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Journal articles on the topic 'NTS workflows'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Zweigle, Jonathan, Selina Tisler, Marta Bevilacqua, et al. "Prioritization strategies for non-target screening in environmental samples by chromatography – High-resolution mass spectrometry: A tutorial." Journal of Chromatography A 1751 (June 21, 2025): 465944. https://doi.org/10.1016/j.chroma.2025.465944.

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Non-target screening (NTS) using chromatography coupled to high-resolution mass spectrometry (HRMS), has become fundamental for detecting and prioritizing chemicals of emerging concern (CECs) in complex environmental matrices. The vast number of generated features (<em>m/z</em>, retention time, and intensity) necessitate effective prioritization strategies to identify environmentally and toxicologically relevant CECs. Since compound identification remains a major bottleneck in NTS, prioritization is critical to focus identification efforts where they matter most. This tutorial presents seven p

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Panse, Christian, Seema Sharma, Romain Huguet, Dennis Vughs, Jonas Grossmann, and Andrea Mizzi Brunner. "Ultraviolet Photodissociation for Non-Target Screening-Based Identification of Organic Micro-Pollutants in Water Samples." Molecules 25, no. 18 (2020): 4189. http://dx.doi.org/10.3390/molecules25184189.

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Non-target screening (NTS) based on the combination of liquid chromatography coupled to high-resolution mass spectrometry has become the key method to identify organic micro-pollutants (OMPs) in water samples. However, a large number of compounds remains unidentified with current NTS approaches due to poor quality fragmentation spectra generated by suboptimal fragmentation methods. Here, the potential of the alternative fragmentation technique ultraviolet photodissociation (UVPD) to improve identification of OMPs in water samples was investigated. A diverse set of water-relevant OMPs was selec

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3

Liu, Yong Shan, Yan Qing Shen, and Tian Bao Hao. "Research on Reliability Modeling of Cross-Organizational Workflows Based on Hierarchical Colored Petri Nets." Advanced Materials Research 186 (January 2011): 505–9. http://dx.doi.org/10.4028/www.scientific.net/amr.186.505.

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To reduce the complexity of cross-organizational workflow modeling and verification, a reliable modeling method of cross-organizational workflows based on hierarchical colored Petri nets is proposed. At the foundation of discussing formal definitions of global and local workflows, the paper develops reliability modeling constraints of cross-organizational workflows from structure to logic. Under these constraints, a top-down cross-organizational workflow model is built. Those substitution transitions which input places were safe in global workflow are refined by reliable local workflows to gua

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Rodríguez, Ricardo J., Rafael Tolosana-Calasanz, and Omer F. Rana. "A Dynamic Data-throttling Approach to Minimize Workflow Imbalance." ACM Transactions on Internet Technology 19, no. 3 (32) (2019): 1–21. https://doi.org/10.1145/3278720.

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Scientific workflows enable scientists to undertake analysis on large datasets and perform complex scientific simulations. These workflows are often mapped onto distributed and parallel computational infrastructures to speed up their executions. Prior to its execution, a workflow structure may suffer transformations to accommodate the computing infrastructures, normally involving task clustering and partitioning. However, these transformations may cause workflow imbalance because of the difference between execution task times (runtime imbalance) or because of unconsidered data dependencies tha

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VAN DER AALST, W. M. P. "THE APPLICATION OF PETRI NETS TO WORKFLOW MANAGEMENT." Journal of Circuits, Systems and Computers 08, no. 01 (1998): 21–66. http://dx.doi.org/10.1142/s0218126698000043.

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Workflow management promises a new solution to an age-old problem: controlling, monitoring, optimizing and supporting business processes. What is new about workflow management is the explicit representation of the business process logic which allows for computerized support. This paper discusses the use of Petri nets in the context of workflow management. Petri nets are an established tool for modeling and analyzing processes. On the one hand, Petri nets can be used as a design language for the specification of complex workflows. On the other hand, Petri net theory provides for powerful analys

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6

WANG, JIACUN, and DEMIN LI. "RESOURCE ORIENTED WORKFLOW NETS AND WORKFLOW RESOURCE REQUIREMENT ANALYSIS." International Journal of Software Engineering and Knowledge Engineering 23, no. 05 (2013): 677–93. http://dx.doi.org/10.1142/s0218194013400135.

