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Four Steps Towards Sound Business Process Models [chapter]

Juliane Dehnert
2003 Lecture Notes in Computer Science  
The key concept for the proposed process model is the use of pragmatic correctness criteria, namely relaxed soundness and robustness.  ...  The proposed process model supports this refinement step, applying methods from controller synthesis.  ...  Based on these notions, it is now possible to express non-controllable choice robustness of a WF-system. Definition 5.5 (Non-controllable choice robustness).  ... 
doi:10.1007/978-3-540-40022-6_4 fatcat:o3bg66egyrfx5dwva65j3mfuey

BRIDGING THE GAP BETWEEN BUSINESS MODELS AND WORKFLOW SPECIFICATIONS

JULIANE DEHNERT, WIL M. P. VAN DER AALST
2004 International Journal of Cooperative Information Systems  
The methodology consists of five steps and is illustrated using event-driven process chains as a business process modeling language and Petri nets as the workflow specification language.  ...  This paper presents a methodology to bridge the gap between business process modeling and workflow specification.  ...  Based on these notions, it is now possible to express non-controllable choice robustness of a WF-system. Definition 16 (Non-controllable choice robustness).  ... 
doi:10.1142/s0218843004000973 fatcat:bdgal4t6yrafroajlz5hni4ire

Security Provisioning in Pervasive Environments Using Multi-objective Optimization [chapter]

Rinku Dewri, Indrakshi Ray, Indrajit Ray, Darrell Whitley
2008 Lecture Notes in Computer Science  
We propose the use of workflow profiles to capture the contexts in which a communication channel is used in a pervasive environment.  ...  Our approach is based on the formulation of a set of constrained multi-objective optimization problems to minimize the residual damage and the cost of security provisioning.  ...  The views and conclusions contained in this document are those of the authors and should not be interpreted as representing official policies of the U.S.  ... 
doi:10.1007/978-3-540-88313-5_23 fatcat:aisqsybj7ngfpmntegcibp722q

Transactional Workflows or Workflow Transactions? [chapter]

Paul Grefen
2002 Lecture Notes in Computer Science  
The fact that these processes require robustness and clear semantics has generally been observed and has lead to the combination of workflow and transaction concepts.  ...  To deal with this problem, we describe a clear taxonomy of transactional workflow models, based on the relation between workflow and transaction concepts.  ...  Maarten Fokkinga is acknowledged for his assistance with respect to language concepts and his feedback on the draft version of this paper.  ... 
doi:10.1007/3-540-46146-9_7 fatcat:5parvw4y25hxndebbog54k3spe

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

Lars M.T. Eijssen, Varshna S. Goelela, Thomas Kelder, Michiel E. Adriaens, Chris T. Evelo, Marijana Radonjic
2015 BMC Genomics  
This module can be used together with existing modules for statistical and pathway analysis to provide a full workflow for Illumina gene expression data analysis.  ...  The module can be used as a starting point for statistical evaluation and pathway analysis provided on the website or to generate processed input data for a broad range of applications in life sciences  ...  Funding bodies did not have any role in study design, collection, analysis and interpretation of data, in the writing of the manuscript, and in the decision to submit the manuscript for publication.  ... 
doi:10.1186/s12864-015-1689-8 pmid:26122086 pmcid:PMC4486126 fatcat:is5jugdo7bfufcx3vdryzulhfe

Process mining: a research agenda

W.M.P. van der Aalst, A.J.M.M. Weijters
2004 Computers in industry (Print)  
In this paper, we try to put the topic of process mining into context, discuss the main issues around process mining, and finally we introduce the papers in this special issue.  ...  Technologies such as Workflow Management (WFM), Enterprise Application Integration (EAI), Enterprise Resource Planning (ERP), and Web Services (WS) typically focus on the realization of IT support rather  ...  However, many processes cannot be expressed in terms of a free-choice net.  ... 
doi:10.1016/j.compind.2003.10.001 fatcat:areplhnmu5cnxcxocifypwqpbi

Fast reconstruction of compact context-specific metabolic networks via integration of microarray data [article]

Maria Pires Pacheco, Thomas Sauter
2014 arXiv   pre-print
Barcode uses prior knowledge on the intensity distribution of each probe set for a given microarray platform to segregate between expressed genes and non-expressed genes.  ...  This will allow the use of metabolic modelling as routine process for the analysis of microarray data e.g. in the field of personalized medicine.  ...  The research was funded by the Life Sciences Research Unit, University of Luxembourg.  ... 
arXiv:1407.6534v1 fatcat:jh4ojztwkrdijbqj43mdirl3qi

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation

Jake J. Reske, Mike R. Wilson, Ronald L. Chandler
2020 Epigenetics & Chromatin  
We further show this workflow identifies sites of differential chromatin accessibility that correlate with gene expression and is sensitive to differential analysis using negative controls.  ...  ATAC-seq users should be aware of the interpretations of potential bias within experimental data and the assumptions of the normalization method implemented.  ...  Generalized ATAC-seq workflow for differential chromatin accessibility analysis Various studies have described ATAC-seq quality control and data processing for non-computational scientists, but few emphasize  ... 
doi:10.1186/s13072-020-00342-y pmid:32321567 fatcat:pwewvgfotvfdtceljdalqbskk4

