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docs: update README.md with JOSS badge #579
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1f6df2e
Update README.md with JOSS badge
gcroci2 db3d061
update CITATION.cff with JOSS paper data
gcroci2 fbef968
Delete .zenodo.json
gcroci2 577b8b4
reinsert zenodo file
gcroci2 f01a808
update readme.dev.mdf
gcroci2 14ccafe
Merge branch 'main' into gcroci2-patch-2
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,72 +1,88 @@ | ||
| # This CITATION.cff file was generated with cffinit. | ||
| # Visit https://bit.ly/cffinit to generate yours today! | ||
|
|
||
| cff-version: 1.2.0 | ||
| doi: 10.5281/zenodo.6674124 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning" | ||
| message: >- | ||
| If you use this software, please cite it using the | ||
| metadata from this file. | ||
| type: software | ||
| cff-version: "1.2.0" | ||
| authors: | ||
| - given-names: Giulia | ||
| family-names: Crocioni | ||
| email: [email protected] | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| - family-names: Bodor | ||
| given-names: Dani L. | ||
| orcid: "https://orcid.org/0000-0003-2109-2349" | ||
| - family-names: Baakman | ||
| given-names: Coos | ||
| orcid: "https://orcid.org/0000-0003-4317-1566" | ||
| - family-names: Parizi | ||
| given-names: Farzaneh M. | ||
| orcid: "https://orcid.org/0000-0003-4230-7492" | ||
| - family-names: Rademaker | ||
| given-names: Daniel-T. | ||
| orcid: "https://orcid.org/0000-0003-1959-1317" | ||
| - family-names: Ramakrishnan | ||
| given-names: Gayatri | ||
| orcid: "https://orcid.org/0000-0001-8203-2783" | ||
| - family-names: Burg | ||
| given-names: Sven A. | ||
| name-particle: van der | ||
| orcid: "https://orcid.org/0000-0003-1250-6968" | ||
| - family-names: Marzella | ||
| given-names: Dario F. | ||
| orcid: "https://orcid.org/0000-0002-0043-3055" | ||
| - family-names: Teixeira | ||
| given-names: João M. C. | ||
| orcid: "https://orcid.org/0000-0002-9113-0622" | ||
| - family-names: Xue | ||
| given-names: Li C. | ||
| orcid: "https://orcid.org/0000-0002-2613-538X" | ||
| contact: | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| doi: 10.5281/zenodo.10566809 | ||
| message: If you use this software, please cite our article in the | ||
| Journal of Open Source Software. | ||
| preferred-citation: | ||
| authors: | ||
| - family-names: Crocioni | ||
| given-names: Giulia | ||
| orcid: "https://orcid.org/0000-0002-0823-0121" | ||
| - given-names: Dani L. | ||
| family-names: Bodor | ||
| email: [email protected] | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Bodor | ||
| given-names: Dani L. | ||
| orcid: "https://orcid.org/0000-0003-2109-2349" | ||
| - given-names: Coos | ||
| family-names: Baakman | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Baakman | ||
| given-names: Coos | ||
| orcid: "https://orcid.org/0000-0003-4317-1566" | ||
| - given-names: Farzaneh Meimandi | ||
| family-names: Parizi | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Parizi | ||
| given-names: Farzaneh M. | ||
| orcid: "https://orcid.org/0000-0003-4230-7492" | ||
| - given-names: Daniel-T. | ||
| family-names: Rademaker | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Rademaker | ||
| given-names: Daniel-T. | ||
| orcid: "https://orcid.org/0000-0003-1959-1317" | ||
| - given-names: Gayatri | ||
| family-names: Ramakrishnan | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Ramakrishnan | ||
| given-names: Gayatri | ||
| orcid: "https://orcid.org/0000-0001-8203-2783" | ||
| - given-names: Sven A. | ||
| family-names: van der Burg | ||
| affiliation: Netherlands eScience Center, Amsterdam, The Netherlands | ||
| - family-names: Burg | ||
| given-names: Sven A. | ||
| name-particle: van der | ||
| orcid: "https://orcid.org/0000-0003-1250-6968" | ||
| - given-names: Dario F. | ||
| family-names: Marzella | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Marzella | ||
| given-names: Dario F. | ||
| orcid: "https://orcid.org/0000-0002-0043-3055" | ||
| - given-names: João M.C. | ||
| family-names: Teixeira | ||
| affiliation: Independent Researcher | ||
| - family-names: Teixeira | ||
| given-names: João M. C. | ||
| orcid: "https://orcid.org/0000-0002-9113-0622" | ||
| - given-names: Li C. | ||
| family-names: Xue | ||
| affiliation: Center for Molecular Bioinformatics, Radboud Universitair Medisch Centrum, Nijmegen, Gelderland, The Netherlands | ||
| - family-names: Xue | ||
| given-names: Li C. | ||
| orcid: "https://orcid.org/0000-0002-2613-538X" | ||
| abstract: >- | ||
| DeepRank2 is an open-source deep learning | ||
| framework for data mining of protein-protein interfaces | ||
| or single-residue variants. | ||
| keywords: | ||
| - Python | ||
| - PyTorch | ||
| - structural biology | ||
| - geometric deep learning | ||
| - 3D protein structures | ||
| - protein-protein interfaces | ||
| - single-residue variants | ||
| - graph neural networks | ||
| - convolutional neural networks | ||
| - DeepRank | ||
| license: Apache-2.0 | ||
| commit: 4e8823758ba03f824b4281f5689cb6a335ab2f6c | ||
| version: "3.0.1" | ||
| date-released: "2024-02-22" | ||
| date-published: 2024-02-27 | ||
| doi: 10.21105/joss.05983 | ||
| issn: 2475-9066 | ||
| issue: 94 | ||
| journal: Journal of Open Source Software | ||
| publisher: | ||
| name: Open Journals | ||
| start: 5983 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep | ||
| Learning" | ||
| type: article | ||
| url: "https://joss.theoj.org/papers/10.21105/joss.05983" | ||
| volume: 9 | ||
| title: "DeepRank2: Mining 3D Protein Structures with Geometric Deep | ||
| Learning" |
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won't look in detail at these changes, will assume all is well.