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Petri nets are a powerful formalism in modeling workflows. A workflow determines the flow of work according to pre-defined business process. In many situations, business processes are constrained by scarce resources. The lack of resources can cause contention, the need for some tasks to wait for others to complete, which slows down the accomplishment of larger goals. In our previous work, a resource-constrained workflow model was introduced and a resource requirement analysis approach was developed for emergency response workflows, in which support of on-the-fly workflow change is critical [14

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Rábová, Ivana. "Using UML and Petri nets for visualization of business document flow." Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis 60, no. 2 (2012): 299–306. http://dx.doi.org/10.11118/actaun201260020299.

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The article deals with two principles of business workflow modeling, Petri nets and UML notation, that are the acceptable approaches to business modeling and can be used also for business documents workflow. The special type of Petri nets, WF-nets and UML activity diagrams are used in this article and both modeling ways are presented on the concrete business workflow and then there are presented and specified their advantage and disadvantage for business documents flows. At beginning it is explained the word workflow in context business documents, its features, principles and using in business

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8

Veldman, Abigail, Mensiena B. G. Kiewiet, Margaretha Rebecca Heiner-Fokkema, et al. "Towards Next-Generation Sequencing (NGS)-Based Newborn Screening: A Technical Study to Prepare for the Challenges Ahead." International Journal of Neonatal Screening 8, no. 1 (2022): 17. http://dx.doi.org/10.3390/ijns8010017.

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Newborn screening (NBS) aims to identify neonates with severe conditions for whom immediate treatment is required. Currently, a biochemistry-first approach is used to identify these disorders, which are predominantly inherited meta1bolic disorders (IMD). Next-generation sequencing (NGS) is expected to have some advantages over the current approach, for example the ability to detect IMDs that meet all screening criteria but lack an identifiable biochemical footprint. We have now designed a technical study to explore the use of NGS techniques as a first-tier approach in NBS. Here, we describe th

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Mans, Ronny, Wil van der Aalst, Nick Russell, Piet Bakker, and Arnold Moleman. "Lightweight Interacting Patient Treatment Processes." International Journal of Knowledge-Based Organizations 2, no. 4 (2012): 1–19. http://dx.doi.org/10.4018/ijkbo.2012100101.

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Processes concerning the diagnosis and treatment of patients cannot be straightjacketed into traditional production-like workflows. They can be best characterized as weakly-connected interacting light-weight workflows where tasks reside at different levels of granularity, and for each individual patient a doctor proceeds in a step-by-step way deciding what next steps be taken. Classical workflow notations fall short in supporting these patient processes as they have been designed to support monolithic processes. Classical notations (WF-nets (work flow nets), BPMN (Business Process Model and No

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10

Zheng, Changyou, Yi Yao, Song Huang, and Zhengping Ren. "Modeling Workflow Systems Constrained by Inputs and Outputs − An Approach Based on Petri Nets." Cybernetics and Information Technologies 15, no. 4 (2015): 27–41. http://dx.doi.org/10.1515/cait-2015-0052.

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Abstract Workflow systems are widely used in our daily life so that the validity, dependability and security with which they need to be assured are important. However, existing researches mainly focus on correctness validation, performance analysis and assignment scheduling, but the testing methods have been seldom suited. In this paper a formalized definition of workflows constrained by an input and output is presented, and based on that, a Petri Net-based model (I/O_WF_Net) is proposed. In I/O_WF_Net, the activities of the workflow can be modeled as transitions of a Petri Net, and the inputs

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11

Bottoni, Paolo, Fabio De Rosa, Kathrin Hoffmann, and Massimo Mecella. "Applying Algebraic Approaches for Modeling Workflows and their Transformations in Mobile Networks." Mobile Information Systems 2, no. 1 (2006): 51–76. http://dx.doi.org/10.1155/2006/704187.

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In emergency scenarios we can obtain a more effective coordination among team members, each of them equipped with hand-held devices, through the use of workflow management software. Team members constitute a Mobile Ad-hoc NETwork (MANET), whose topology both influences and is influenced by the workflow. In this paper we propose an algebraic approach for modeling workflow progress as well as its modifications as required by topology transformations. The approach is based on Algebraic Higher-Order Nets and sees both workflows and topologies as tokens, allowing their concurrent modification.

