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Programming models to support data science workflows

Authors: Ramón-Cortés Vilarrodona, Cristián

Contributors: University/Department: Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors

Thesis Advisors: Badia Sala, Rosa M. (Rosa Maria), Ejarque Artigas, Jorge

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Distributed computing, High-performance computing, Data science pipelines, Task-ba workflows, Dataflows, Containers (Computer sicience), COMPSs, PyCOMPSs, AutoParallel, Docker, Àrees temàtiques de la UPC::Informàtica

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/669728
https://dx.doi.org/10.5821/dissertation-2117-330142

Methyl•••Methyl Interactions in Proteins: Insights from Structural and Computational Studies.

Authors: Dutta J Sahu AK Jena S et al.

Source: Journal of chemical information and modeling [J Chem Inf Model] 2025 May 12; Vol. 65 (9), pp. 4729-4739. Date of Electronic Publication: 2025 Apr 21.

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 101230060 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-960X (Electronic) Linking ISSN: 15499596 NLM ISO Abbreviation: J Chem Inf Model Subsets: MEDLINE

MeSH Terms: Proteins*/chemistry , Proteins*/metabolism, Models, Molecular ; Quantum Theory ; Protein Conformation

AI-Driven Analysis of Drug Marketing Efficiency: Unveiling FDA Approval to Market Release Dynamics.

Authors: Takefuji Y; Faculty of Data Science, Musashino University, 3-3-3 Ariake Koto-Ku, Tokyo, 135-8181, Japan. takefuji@keio.jp.

Source: The AAPS journal [AAPS J] 2025 Feb 20; Vol. 27 (2), pp. 48. Date of Electronic Publication: 2025 Feb 20.

Publication Type: Journal Article

Journal Info: Publisher: American Association of Pharmaceutical Scientists Country of Publication: United States NLM ID: 101223209 Publication Model: Electronic Cited Medium: Internet ISSN: 1550-7416 (Electronic) Linking ISSN: 15507416 NLM ISO Abbreviation: AAPS J Subsets: MEDLINE

MeSH Terms: Drug Industry*/methods , Drug Industry*/legislation & jurisprudence , Marketing*/methods , United States Food and Drug Administration* , Drug Approval* , Artificial Intelligence*, United States ; Humans ; Time Factors

Evolutionary Insights from Sequence Analysis of Interleukin 17A (IL17A).

Authors: Santos JC; Department of Biological Sciences, College of Liberal Arts and Sciences, St. John's University, Jamaica, Queens, NY, USA. santosj@stjohns.edu.

Source: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2026; Vol. 2983, pp. 397-447.

Publication Type: Journal Article

Journal Info: Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE

MeSH Terms: Interleukin-17*/genetics , Sequence Analysis, DNA*/methods , Computational Biology*/methods , Evolution, Molecular*, Phylogeny ; Humans ; Software ; Sequence Alignment

Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework.

Authors: Saraiva BM Cunha I Brito AD et al.

Source: Nature methods [Nat Methods] 2025 Feb; Vol. 22 (2), pp. 283-286. Date of Electronic Publication: 2025 Jan 02.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE

MeSH Terms: Image Processing, Computer-Assisted*/methods , Microscopy*/methods , Software*, Algorithms ; Humans

Identification of Novel Microcystins Using High-Resolution MS and MSⁿ with Python Code.

Authors: Baliu-Rodriguez D Peraino NJ Premathilaka SH et al.

Source: Environmental science & technology [Environ Sci Technol] 2022 Feb 01; Vol. 56 (3), pp. 1652-1663. Date of Electronic Publication: 2022 Jan 12.

Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 0213155 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1520-5851 (Electronic) Linking ISSN: 0013936X NLM ISO Abbreviation: Environ Sci Technol Subsets: MEDLINE

MeSH Terms: Microcystins*/analysis , Tandem Mass Spectrometry*, Chromatography, Liquid ; Fresh Water ; Harmful Algal Bloom

Development of a Novel Automated Workflow in Fiji ImageJ for Batch Analysis of Confocal Imaging Data to Quantify Protein Colocalization Using Manders Coefficient.

Authors: Aditya V Tambe V Yue W

Source: Bio-protocol [Bio Protoc] 2025 Apr 05; Vol. 15 (7), pp. e5285. Date of Electronic Publication: 2025 Apr 05 (Print Publication: 2025).

