Search Results - Example Software Workflow

A novel workflow utilizing open-source software tools in the environmental fate studies: The example of imatinib biotransformation by Tkalec, Žiga, Negreira, Noelia, López de Alda, Miren, Barceló, Damià, Kosjek, Tina

“…) as an example, we developed an efficient workflow to describe IMA biodegradation with activated sludge…”
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Watchdog – a workflow management system for the distributed analysis of large-scale experimental data by Kluge, Michael, Friedel, Caroline C.

“… To support these analyses, a number of workflow management systems (WMSs) have been developed to allow automated execution of corresponding analysis workflows…”
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AmphoraNet: The webserver implementation of the AMPHORA2 metagenomic workflow suite by Kerepesi, Csaba, Bánky, Dániel, Grolmusz, Vince

“… The program suite AMPHORA and its workflow version are examples of publicly available software that yields reliable phylogenetic results for metagenomic data…”
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Intelligent Workflow and Software for Non-Target Analysis of Complex Samples Using a Mixture of Toxic Transformation Products of Unsymmetrical Dimethylhydrazine as an Example by Sholokhova, Anastasia Yu, Matyushin, Dmitriy D., Grinevich, Oksana I., Borovikova, Svetlana A., Buryak, Aleksey K.

“… This is quite an unreliable approach. It was demonstrated that a newly proposed artificial intelligence-based workflow allows for the proposal of structures of UDMH transformation products with a greater…”
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Watchdog - a workflow management system for the distributed analysis of large-scale experimental data by Kluge, Michael, Friedel, Caroline C.

“… To support these analyses, a number of workflow management systems (WMSs) have been developed to allow automated execution of corresponding analysis workflows…”
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Changes in MRI Workflow of Multiple Sclerosis after Introduction of an AI-Software: A Qualitative Study by Rathmann, Eiko, Hemkemeier, Pia, Raths, Susan, Grothe, Matthias, Mankertz, Fiona, Hosten, Norbert, Flessa, Steffen

“…The purpose of this study was to explore the effects of the integration of machine learning into daily radiological diagnostics, using the example of the machine learning software mdbrain…”
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Matlab/R workflows to assess critical choices in Global Sensitivity Analysis using the SAFE toolbox by Noacco, Valentina, Sarrazin, Fanny, Pianosi, Francesca, Wagener, Thorsten

“…). The present paper focuses on the implementation of GSA and provides a set of workflow scripts to assess the critical choices that GSA users need to make before and while executing GSA…”
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Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework by Jagtap, Pratik D, Johnson, James E, Onsongo, Getiria, Sadler, Fredrik W, Murray, Kevin, Wang, Yuanbo, Shenykman, Gloria M, Bandhakavi, Sricharan, Smith, Lloyd M, Griffin, Timothy J

“… Using analysis of whole human saliva as an example, we demonstrate Galaxy’s flexibility through the creation of a modular workflow incorporating…”
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Processing strategies and software solutions for data-independent acquisition in mass spectrometry by Bilbao, Aivett, Varesio, Emmanuel, Luban, Jeremy, Strambio-De-Castillia, Caterina, Hopfgartner, Gérard, Müller, Markus, Lisacek, Frédérique

“…Data‐independent acquisition (DIA) offers several advantages over data‐dependent acquisition (DDA) schemes for characterizing complex protein digests analyzed…”
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Automated Image Processing Workflow for Morphological Analysis of Fluorescence Microscopy Cell Images by Voigt, Sven P., Ravikumar, K., Basu, Bikramjit, Kalidindi, Surya R.