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12

Shen-Gunther, Jane, Hong Cai, and Yufeng Wang. "HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics." International Journal of Molecular Sciences 23, no. 15 (2022): 8132. http://dx.doi.org/10.3390/ijms23158132.

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Human papillomavirus (HPV) integration within the host genome may contribute to carcinogenesis through various disruptive mechanisms. With next-generation sequencing (NGS), identification of viral and host genomic breakpoints and chimeric sequences are now possible. However, a simple, streamlined bioinformatics workflow has been non-existent until recently. Here, we tested two new, automated workflows in CLC Microbial Genomics, i.e., Viral Hybrid Capture (VHC) Data Analysis and Viral Integration Site (VIS) Identification for software performance and efficiency. The workflows embedded with HPV

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13

Parker, Kyle, Hillary Wood, Joseph A. Russell, et al. "Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications." Tropical Medicine and Infectious Disease 8, no. 2 (2023): 121. http://dx.doi.org/10.3390/tropicalmed8020121.

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Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted b

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14

Clempner, Julio. "An analytical method for well-formed workflow/Petri net verification of classical soundness." International Journal of Applied Mathematics and Computer Science 24, no. 4 (2014): 931–39. http://dx.doi.org/10.2478/amcs-2014-0068.

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Abstract In this paper we consider workflow nets as dynamical systems governed by ordinary difference equations described by a particular class of Petri nets. Workflow nets are a formal model of business processes. Well-formed business processes correspond to sound workflow nets. Even if it seems necessary to require the soundness of workflow nets, there exist business processes with conditional behavior that will not necessarily satisfy the soundness property. In this sense, we propose an analytical method for showing that a workflow net satisfies the classical soundness property using a Petr

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15

Tiplea, Ferucio Laurenţiu, and Corina Bocaneala. "Priority Workflow Nets." IEEE Transactions on Systems, Man, and Cybernetics: Systems 43, no. 2 (2013): 402–15. http://dx.doi.org/10.1109/tsmca.2012.2198465.

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16

Wang, Jing, ShuXia Yu, and YuYue Du. "The Equivalency between Logic Petri Workflow Nets and Workflow Nets." Scientific World Journal 2015 (2015): 1–7. http://dx.doi.org/10.1155/2015/121492.

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Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in

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17

JianQiang Li, YuShun Fan, and MengChu Zhou. "Timing constraint workflow nets for workflow analysis." IEEE Transactions on Systems, Man, and Cybernetics - Part A: Systems and Humans 33, no. 2 (2003): 179–93. http://dx.doi.org/10.1109/tsmca.2003.811771.

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18

Zhou, Huan, Chuang Lin, Kun Meng, and Yarui Chen. "Stochastic Workflow Nets Based Workflow Pattern Modeling." Chinese Journal of Electronics 23, no. 1 (2014): 6–12. https://doi.org/10.23919/cje.2014.10848006.

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19

Yamaguchi, Shingo, and Mohd Anuaruddin Bin Ahmadon. "Process tree-based analysis method of DECLARE relation constraints in acyclic bridge-less well-structured workflow nets." ECTI Transactions on Computer and Information Technology (ECTI-CIT) 13, no. 2 (2019): 104–11. http://dx.doi.org/10.37936/ecti-cit.2019132.203107.

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In this paper, we proposed a method to analyze workflows’ constraints whose templates are defined in a declarative language called DECLARE. Checking such constraints is important but known to be intractable in general. Our results show three things. First, utilizing a tree representation of workflow process called {\it process tree}, we provided necessary and sufficient conditions on the constraints. Second, those conditions enable us to not only check a given constraint in polynomial time but also find a clue for improving the net if it violates the constraint. Third, we revealed the relation

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20

Akdemir, Ümit Özgür, and Neşe İlgin Karabacak. "Daily Workflow and Protocol Optimization in Positron Emission Tomography/Magnetic Resonance Imaging Use." Nükleer Tıp Seminerleri 3, no. 1 (2017): 12–21. http://dx.doi.org/10.4274/nts.003.