Publication Type: Journal Article

Journal Info: Publisher: Bio-protocol LLC Country of Publication: United States NLM ID: 101635102 Publication Model: eCollection Cited Medium: Internet ISSN: 2331-8325 (Electronic) Linking ISSN: 23318325 NLM ISO Abbreviation: Bio Protoc Subsets: PubMed not MEDLINE

Factors Influencing Continued Usage of Intracavernosal injections for Erectile Dysfunction: A Retrospective Analysis.

Authors: Ledesma BR Codrington J Velasquez D et al.

Source: The world journal of men's health [World J Mens Health] 2025 Apr; Vol. 43 (2), pp. 407-414. Date of Electronic Publication: 2024 Sep 23.

Publication Type: Journal Article

Journal Info: Publisher: Korean Society for Sexual Medicine and Andrology Country of Publication: Korea (South) NLM ID: 101596899 Publication Model: Print-Electronic Cited Medium: Print ISSN: 2287-4208 (Print) Linking ISSN: 22874208 NLM ISO Abbreviation: World J Mens Health Subsets: PubMed not MEDLINE

Tutorial on WDK-VENUS: A Streamlined and Modular Workflow for High-Temperature Dynamics and Kinetics of Atom-Diatom Collisions.

Authors: Yang J Li J

Source: ACS physical chemistry Au [ACS Phys Chem Au] 2025 Dec 26; Vol. 6 (1), pp. 1-12. Date of Electronic Publication: 2025 Dec 26 (Print Publication: 2026).

Publication Type: Journal Article

Journal Info: Publisher: American Chemical Society Country of Publication: United States NLM ID: 9918300980006676 Publication Model: eCollection Cited Medium: Internet ISSN: 2694-2445 (Electronic) Linking ISSN: 26942445 NLM ISO Abbreviation: ACS Phys Chem Au Subsets: PubMed not MEDLINE

porE: A code for deterministic and systematic analyses of porosities.

Authors: Trepte K Schwalbe S

Source: Journal of computational chemistry [J Comput Chem] 2021 Apr 05; Vol. 42 (9), pp. 630-643. Date of Electronic Publication: 2021 Jan 28.

Publication Type: Journal Article

Journal Info: Publisher: Wiley Country of Publication: United States NLM ID: 9878362 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-987X (Electronic) Linking ISSN: 01928651 NLM ISO Abbreviation: J Comput Chem Subsets: MEDLINE; PubMed not MEDLINE

A tidal disruption event from an intermediate-mass black hole revealed by comprehensive multi-wavelength observations.

Authors: Wang J Huang M Xue Y et al.

Source: Nature communications [Nat Commun] 2026 Jan 24. Date of Electronic Publication: 2026 Jan 24.

Publication Type: Journal Article

Journal Info: Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE

Ichor: A Python library for computational chemistry data management and machine learning force field development.

Authors: Manchev YT Burn MJ Popelier PLA

Source: Journal of computational chemistry [J Comput Chem] 2024 Dec 15; Vol. 45 (32), pp. 2912-2928. Date of Electronic Publication: 2024 Aug 31.

Publication Type: Journal Article

Journal Info: Publisher: Wiley Country of Publication: United States NLM ID: 9878362 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1096-987X (Electronic) Linking ISSN: 01928651 NLM ISO Abbreviation: J Comput Chem Subsets: MEDLINE; PubMed not MEDLINE

Unveiling livestock trade trends: A beginner's guide to generative AI-powered visualization.

Authors: Takefuji Y; Faculty of Data Science, Musashino University, 3-3-3 Ariake Koto-ku, Tokyo 135-8181, Japan. Electronic address: takefuji@keio.jp.

Source: Research in veterinary science [Res Vet Sci] 2024 Nov; Vol. 180, pp. 105435. Date of Electronic Publication: 2024 Oct 10.

Publication Type: Journal Article

Journal Info: Publisher: British Veterinary Association Country of Publication: England NLM ID: 0401300 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1532-2661 (Electronic) Linking ISSN: 00345288 NLM ISO Abbreviation: Res Vet Sci Subsets: MEDLINE

MeSH Terms: Commerce*/trends , Livestock*, Animal Husbandry/methods ; Animal Husbandry/trends ; Animals ; Japan ; United States ; Artificial Intelligence

Highdicom: a Python Library for Standardized Encoding of Image Annotations and Machine Learning Model Outputs in Pathology and Radiology.

Authors: Bridge CP Gorman C Pieper S et al.

Source: Journal of digital imaging [J Digit Imaging] 2022 Dec; Vol. 35 (6), pp. 1719-1737. Date of Electronic Publication: 2022 Aug 22.

