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Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.

التفاصيل البيبلوغرافية
العنوان: Using interactive Jupyter Notebooks and BioConda for FAIR and reproducible biomolecular simulation workflows.
المؤلفون: Genís Bayarri, Pau Andrio, Josep Lluís Gelpí, Adam Hospital, Modesto Orozco
المصدر: PLoS Computational Biology, Vol 20, Iss 6, p e1012173 (2024)
بيانات النشر: Public Library of Science (PLoS), 2024.
سنة النشر: 2024
المجموعة: LCC:Biology (General)
مصطلحات موضوعية: Biology (General), QH301-705.5
الوصف: Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations. Workflows can be launched with myBinder or easily installed in a local system. The collection of notebooks aims to provide a compilation of demonstration workflows, and it is continuously updated and expanded with examples using new methodologies and tools.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1553-734X
1553-7358
Relation: https://doaj.org/toc/1553-734X; https://doaj.org/toc/1553-7358
DOI: 10.1371/journal.pcbi.1012173
URL الوصول: https://doaj.org/article/3d06dcac195746eab6375d2b780d6aec
رقم الأكسشن: edsdoj.3d06dcac195746eab6375d2b780d6aec
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:1553734X
15537358
DOI:10.1371/journal.pcbi.1012173