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ssbio: A Python Framework for Structural Systems Biology [article]

Nathan Mih, Elizabeth Brunk, Ke Chen, Edward Catoiu, Anand Sastry, Erol Kavvas, Jonathan M Monk, Zhen Zhang, Bernhard O Palsson
2017 bioRxiv   pre-print
Interactive notebooks can be launched using Binder at https://mybinder.org/v2/gh/SBRG/ssbio/master?filepath=Binder.ipynb.  ...  Documentation and Jupyter notebook tutorials are available at http://ssbio.readthedocs.io/en/latest/.  ...  Laurence Yang, Yara Seif, JC Lachance, and Jared Broddrick for insight into desired functionalities of the package. We would also like to thank Marc Abrams for proofreading of the manuscript.  ... 
doi:10.1101/165506 fatcat:4x3chxxgabbufb2cfvsketjsjy

OSSCAR, an open platform for collaborative development of computational tools for education in science [article]

Dou Du and Taylor J. Baird and Sara Bonella and Giovanni Pizzi
2022 arXiv   pre-print
In this paper we present the Open Software Services for Classrooms and Research (OSSCAR) platform.  ...  Examples from courses in the domains of physics, chemistry, and materials science are shown to demonstrate the style and level of interactivity of typical applications.  ...  We acknowledge CECAM for dedicated OSSCAR dissemination activities.  ... 
arXiv:2203.12019v1 fatcat:a4yhbgwokrd2nhhbkbbr6djrsa

BioExcel-2 Deliverable 2.3 – First release of demonstration workflows

Adam Hospital, Genis Bayarri, Stian Soiland-Reyes, Jose Lluis Gelpi, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier, Rosa Maria Badia, Rodrigo Vargas, Alexandre Bonvin
2020 Zenodo  
The section is divided in three subsections, according to different workflow categories: Jupyter Notebook tutorials, library versatility tutorials, and pre-exascale demonstration workflows.  ...  The Jupyter Notebook tutorials illustrate the power of the BioExcel Building Blocks software library through biomolecular simulation tools interoperability, with examples on how to parameterize a small  ...  This graphical interface makes Jupyter Notebooks perfect for educational purposes with tutorials made of interactive programming code accompanied by text information and/or documentation, versatile charts  ... 
doi:10.5281/zenodo.4540432 fatcat:srr5ywi5x5hbvecqlfxqngeapi

Appyters: turning Jupyter Notebooks into data-driven web apps

Daniel J.B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman (+12 others)
2021 Patterns  
Jupyter Notebooks have transformed the communication of data analysis pipelines by facilitating a modular structure that brings together code, markdown text, and interactive visualizations.  ...  Here, we extended Jupyter Notebooks to broaden their accessibility with Appyters. Appyters turn Jupyter Notebooks into fully functional standalone web-based bioinformatics applications.  ...  Another example is Single Cell Explorer, a single-cell RNA-seq (scRNA-seq) data analysis environment. 3 NGLview is a Jupyter widget developed to view molecular structures inside Jupyter Notebooks. 4  ... 
doi:10.1016/j.patter.2021.100213 pmid:33748796 pmcid:PMC7961182 fatcat:n2xqpmun45dddfqn756hagj72m

AiiDAlab – an ecosystem for developing, executing, and sharing scientific workflows

Aliaksandr V. Yakutovich, Kristjan Eimre, Ole Schütt, Leopold Talirz, Carl S. Adorf, Casper W. Andersen, Edward Ditler, Dou Du, Daniele Passerone, Berend Smit, Nicola Marzari, Giovanni Pizzi (+1 others)
2021 Computational materials science  
Computational workflows can be bundled together with user-friendly graphical interfaces and made available through the AiiDAlab app store.  ...  A B S T R A C T Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science.  ...  We acknowledge PRACE for awarding us simulation time on Piz Daint at CSCS (project ID 2016153543) and Marconi at CINECA (project ID 2016163963), and the support of Swiss Platform for Advanced Scientific  ... 
doi:10.1016/j.commatsci.2020.110165 fatcat:yj5fdrpjtbc3vholgf2t6eoiqu