Publication Type: Journal Article; Research Support, N.I.H., Extramural

Journal Info: Publisher: Springer Country of Publication: United States NLM ID: 9100529 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1618-727X (Electronic) Linking ISSN: 08971889 NLM ISO Abbreviation: J Digit Imaging Subsets: MEDLINE

MeSH Terms: Radiology* , Radiology Information Systems*, Humans ; Ecosystem ; Data Curation ; Tomography, X-Ray Computed ; Machine Learning

Assessment of stabilizing feedback control of walking: A tutorial.

Authors: van Dieën JH Bruijn SM Afschrift M

Source: Journal of electromyography and kinesiology : official journal of the International Society of Electrophysiological Kinesiology [J Electromyogr Kinesiol] 2024 Oct; Vol. 78, pp. 102915. Date of Electronic Publication: 2024 Jun 22.

Publication Type: Journal Article

Journal Info: Publisher: Elsevier Country of Publication: England NLM ID: 9109125 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1873-5711 (Electronic) Linking ISSN: 10506411 NLM ISO Abbreviation: J Electromyogr Kinesiol Subsets: MEDLINE

MeSH Terms: Electromyography*/methods , Gait*/physiology , Walking*/physiology, Biomechanical Phenomena/physiology ; Gait Analysis/methods ; Muscle, Skeletal/physiology ; Postural Balance/physiology ; Humans

VizGenie: Toward Self-Refining, Domain-Aware Workflows for Next-Generation Scientific Visualization.

Authors: Biswas A Turton TL Ranasinghe NR et al.

Source: IEEE transactions on visualization and computer graphics [IEEE Trans Vis Comput Graph] 2026 Jan; Vol. 32 (1), pp. 1021-1031.

Publication Type: Journal Article

Journal Info: Publisher: IEEE Computer Society Country of Publication: United States NLM ID: 9891704 Publication Model: Print Cited Medium: Internet ISSN: 1941-0506 (Electronic) Linking ISSN: 10772626 NLM ISO Abbreviation: IEEE Trans Vis Comput Graph Subsets: MEDLINE; PubMed not MEDLINE

Benchmarking Large Language Models for Predictive Modeling in Biomedical Research With a Focus on Reproductive Health.

Authors: Sarwal R Tarca V Dubin C et al.

Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Jul 10. Date of Electronic Publication: 2025 Jul 10.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE

MEG and EEG data analysis with MNE-Python

Authors: Gramfort, Alexandre Luessi, Martin Hamalainen, Matti et al.

Source: Gramfort, A., M. Luessi, E. Larson, D. A. Engemann, D. Strohmeier, C. Brodbeck, R. Goj, et al. 2013. “MEG and EEG data analysis with MNE-Python.” Frontiers in Neuroscience 7 (1): 267. doi:10.3389/fnins.2013.00267. http://dx.doi.org/10.3389/fnins.2013.00267.

Subject Terms: Methods Article, electroencephalography (EEG), magnetoencephalography (MEG), neuroimaging, software, python, open-source

File Description: application/pdf

Relation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872725/pdf/; Frontiers in Neuroscience

Access URL: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879699

From Spreadsheets and Bespoke Models to Enterprise Data Warehouses: GPT-enabled Clinical Data Ingestion into i2b2.

Authors: Wang TD Murphy SN Castro VM et al.

Source: MedRxiv : the preprint server for health sciences [medRxiv] 2025 Apr 19. Date of Electronic Publication: 2025 Apr 19.

Publication Type: Journal Article; Preprint

Journal Info: Country of Publication: United States NLM ID: 101767986 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: medRxiv Subsets: PubMed not MEDLINE

Automated detection of mouth opening in newborn infants.

Authors: Zeng G Ahn YA Leung TS et al.

Source: Behavior research methods [Behav Res Methods] 2025 Oct 27; Vol. 57 (12), pp. 322. Date of Electronic Publication: 2025 Oct 27.

Publication Type: Journal Article

Journal Info: Publisher: Springer Country of Publication: United States NLM ID: 101244316 Publication Model: Electronic Cited Medium: Internet ISSN: 1554-3528 (Electronic) Linking ISSN: 1554351X NLM ISO Abbreviation: Behav Res Methods Subsets: MEDLINE

MeSH Terms: Mouth*/physiology , Infant Behavior*, Humans ; Infant, Newborn ; Female ; Male ; Support Vector Machine ; Video Recording ; Facial Expression ; Algorithms ; Gestures