workflow is questioned. Engineers and music producers of today are increasingly divorced from the tangibility of music production. Making music no longer requires you to reach over and turn a knob. Ideas of authenticity in music production are being redefined. Calculations from the mathematical algorithm with the pretty pictures are increasingly being chosen over hardware containing transformers and tubes. Are mouse clicks and movements equivalent or inferior to the master brush strokes we are seeking to conjure? We are making audio production decisions visually by constantly looking at a screen rather than listening. Have we compromised our music objectives and values by removing the ‘hands-on’ nature of music making? DAW interfaces are making our musical decisions for us not necessarily in our best interests. Technological innovation has presented opportunities as well as challenges for education. What do music production students actually need to learn in a formalised education environment, and to what extent do they need to know it? In this brave new world of omnipresent music creation tools, do we still need tangibility in music production? Interviews with prominent Australian music producers that work in a variety of fields will be featured in this paper, and will provide insight in answering these questions and move towards developing an understanding how tangibility can be rediscovered in the next generation of music production.

Keywords: analogue, digital, digital audio workstation, music production, plugins, tangibility, technology, workflow

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Authors: U. Borasi, Amit Kr. Jain, Rakesh, Piyush Jain

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Data collection, data preparation, model training, model evaluation, and deployment are all processes in a typical machine learning workflow. Training data needs to be gathered and organised. This often entails collecting a sizable dataset and cleaning it to remove or correct any inaccurate or missing information. Preparing the data for use in the machine learning model requires pre-processing it after it has been acquired. This often entails actions like scaling or normalising the data, handling outliers, selecting appropriate features, reducing dimensionality, etc. This pre-processed data is then used to train a model on some machine learning algorithm. After the model has been trained, it needs to be assessed by determining metrics like accuracy, precision, and recall, utilising a test dataset. Every time a new model is built, both data pre-processing and model training—two crucial processes in the Machine learning (ML) workflow—must be carried out. Thus, there are various Machine Learning algorithms that can be employed for every single approach to data pre-processing, generating a large set of combinations to choose from. Example: for every method to handle missing values (dropping records, replacing with mean, etc.), for every scaling technique, and for every combination of features selected, a different algorithm can be used. As a result, in order to get the optimum outcomes, these tasks are frequently repeated in different combinations. This paper suggests a simple architecture for organizing this largely produced “combination set of pre-processing steps and algorithms” into an automated workflow which simplifies the task of carrying out all possibilities.

Keywords: machine learning, automation, AUTOML, architecture, operator pool, configuration, scheduler

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Authors: Yiping Meng, Yiming Sun

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The traditional construction industry is unable to meet the requirements for novel fabrication and construction. Automated construction and digital design have emerged as industry development trends that compensate for this shortcoming under the backdrop of Industrial Revolution 4.0. Benefitting from more flexible working space and more various end-effector tools compared to CNC methods, robot fabrication and construction techniques have been used in irregular architectural design. However, there is a lack of a systematic and comprehensive design and optimisation workflow considering geometric form, material, and fabrication methods. This paper aims to propose a design optimisation workflow for improving the rationality of a free-form timber structure fabricated by the robotic arm. Firstly, the free-form surface is described by NURBS, while its structure is calculated using the finite element analysis method. Then, by considering the characteristics and limiting factors of robotic timber fabrication, strain energy and robustness are set as optimisation objectives to optimise structural morphology by gradient descent method. As a result, an optimised structure with axial force as the main force and uniform stress distribution is generated after the structure morphology optimisation process. With the decreased strain energy and the improved robustness, the generated structure's bearing capacity and mechanical properties have been enhanced. The results prove the feasibility and effectiveness of the proposed optimisation workflow for free-form timber structure morphology design.