BioExcel-2 Deliverable 2.1 – State of the Art and Initial Roadmap

Adam Hospital, Stian Soiland-Reyes, Josep Lluís Gelpí, Pau Andrio, Daniele Lezzi, Sarah Butcher, Ania Niewielska, Yvonne Westermaier
2019 Zenodo  
notebooks.  ...  Workflow managers, especially the ones focused on the HPC and exascale supercomputers are also reviewed, presenting a collaboration with the Molecular Science Software Institute (MolSSI).  ...  Jupyter Notebooks & Binder Jupyter Notebooks are (2015, v1.0) are an extension of the iPython (interactive Python) initiative, a command shell for interactive computing in multiple programming languages  ... 
doi:10.5281/zenodo.4604607 fatcat:u3yplgrepzfytda2zwzu37phge

AiiDAlab – an ecosystem for developing, executing, and sharing scientific workflows [article]

Aliaksandr V. Yakutovich, Kristjan Eimre, Ole Schütt, Leopold Talirz, Carl S. Adorf, Casper W. Andersen, Edward Ditler, Dou Du, Daniele Passerone, Berend Smit, Nicola Marzari, Giovanni Pizzi (+1 others)
2020 arXiv   pre-print
Computational workflows can be bundled together with user-friendly graphical interfaces and made available through the AiiDAlab app store.  ...  Cloud platforms allow users to execute tasks directly from their web browser and are a key enabling technology not only for commerce but also for computational science.  ...  We acknowledge PRACE for awarding us simulation time on Piz Daint at CSCS (project ID 2016153543) and Marconi at CINECA (project ID 2016163963), and the support of Swiss Platform for Advanced Scientific  ... 
arXiv:2010.02731v1 fatcat:big7wvp6dnb7hg33hthi76gbli

SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking

Samuel Murail, Sjoerd J. de Vries, Julien Rey, Gautier Moroy, Pierre Tufféry
2021 Frontiers in Molecular Biosciences  
In silico assessment of protein receptor interactions with small ligands is now part of the standard pipeline for drug discovery, and numerous tools and protocols have been developed for this purpose.  ...  The SeamDock online service integrates different docking tools in a common framework that allows ligand global and/or local docking and a hierarchical approach combining the two for easy interaction site  ...  ACKNOWLEDGMENTS We are grateful to the authors of NGL view, Rdkit, Autodock, Autodock Vina, Qvina, and Smina for making their methods available for implementation in the SeamDock server and docking_py  ... 
doi:10.3389/fmolb.2021.716466 pmid:34604303 pmcid:PMC8484321 fatcat:ahts2gv6n5durc7mdxxv6vldxe

Towards Molecular Simulations that are Transparent, Reproducible, Usable By Others, and Extensible (TRUE) [article]

Matthew W. Thompson, Justin B. Gilmer, Ray A. Matsumoto, Co D. Quach, Parashara Shamaprasad, Alexander H. Yang, Christopher R. Iacovella, Clare McCabe, Peter T. Cummings
2020 arXiv   pre-print
To address the issue of reproducibility and to provide tools for computational screening, we have been developing the open-source Molecular Simulation and Design Framework (MoSDeF) software suite.  ...  , requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation.  ...  In a single Python script (or Jupyter notebook), each step of a molecular simulation workflow (generation of particle coordinates, application of a force field, running of a molecular simulation, and analysis  ... 
arXiv:2003.02031v2 fatcat:fgzrnt3lf5fcdmr5hsps33fs4y

Molecular docking and machine learning analysis of Abemaciclib in colon cancer

Jose Liñares-Blanco, Cristian R. Munteanu, Alejandro Pazos, Carlos Fernandez-Lozano
2020 BMC Molecular and Cell Biology  
We observed four interactions of interest: GLTP - Nilotinib, PTPRN - Venetoclax, VEGFA - Venetoclax and FABP6 - Abemaciclib.  ...  For these reasons, we propose the validation of the drug Abemaciclib for the treatment of colon cancer.  ...  The sections of the web included interactive tables, plots, pivot table and 3D structures widgets (generated with python jupyter notebooks based on HTML, plotly -https://plotly. com, ipywidgets -https:  ... 
doi:10.1186/s12860-020-00295-w pmid:32640984 fatcat:4lk64hvpfbfyffzqnp3k3ba46e