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21

Akdemir, Ümit Özgür, and Nese İlgin Karabacak. "Daily Workflow and Protocol Optimization in Positron Emission Tomography/Magnetic Resonance Imaging Use." Nuclear Medicine Seminars 3, no. 1 (2017): 12–21. http://dx.doi.org/10.4274/nts.2017.003.

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22

Muscarella, Fabrizio, De Bonis, et al. "Automated Workflow for Somatic and Germline Next Generation Sequencing Analysis in Routine Clinical Cancer Diagnostics." Cancers 11, no. 11 (2019): 1691. http://dx.doi.org/10.3390/cancers11111691.

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Thanks to personalized medicine trends and collaborations between industry, clinical research groups and regulatory agencies, next generation sequencing (NGS) is turning into a common practice faster than one could have originally expected. When considering clinical applications of NGS in oncology, a rapid workflow for DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue samples, as well as producing high quality library preparation, can be real challenges. Here we consider these targets and how applying effective automation technology to NGS workflows may help improve yield, tim

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23

Ramesh, Siddhi, Monica Pomaville, Kristina Doytcheva, et al. "Interpretable artificial intelligence-based analysis for morphologic classification of neuroblastic tumors." Journal of Clinical Oncology 42, no. 16_suppl (2024): 10023. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.10023.

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10023 Background: Rapid and accurate identification of morphologic features of neuroblastic tumors (NTs) is critical for risk stratification and therapeutic decision making. The prognostic value of features like neuroblast differentiation, mitosis-karyorrhexis index (MKI), and Schwannian stromal presence is well established. Deep learning permits objective histopathological analysis, streamlining workflows for pathologists, notably in rare cancers. In rare cancers, our method minimizes bias and optimizes limited data using transfer and self-supervised learning (SSL) for feature extraction, wit

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24

Cadang, Lance, Chi Yan Janet Tam, Benjamin Nathan Moore, Juergen Fichtl, and Feng Yang. "A Highly Efficient Workflow for Detecting and Identifying Sequence Variants in Therapeutic Proteins with a High Resolution LC-MS/MS Method." Molecules 28, no. 8 (2023): 3392. http://dx.doi.org/10.3390/molecules28083392.

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Large molecule protein therapeutics have steadily grown and now represent a significant portion of the overall pharmaceutical market. These complex therapies are commonly manufactured using cell culture technology. Sequence variants (SVs) are undesired minor variants that may arise from the cell culture biomanufacturing process that can potentially affect the safety and efficacy of a protein therapeutic. SVs have unintended amino acid substitutions and can come from genetic mutations or translation errors. These SVs can either be detected using genetic screening methods or by mass spectrometry

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25

Ouenes, Ahmed, Nicholas M. Umholtz, and Yamina E. Aimene. "Using geomechanical modeling to quantify the impact of natural fractures on well performance and microseismicity: Application to the Wolfcamp, Permian Basin, Reagan County, Texas." Interpretation 4, no. 2 (2016): SE1—SE15. http://dx.doi.org/10.1190/int-2015-0134.1.

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We have evaluated workflows to quantify the mechanical impact of natural fractures (NFs) on the production performance of hydraulically stimulated stages in shale wells. Variations in fracture orientation and density can enhance or degrade the transport and effectiveness of fracturing fluids. Specifically, we studied the effect of a complex fault splay system on a horizontal Wolfcamp B reservoir well. A general workflow that combines geophysics, geology, and geomechanics (3G) was evaluated and applied to the well. The benefits of the 3G workflow are threefold. First, the quantitative impact of

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26

Esparza, Javier, Martin Leucker, and Maximilian Schlund. "Learning Workflow Petri Nets." Fundamenta Informaticae 113, no. 3-4 (2011): 205–28. http://dx.doi.org/10.3233/fi-2011-607.

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27

van Hee, Kees, Natalia Sidorova, and Marc Voorhoeve. "Resource-Constrained Workflow Nets." Fundamenta Informaticae 71, no. 2-3 (2006): 243–57. https://doi.org/10.3233/fun-2006-712-306.

