A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
ssbio: A Python Framework for Structural Systems Biology
[article]
2017
bioRxiv
pre-print
Preserved Fulltext
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]
2022
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2020
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
Patterns
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
Computational materials science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2019
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2021
Frontiers in Molecular Biosciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2020
arXiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Other Versions
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
2020
BMC Molecular and Cell Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2016
Proceedings of the 15th Python in Science Conference
unpublished
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2016
PROC. OF THE 15th PYTHON IN SCIENCE CONF
unpublished
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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]
2021
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
Molecules
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 16 results