Keywords: robotic fabrication, free-form timber structure, Multi-objective optimisation, Structural morphology, rational design

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Authors: Patrick Ho

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Bloodstain Pattern Analysis (BPA) forensic evidence can be complex, requiring effective courtroom presentation to ensure clear and comprehensive understanding of the analyst’s findings. BPA witness statements can often involve reference to spatial information (such as location of rooms, objects, walls) which, when coupled with classified blood patterns, may illustrate the reconstructed movements of suspects and injured parties. However, it may be difficult to communicate this information through photography alone, despite this remaining the UK’s established method for presenting BPA evidence. Through an academic-police partnership between the University of Warwick and West Midlands Police (WMP), an integrated 3D scanning and HDR photography workflow for BPA was developed. Homicide scenes were laser scanned and, after processing, the 3D models were utilised in the BPA peer-review process. The same 3D models were made available for court but were not always utilised. This workflow has improved the ease of presentation for analysts and provided 3D scene models that assist with the investigation. However, the effects of incorporating 3D scene models in judicial processes may need to be studied before they are adopted more widely. 3D models from a simulated crime scene and West Midlands Police cases approved for conference disclosure are presented. We describe how the workflow was developed and integrated into established practices at WMP, including peer-review processes and witness statement delivery in court, and explain the impact the work has had on the Criminal Justice System in the West Midlands.

Keywords: bloodstain pattern analysis, forensic science, criminal justice, 3D scanning

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Authors: Robnier Reyes, Andrew J. P. Marques, Joel Ramjist, Chris R. Pasarikovski, Victor X. D. Yang

Abstract:

Over the past three decades, surgical robotic systems have demonstrated their ability to improve surgical outcomes. The LBR Med is a collaborative robotic arm that is meant to work with a surgeon to streamline surgical workflow. It has 7 degrees of freedom and thus can be easily oriented. Position and torque sensors at each joint allow it to maintain a position accuracy of 150 µm with real-time force and torque feedback, making it ideal for complex surgical procedures. Spinal fusion procedures involve the placement of as many as 20 pedicle screws, requiring a great deal of accuracy due to proximity to the spinal canal and surrounding vessels. Any deviation from intended path can lead to major surgical complications. Assistive surgical robotic systems are meant to serve as collaborative devices easing the workload of the surgeon, thereby improving pedicle screw placement by mitigating fatigue related inaccuracies. Moreover, robotic spinal systems have shown marked improvements over conventional freehanded techniques in both screw placement accuracy and fusion quality and have greatly reduced the need for screw revision, intraoperatively and post-operatively. However, current assistive spinal fusion robots, such as the ROSA Spine, are limited in functionality to positioning surgical instruments. While they offer a small degree of improvement in pedicle screw placement accuracy, they do not alleviate surgeon fatigue, nor do they provide real-time force and torque feedback during screw insertion. We propose a semi-autonomous surgical robot workflow for spinal fusion where the surgeon guides the robot to its initial position and orientation, and the robot drives the pedicle screw accurately into the vertebra. Here, we demonstrate feasibility by inserting pedicle screws into ex-vivo bovine rib bone. The robot monitors position, force and torque with respect to predefined values selected by the surgeon to ensure the highest possible spinal fusion quality. The workflow alleviates the strain on the surgeon by having the robot perform the screw placement while the ability to monitor the process in real-time keeps the surgeon in the system loop. The approach we have taken in terms of level autonomy for the robot reflects its ability to safely collaborate with the surgeon in the operating room without external navigation systems.

Keywords: ex vivo bovine bone, pedicle screw, surgical robot, surgical workflow

Procedia PDF Downloads 124

Authors: Mhaned Oubounyt, Jan Baumbach

Abstract:

Differences in co-expression networks between two or multiple cells (sub)types across conditions is a pressing problem in single-cell RNA sequencing (scRNA-seq). A key challenge is to define those co-variations that differ between or among cell types and/or conditions and phenotypes to examine small regulatory networks that can explain mechanistic differences. To this end, we developed SCANet, an all-in-one Python package that uses state-of-the-art algorithms to facilitate the workflow of a combined single-cell GCN (Gene Correlation Network) and GRN (Gene Regulatory Networks) pipeline, including inference of gene co-expression modules from scRNA-seq, followed by trait and cell type associations, hub gene detection, co-regulatory networks, and drug-gene interactions. In an example case, we illustrate how SCANet can be applied to identify regulatory drivers behind a cytokine storm associated with mortality in patients with acute respiratory illness. SCANet is available as a free, open-source, and user-friendly Python package that can be easily integrated into systems biology pipelines.

Keywords: single-cell, co-expression networks, drug-gene interactions, co-regulatory networks

Procedia PDF Downloads 98