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We study concurrent processes modelled as workflow Petri nets extended with resource constrains. Resources are durable units that can be neither created nor destroyed: they are claimed during the handling procedure and then released again. Typical kinds of resources are manpower, machinery, computer memory. We define structural criteria based on traps and siphons for the correctness of workflow nets with resource constraints. We also extend the soundness notion for workflow nets to the workflow nets with resource constraints; extra conditions concern the durability of resources. We prove some

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Lomazova, Irina A. "Interacting Workflow Nets for Workflow Process Re-Engineering." Fundamenta Informaticae 101, no. 1-2 (2010): 59–70. http://dx.doi.org/10.3233/fi-2010-275.

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29

Wahba, Ashraf, Tony Ho, Sarah Johns, et al. "Abstract 2291: Bravo automation of Agilent Avida targeted enrichment for high-throughput detection of genomic alteration and DNA methylation." Cancer Research 84, no. 6_Supplement (2024): 2291. http://dx.doi.org/10.1158/1538-7445.am2024-2291.

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Abstract Background: Current genomic and epigenomic profiling of cancer tissue DNA or cfDNA (cell-free DNA) in liquid biopsy relies upon separate, time- and sample-consuming technologies for somatic variant detection or methylation analysis. Here we describe workflow and performance of the Agilent Bravo automated liquid handling platform with the Agilent Avida targeted enrichment solution for next generation sequencing of somatic variants and methylation profiling. This solution can effectively analyze low-input tumor DNA or cfDNA samples. The Avida Duo workflow enables highly sensitive detect

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Liu, Wei, YuYue Du, MengChu Zhou, and Chun Yan. "Transformation of Logical Workflow Nets." IEEE Transactions on Systems, Man, and Cybernetics: Systems 44, no. 10 (2014): 1401–12. http://dx.doi.org/10.1109/tsmc.2014.2311392.

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31

JIAO, LI, and TO-YAT CHEUNG. "COMPOSITIONAL VERIFICATION FOR WORKFLOW NETS." Journal of Circuits, Systems and Computers 15, no. 04 (2006): 551–70. http://dx.doi.org/10.1142/s0218126606003167.

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A workflow is the automation of business processes that describe activities in a business context. Petri nets have been widely used as a workflow modeling technique. Workflow nets (WF-nets), introduced by van der Aalst [LNCS1248 (1997) 407–426], are a class of Petri nets tailored towards workflow analysis. Soundness is used as the least correctness criterion for WF-nets in order to ensure that a process can terminate properly. This paper extends WF-nets by considering resources and allowing for multi-cases in a process. For the extended model, the relationship between soundness and standard be

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Kotb, Y. T., S. S. Beauchemin, and J. L. Barron. "Workflow Nets for Multiagent Cooperation." IEEE Transactions on Automation Science and Engineering 9, no. 1 (2012): 198–203. http://dx.doi.org/10.1109/tase.2011.2163510.

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33

Lassen, Kristian Bisgaard, and Wil M. P. van der Aalst. "Complexity metrics for Workflow nets." Information and Software Technology 51, no. 3 (2009): 610–26. http://dx.doi.org/10.1016/j.infsof.2008.08.005.

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Wu, Zhong, Michelle Baird, Cornelia Mechlen, Peter Hahn, and Jonathan M. Shaffer. "Abstract 320: Development and automation of a streamlined targeted enrichment method for cancer mutation detection." Cancer Research 84, no. 6_Supplement (2024): 320. http://dx.doi.org/10.1158/1538-7445.am2024-320.

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Abstract Next Generation Sequencing (NGS) of DNA is a powerful tool for the detection of genetic variations, including single nucleotide polymorphisms, copy number variation, and small insertions/deletions. Target enrichment technologies enhance DNA sequencing by enabling users to analyze specific regions of interest only, which helps to effectively increase sequencing depth and sample throughput while minimizing cost. However, many targeted DNA library construction workflows are not optimal for routine genetic testing needs due to inconsistent, lengthy workflow. This poses significant challen

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Prisecaru, Oana Otilia. "Resource workflow nets: an approach to workflow modelling and analysis." Enterprise Information Systems 2, no. 2 (2008): 101–20. http://dx.doi.org/10.1080/17517570802072951.

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Favre, Cédric, Dirk Fahland, and Hagen Völzer. "The relationship between workflow graphs and free-choice workflow nets." Information Systems 47 (January 2015): 197–219. http://dx.doi.org/10.1016/j.is.2013.12.004.