Infectious Disease Metagenomics: Error Mitigation and Best Practices for the Clinical Routine Use of Metagenomic Sequencing

Nur A Hasan, Huai Li, Brian Fanelli, Arne Materna, Manoj Dadlani, Rita R Colwell
2019 Journal of Biomolecular Techniques  
The use of internal standards, including positive and negative controls are an important part of quality control.  ...  Despite its potential for clinical microbiology, many laboratories are challenged by the method's disruptive effect on traditional lab workflows and by the complexities inherent to establishing a robust  ...  Overall, these findings illustrate the importance of utilizing controls at multiple stages of the process, to better assess the impact of the findings of any human samples.  ... 
pmid:31892891 pmcid:PMC6936895 fatcat:nw2yugjlbrhchi4dlzge5xhlbe

Understanding approaches for web service composition and execution

Vikas Agarwal, Girish Chafle, Sumit Mittal, Biplav Srivastava
2008 Proceedings of the 1st Bangalore annual Compute conference on - Compute '08  
Of particular interest is the Web Service Composition and Execution (WSCE) process -the creation of a workflow that realizes the functionality of a new service and its subsequent deployment and execution  ...  To this end, we present an analysis that includes formalization of the WSCE process, a classification of existing solutions into four distinct categories (approaches), and an in-depth evaluation of these  ...  ., OWL expression for functional specification and Quality-of-service (QoS) expression for specifying non-functional parameters.  ... 
doi:10.1145/1341771.1341773 dblp:conf/compute/AgarwalCMS08 fatcat:qppqfssivbfaxfl4aknsajsksy

BeadArray Expression Analysis Using Bioconductor

Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch, Fran Lewitter
2011 PLoS Computational Biology  
Illumina whole-genome expression BeadArrays are a popular choice in gene profiling studies.  ...  The key steps of importing data, performing quality assessments, preprocessing, and annotation in the common setting of assessing differential expression in designed experiments will be covered.  ...  Acknowledgments We thank Sean Davis for help on retrieving MAQC data from GEO, James Hadfield and Michelle Osbourne from the Cancer Research UK Cambridge Research Institute for generating the HT-12 data  ... 
doi:10.1371/journal.pcbi.1002276 pmid:22144879 pmcid:PMC3228778 fatcat:m6eamfhn2fbfxnz6h6bdjvugja

The BioVel Project: Robust phylogenetic workflows running on the GRID

Saverio Vicario, Bachir Balech, Giacinto Donvito, Pasquale Notarangelo, Graziano Pesole
2012 EMBnet journal  
Acknowledgements We would like to thanks FP7 funding that with the grant 283359 made possible this work  ...  the system, and in same time non-expert scientists to use those services.  ...  Expressing the high level formalization of the algorithm in a workflow language, allows scientists interested in setting up algorithm's parameters but not expert in grid technology to improve and update  ... 
doi:10.14806/ej.18.b.557 fatcat:cz5xycecsrepxdiaiueh6szwem

An Efficient Robust Optimization Workow using Multiscale Simulation and Stochastic Gradients

Rafael J. de Moraes, Rahul-Mark Fonseca, Mircea A. Helici, Arnold W. Heemink, Jan Dirk Jansen
2018 Journal of Petroleum Science and Engineering  
In the workflow, the construction of the basis fuctions is performed at an offline stage and they are not reconstructed/updated throughout the optimization process.  ...  We present an efficient workflow that combines multiscale (MS) forward simulation and stochastic gradient computation -MS-StoSAG -for the optimization of well controls applied to waterflooding under geological  ...  The authors would like to thank Dr. Hadi Hajibeygi for useful discussions related to multiscale simulation.  ... 
doi:10.1016/j.petrol.2018.09.047 fatcat:mduxcpqku5dntnrubi52scxuau

Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis

Wei-Feng Guo, Xiangtian Yu, Qian-Qian Shi, Jing Liang, Shao-Wu Zhang, Tao Zeng
2021 PLoS Computational Biology  
By widely comparing analysis of existing SSC analysis workflows, we provided the following recommendations and banchmarking workflows.  ...  Here, we conducted a performance assessment for 16 SSC analysis workflows by using the combination of 4 sample-specific network reconstruction methods and 4 representative structural control methods.  ...  Note 3: Robustness of network structural control methods for different reference networks Besides, to comprehensively evaluate the robustness of structural control methods when different reference networks  ... 
doi:10.1371/journal.pcbi.1008962 pmid:33956788 pmcid:PMC8130943 fatcat:pyrrznslr5cbjlm2uozdqddr3u

Robust summarization and inference in proteome-wide label-free quantification [article]

Adriaan Sticker, Ludger Goeminne, Lennart Martens, Lieven Clement
2019 bioRxiv   pre-print
AbstractLabel-Free Quantitative mass spectrometry based workflows for differential expression (DE) analysis of proteins impose important challenges on the data analysis due to peptide-specific effects  ...  processing.  ...  Acknowledgments We thank the students of the Statistical Genomics course  ... 
doi:10.1101/668863 fatcat:ztj3zwh7wbfw7bb43zmqeqewc4
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