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Compatibility with google colab
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gbayarri committed May 6, 2024
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84 changes: 84 additions & 0 deletions CITATION.cff
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# YAML 1.2
---
abstract: "BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments."
authors:
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Andrio"
given-names: "Pau"
orcid: "https://orcid.org/0000-0003-2116-3880"
-
affiliation: "Institute for Research in Biomedicine (IRB Barcelona)"
family-names: "Hospital"
given-names: "Adam"
orcid: "https://orcid.org/0000-0002-8291-8071"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Conejero"
given-names: "Javier"
orcid: "https://orcid.org/0000-0001-6401-6229"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Jordà"
given-names: "Luis"
orcid: "https://orcid.org/0000-0002-9407-9703"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Del Pino"
given-names: "Marc"
orcid: "https://orcid.org/0000-0001-5565-7577"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Laia"
given-names: "Codó"
orcid: "https://orcid.org/0000-0002-6797-8746"
-
affiliation: "School of computer Science, the University of Manchester"
family-names: Werkhoven
given-names: Ben
name-particle: van
orcid: "https://orcid.org/0000-0002-7508-3272"
-
affiliation: "University of Manchester (UOM)"
family-names: "Soiland-Reyes"
given-names: "Stian"
orcid: "https://orcid.org/0000-0001-9842-9718"
-
affiliation: "University of Manchester (UOM)"
family-names: "Goble"
given-names: "Carole"
orcid: "https://orcid.org/0000-0003-1219-2137"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Lezzi"
given-names: "Daniele"
orcid: "https://orcid.org/0000-0001-5081-7244"
-
affiliation: "Barcelona Supercomputing Center (BSC)"
family-names: "Rosa M"
given-names: "Badia"
orcid: "https://orcid.org/0000-0003-2941-5499"
-
affiliation: "Institute for Research in Biomedicine (IRB Barcelona), University of Barcelona (UB)"
family-names: "Orozco"
given-names: "Modesto"
orcid: "https://orcid.org/0000-0002-8608-3278"
-
affiliation: "Barcelona Supercomputing Center (BSC), University of Barcelona (UB)"
family-names: "Gelpí"
given-names: "Josep Ll."
orcid: "https://orcid.org/0000-0002-0566-7723"
email: "gelpi@ub.edu"

cff-version: "1.2.0"
date-released: "2019-09-10"
keywords:
- "BioExcel"
- "BioBB"
- "Bioinformatics"
- "Computational Biology"
- "Biomolecular Workflows"
license: "Apache-2.0"
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/bioexcel/biobb"
title: "BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows"
10 changes: 7 additions & 3 deletions README.md
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[![](https://readthedocs.org/projects/biobb-wf-protein-complex-md-setup/badge/?version=latest)](https://biobb-wf-protein-complex-md-setup.readthedocs.io/en/latest/?badge=latest)
[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_protein-complex_md_setup/HEAD?labpath=biobb_wf_protein-complex_md_setup%2Fnotebooks%2Fbiobb_Protein-Complex_MDsetup_tutorial.ipynb)
[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_protein-complex_md_setup/blob/main/biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb)

# Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Expand Down Expand Up @@ -47,16 +48,19 @@ Click here to [view tutorial in Read the Docs](https://biobb-wf-protein-complex-

Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_protein-complex_md_setup/HEAD?labpath=biobb_wf_protein-complex_md_setup%2Fnotebooks%2Fbiobb_Protein-Complex_MDsetup_tutorial.ipynb)

Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_protein-complex_md_setup/blob/main/biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb)


***

## Version
2023.3
2024.1

## Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).

* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)

Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
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Expand All @@ -23,4 +23,32 @@ a:visited { color:#9e8830; }
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dl.first.docutils {

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$('.wy-side-nav-search .icon.icon-home').html('<img src="' + path + '_static/logo.png" class="logo" alt="Logo">');
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10 changes: 7 additions & 3 deletions biobb_wf_protein-complex_md_setup/docs/source/readme.md
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[![](https://readthedocs.org/projects/biobb-wf-protein-complex-md-setup/badge/?version=latest)](https://biobb-wf-protein-complex-md-setup.readthedocs.io/en/latest/?badge=latest)
[![](https://img.shields.io/badge/launch-myBinder-579ACA.svg?logo=data:image/png;base64,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)](https://mybinder.org/v2/gh/bioexcel/biobb_wf_protein-complex_md_setup/HEAD?labpath=biobb_wf_protein-complex_md_setup%2Fnotebooks%2Fbiobb_Protein-Complex_MDsetup_tutorial.ipynb)
[![](https://img.shields.io/badge/Google%20Colab-Open-orange?logo=google-colab)](https://colab.research.google.com/github/bioexcel/biobb_wf_protein-complex_md_setup/blob/main/biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb)

# Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)

Expand Down Expand Up @@ -47,16 +48,19 @@ Click here to [view tutorial in Read the Docs](https://biobb-wf-protein-complex-

Click here to [execute tutorial in Binder](https://mybinder.org/v2/gh/bioexcel/biobb_wf_protein-complex_md_setup/HEAD?labpath=biobb_wf_protein-complex_md_setup%2Fnotebooks%2Fbiobb_Protein-Complex_MDsetup_tutorial.ipynb)

Click here to [open tutorial in Google Colab](https://colab.research.google.com/github/bioexcel/biobb_wf_protein-complex_md_setup/blob/main/biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb)


***

## Version
2023.3
2024.1

## Copyright & Licensing
This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).

* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)

Licensed under the
[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.
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