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Shen-Gunther, Jane, and Acarizia Easley. "HPV, HBV, and HIV-1 Viral Integration Site Mapping: A Streamlined Workflow from NGS to Genomic Insights of Carcinogenesis." Viruses 16, no. 6 (2024): 975. http://dx.doi.org/10.3390/v16060975.

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Viral integration within the host genome plays a pivotal role in carcinogenesis. Various disruptive mechanisms are involved, leading to genomic instability, mutations, and DNA damage. With next-generation sequencing (NGS), we can now precisely identify viral and host genomic breakpoints and chimeric sequences, which are useful for integration site analysis. In this study, we evaluated a commercial hybrid capture NGS panel specifically designed for detecting three key viruses: HPV, HBV, and HIV-1. We also tested workflows for Viral Hybrid Capture (VHC) and Viral Integration Site (VIS) analysis,

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Patel, Areeba, Felix Hinz, Helin Dogan, et al. "PATH-64. COMPREHENSIVE CNS TUMOUR MOLECULAR DIAGNOSTICS USING THIRD GENERATION SEQUENCING." Neuro-Oncology 25, Supplement_5 (2023): v183. http://dx.doi.org/10.1093/neuonc/noad179.0693.

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Abstract The WHO classification of CNS tumours 2021 recommends reporting a wide range of molecular alterations for WHO-compatible diagnoses. Conventional workflows warrant considerable investment and long turnaround times limited by batching. Nanopore sequencing enables long read sequencing, real-time targeting and simultaneous base modification detection with compact devices. Rapid-CNS2- a rapid, comprehensive adaptive sampling based sequencing pipeline with a turnaround time of 5 days was previously described. The ad-hoc methylation classification model employed by Rapid-CNS2 is limited to M

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YAMAGUCHI, Shingo. "Refactoring Problem of Acyclic Extended Free-Choice Workflow Nets to Acyclic Well-Structured Workflow Nets." IEICE Transactions on Information and Systems E95.D, no. 5 (2012): 1375–79. http://dx.doi.org/10.1587/transinf.e95.d.1375.

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40

Clempner, Julio B. "Classical workflow nets and workflow nets with reset arcs: using Lyapunov stability for soundness verification." Journal of Experimental & Theoretical Artificial Intelligence 29, no. 1 (2015): 43–57. http://dx.doi.org/10.1080/0952813x.2015.1080472.

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41

Pickle, Loni, Andrew Hatch, Gokhan Yavas, et al. "Abstract 4416: Rapid, low-input, targeted NGS workflow for DNA methylation." Cancer Research 84, no. 6_Supplement (2024): 4416. http://dx.doi.org/10.1158/1538-7445.am2024-4416.

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Abstract DNA methylation is a fundamental epigenetic process that regulates human gene expression. In cancer, methylation changes promote proliferation networks and metastasis. Development of biomarkers for methylation will be enabled by flexible, fast, low-input next generation sequencing workflows. We describe the first Ion AmpliSeq™ Methylation targeted panel and protocol on the turn-key Genexus™ Integrated Sequencer as part an ongoing collaboration with Ontario Institute for Cancer Research (OICR) to detect and predict response in early stage breast cancer and improve diagnostics for Black

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Vitale, Silvia R., Floris H. Groenendijk, Ronald van Marion, et al. "TP53 Mutations in Serum Circulating Cell-Free Tumor DNA As Longitudinal Biomarker for High-Grade Serous Ovarian Cancer." Biomolecules 10, no. 3 (2020): 415. http://dx.doi.org/10.3390/biom10030415.

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The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was us

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43

D’Agaro, Edo. "NGS genome annotation profiling using data analysis workflows." Journal of Biotechnology 256 (August 2017): S11. http://dx.doi.org/10.1016/j.jbiotec.2017.06.039.

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44

Bocăneală, Corina. "Workflow nets for flexible manufacturing systems." Annals of the ”Dunarea de Jos” University of Galati. Fascicle II, Mathematics, Physics, Theoretical Mechanics 42, no. 2 (2019): 183–86. http://dx.doi.org/10.35219/ann-ugal-math-phys-mec.2019.2.09.