“… This study presents a novel workflow for automated analysis of fluorescence microscopy images, which benefits from running multiple segmentation workflows and combining them to produce the best final segmentation…”
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sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data by Kuzniar, Arnold, Maassen, Jason, Verhoeven, Stefan, Santuari, Luca, Shneider, Carl, Kloosterman, Wigard P., de Ridder, Jeroen

“… We present sv-callers , a highly portable workflow that enables parallel execution of multiple SV detection tools, as well as provide users with example analyses of detected SV callsets in a Jupyter Notebook…”
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Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes by Randall, Ricardo S, Jourdain, Claire, Nowicka, Anna, Kaduchová, Kateřina, Kubová, Michaela, Ayoub, Mohammad A., Schubert, Veit, Tatout, Christophe, Colas, Isabelle, Kalyanikrishna, Desset, Sophie, Mermet, Sarah, Boulaflous-Stevens, Aurélia, Kubalová, Ivona, Mandáková, Terezie, Heckmann, Stefan, Lysak, Martin A., Panatta, Martina, Santoro, Raffaella, Schubert, Daniel, Pecinka, Ales, Routh, Devin, Baroux, Célia

“… Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data…”
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Simplifying the development of portable, scalable, and reproducible workflows by Piccolo, Stephen R, Ence, Zachary E, Anderson, Elizabeth C, Chang, Jeffrey T, Bild, Andrea H

“…Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely…”
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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Mukhaleva, Elizaveta, Manookian, Babgen, Chen, Hanyu, Sivaraj, Indira R, Ma, Ning, Wei, Wenyuan, Urbaniak, Konstancja, Gogoshin, Grigoriy, Bhattacharya, Supriyo, Vaidehi, Nagarajan, Rodin, Andrei S, Branciamore, Sergio

“…Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In…”
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Virtual reality-integrated workflow in BIM-enabled projects collaboration and design review: a case study by Zaker, Reza, Coloma, Eloi

“…Introduction A successful project delivery based on building information modeling (BIM) methods is interdependent on an efficient collaboration. This relies…”
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A New Open-Source Software to Help Design Models for Automatic 3D Point Cloud Classification in Coastal Studies by Pellerin Le Bas, Xavier, Froideval, Laurent, Mouko, Adan, Conessa, Christophe, Benoit, Laurent, Perez, Laurent

“…This study introduces a new software, cLASpy_T, that helps design models for the automatic 3D point cloud classification of coastal environments…”
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In Silico Modeling Method for Computational Aquatic Toxicology of Endocrine Disruptors: A Software-Based Approach Using QSAR Toolbox by Bohlen, Marie-Léonie, Jeon, Hyun Pyo, Kim, Young Jun, Sung, Baeckkyoung

“…Computational analyses of toxicological processes enables high-throughput screening of chemical substances and prediction of their endpoints in biological…”
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Code2graph: Automatic Generation of Static Call Graphs for Python Source Code by Gharibi, Gharib, Tripathi, Rashmi, Lee, Yugyung

“…A static call graph is an imperative prerequisite used in most interprocedural analyses and software comprehension tools…”
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Enhancing FAIRdata by providing digital workflows from data generation to the publication of data: an open source approach described for cyclic voltammetry by Herrmann, David, Hodapp, Patrick, Starman, Martin, Huang, Pei-Chi, Lin, Chia-Lin, Le, Lan B. Q, Fischer, Tillmann G, Bizzarri, Claudia, Röse, Philipp, Oppel, Niklas, Klar, Jochen, Tremouilhac, Pierre, Holzhauer, Laura, Herres-Pawlis, Sonja, Hoffmann, Alexander, Seitz, Tobias, Dorn, Alrik, Zeitler, Kirsten, Jung, Nicole, Bräse, Stefan

“… The presented workflow includes concepts, software and infrastructure that can be used to support the whole data life cycle from the measurement of data to the publication of data and metadata in repositories…”
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SGTools: a suite of tools for processing and analyzing large data sets from in situ X‐ray scattering experiments by Zhao, Nie, Yang, Chunming, Bian, Fenggang, Guo, Daoyou, Ouyang, Xiaoping

“… However, data processing software for in situ experiments is relatively rare, especially for grazing‐incidence small‐angle X‐ray scattering (GISAXS…”
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