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations

Richard Gowers, Max Linke, Jonathan Barnoud, Tyler Reddy, Manuel Melo, Sean Seyler, Jan Domański, David Dotson, Sébastien Buchoux, Ian Kenney, Oliver Beckstein
2016 Proceedings of the 15th Python in Science Conference   unpublished
The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks,  ...  especially together with molecular visualization provided by nglview and time series analysis with pandas.  ...  DLD was in part supported by a Molecular  ... 
doi:10.25080/majora-629e541a-00e fatcat:n74rsq6epzhj7gx7xdh4ldub7y

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations

Richard Gowers, Max Linke, Jonathan Barnoud, Tyler Reddy, Manuel Melo, Sean Seyler, Jan Domá, David Dotson, Sébastien Buchoux, Ian Kenney, Oliver Beckstein
2016 PROC. OF THE 15th PYTHON IN SCIENCE CONF   unpublished
The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks,  ...  especially together with molecular visualization provided by nglview and time series analysis with pandas.  ...  DLD was in part supported by a Molecular  ... 
fatcat:m3cueqzeyjdjddh2x3erzho72i

Force field parameters for Fe2+4S2-4 clusters of dihydropyrimidine dehydrogenase, the 5-fluorouracil cancer drug deactivation protein: a step towards in silico pharmacogenomics studies [article]

Maureen Bilinga Tendwa, Lorna Chebon-Bore, Kevin Lobb, Thommas Mutemi Musyoka, Ozlem Tastan Bishop
2021 bioRxiv   pre-print
We previously proposed combined molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins.  ...  However, the presence of Fe2+4S2-4 clusters in DPD poses a challenge for such in silico studies.  ...  Additional analytical approach Molecular graphics were then prepared with PyMOL v1.8 [91] , Anaconda 4.3.1 Jupyter Notebooks [92] , and various open-source Python libraries, such as matplotlib [93]  ... 
doi:10.1101/2021.04.20.440516 fatcat:5gctzagaq5d5pjedkfkkxsasca

Force Field Parameters for Fe2+4S2−4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies

Maureen Bilinga Tendwa, Lorna Chebon-Bore, Kevin Lobb, Thommas Mutemi Musyoka, Özlem Tastan Bishop
2021 Molecules  
We previously proposed combining molecular dynamics (MD) and dynamic residue network (DRN) analysis to decipher the molecular mechanisms of missense mutations in other proteins.  ...  However, the presence of Fe2+4S2−4 clusters in DPD poses a challenge for such in silico studies.  ...  Acknowledgments: The authors thank to the Center for High Performance Computing (CHPC), South Africa, for computational clusters and RUBi colleagues for their constructive discussions.  ... 
doi:10.3390/molecules26102929 pmid:34069161 pmcid:PMC8156676 fatcat:4hzbfptajvcztfd5qfoeahtsdu

OpenPathSampling: A Python framework for path sampling simulations. I. Basics [article]

David W.H. Swenson, Jan-Hendrik Prinz, Frank Noe, John D. Chodera, Peter G. Bolhuis
2018 bioRxiv   pre-print
Interfaces to OpenMM and an internal dynamics engine for simple models are provided in the initial release, but new molecular simulation packages can easily be added.  ...  Here, we introduce an easy-to-use Python framework called OpenPathSampling (OPS) that facilitates path sampling for (bio)molecular systems with minimal effort and yet is still extensible.  ...  Up-to-date versions of the examples are available as interactive Jupyter notebooks on the website http://openpathsampling.org. .  ... 
doi:10.1101/351494 fatcat:j5httxt66zhkldu6evmulycmgy
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