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Soffer, Pnina, Maya Kaner, and Yair Wand. "Assigning Ontological Meaning to Workflow Nets." Journal of Database Management 21, no. 3 (2010): 1–35. http://dx.doi.org/10.4018/jdm.2010070101.

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A common way to represent organizational domains is the use of business process models. A Workflow-net (WF-net) is an application of Petri Nets (with additional rules) that model business process behavior. However, the use of WF-nets to model business processes has some shortcomings. In particular, no rules exist beyond the general constraints of WF-nets to guide the mapping of an actual process into a net. Syntactically correct WF-nets may provide meaningful models of how organizations conduct their business processes. Moreover, the processes represented by these nets may not be feasible to e

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Tiplea, Ferucio L., and Raluca A. Diaconu. "Petri Net Computers and Workflow Nets." IEEE Transactions on Systems, Man, and Cybernetics: Systems 45, no. 3 (2015): 496–507. http://dx.doi.org/10.1109/tsmc.2014.2347933.

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Chrz�stowski-Wachtel, Piotr, Paweł Findeisen, and Grzegorz Wolny. "Time Distribution in Structural Workflow Nets." Fundamenta Informaticae 85, no. 1-4 (2008): 67–87. https://doi.org/10.3233/fun-2008-851-406.

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Workflows with transition execution times having exponential distributions are considered. The aim is to determine the overall execution time without looking into the reachability space and its analysis using Markov processes. We concentrate on the so called structural workflows, which are represented with Petri nets constructed by means of specific refinement rules. With each refinement rule (sequence, choice, parallelization, loop) we associate formulas which allow to compute the overall execution time distribution. The class of exponential distributions is too narrow to keep the result with

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Sedova, Marina, Alexy Ongpin, Jennifer Burke, et al. "Abstract 764: Fully automated sample-to-report NGS workflow for comprehensive genomic profiling for myeloid neoplasms." Cancer Research 82, no. 12_Supplement (2022): 764. http://dx.doi.org/10.1158/1538-7445.am2022-764.

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Abstract Introduction: Myeloid malignancies are associated with a broad and diverse set of genomic alterations, including SNVs, insertions, deletions and gene fusions. Comprehensive characterization of genetic mutations in hematological disorders currently requires a variety of diagnostic tests and takes multiple days to complete. We developed a fully automated NGS Myeloid Assay that offers an easy to use sample-to-report workflow and the capability for processing up to 8 samples per day. Methods: The Genexus System is comprised of two software linked instruments, the Genexus Purification Syst

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Song, Chen, Margaret R. Heider, Jian Sun, et al. "Abstract 1907: A novel DNA library prep method enables high sensitivity variant detection from matched fresh frozen and FFPE patient tissues." Cancer Research 85, no. 8_Supplement_1 (2025): 1907. https://doi.org/10.1158/1538-7445.am2025-1907.

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Abstract In cancer genomics, a common source of DNA is formalin-fixed, paraffin-embedded (FFPE) tissue from patient surgical samples, where in most cases high quality fresh or frozen tissue samples are not available. FFPE DNA poses many notable challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction methods. It is difficult to obtain libraries with sufficient coverage and the sequencing artifacts arising from damaged DNA bases confound somatic variant detection. Additionally, many laboratories process FFPE tumor samp

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Saunders, Lauren P., James Erickson, Margaret R. Heider, Jian Sun, Adrian Reich, and Ben Lepene. "Abstract 7139: An optimized extraction and library preparation workflow for sensitive mutation detection in clinical cfDNA samples." Cancer Research 85, no. 8_Supplement_1 (2025): 7139. https://doi.org/10.1158/1538-7445.am2025-7139.

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Abstract Monitoring cell-free DNA (cfDNA) - small DNA fragments circulating in the bloodstream - provides valuable insights into various tissues throughout the body and diverse health conditions. cfDNA has been particularly useful in tracking cancer progression, although its low abundance can lead to low mutation copy frequencies, especially in early-stage cancers where limited tumor presence yields minimal cfDNA in circulation. Optimizing molecular biology techniques for maximal cfDNA recovery and purity as well as high NGS library conversion efficiency is essential to improve detection of lo

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