-
Notifications
You must be signed in to change notification settings - Fork 36
CITATION.cff #478
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Merged
Merged
CITATION.cff #478
Changes from 1 commit
Commits
Show all changes
4 commits
Select commit
Hold shift + click to select a range
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,150 @@ | ||
| cff-version: 1.2.1 | ||
| title: FAIRMD_lipids | ||
| message: >- | ||
| If you use this software, please cite it using the | ||
| metadata from this file. | ||
| type: software | ||
| authors: | ||
| - name: comcon1 | ||
| family-names: Nesterenko | ||
| given-names: Alexey | ||
| - name: ohsOllila | ||
| family-names: Ollila | ||
| given-names: O. H. Samuli | ||
| - name: batukav | ||
| family-names: Kav | ||
| given-names: Batuhan | ||
| - name: MagnusSletten | ||
| - name: larabort | ||
| - name: PicoCentauri | ||
| family-names: Loche | ||
| given-names: Philip | ||
| - name: thraindk | ||
| given-names: Cedric | ||
| - name: markussmiettinen | ||
| family-names: Miettinen | ||
| given-names: Markus | ||
| - name: fsuarezleston | ||
| family-names: Suárez-Lestón | ||
| given-names: Fabián | ||
| - name: pbuslaev | ||
| - name: mdondrup | ||
| family-names: Dondrup | ||
| given-names: Michael | ||
| - name: korbinib | ||
| family-names: Bösl | ||
| given-names: Korbinian | ||
| orcid: https://orcid.org/0000-0003-0498-4273 | ||
| - name: hsantila | ||
| - name: akiirik | ||
| - name: JHoeflich1 | ||
| - name: jagdep-singh | ||
| - name: suviheinonen | ||
| - name: awurl | ||
| family-names: Wurl | ||
| given-names: Anika | ||
| - name: PEFrankel | ||
| - name: hseara | ||
| family-names: Martinez-Seara | ||
| given-names: Hector | ||
| - names: tfmFerreira | ||
| family-names: Ferreira | ||
| given-names: Tiago M. | ||
| - names: yesthisisarne | ||
| - names: MelbourneFL | ||
| identifiers: | ||
| - type: doi | ||
| value: 10.5281/zenodo.7875567 | ||
| description: zenodo archive of version 1.4.0 of FAIRMD_lipids | ||
| repository-code: 'https://github.com/NMRLipids/FAIRMD_lipids' | ||
| url: 'https://databank2.nmrlipids.fi/' | ||
| repository-artifact: 'https://pypi.org/project/fairmd-lipids/' | ||
| abstract: >- | ||
| This is the FAIRMD Lipids — an API package for the | ||
| community-driven catalogue FAIRMD Lipid Databank (formerly | ||
| NMRlipids Databank) containing atomistic MD simulations of | ||
| biologically relevant lipid membranes emerging from the | ||
| NMRlipids Open Collaboration. | ||
| keywords: | ||
| - Membrane | ||
| - Biophysics | ||
| - Molecular dynamics simulation | ||
| - intrinsic disorder | ||
| - Lipid | ||
| license: GPL-3.0 | ||
| commit: 20461841753107a13497cfe2a2635c55a7f83c14 | ||
| version: 1.4.0 | ||
| date-released: '2026-02-16' | ||
| preferred-citation: | ||
| type: article | ||
| authors: | ||
| - family-names: Kiirikki | ||
| given-names: Anne M. | ||
| - family-names: Antila | ||
| given-names: Hanne S. | ||
| - family-names: Bort | ||
| given-names: Lara S. | ||
| - family-names: Buslaev | ||
| given-names: Pavel | ||
| - family-names: Favela-Rosales | ||
| given-names: Fernando | ||
| - family-names: Ferreira | ||
| given-names: Tiago Mendes | ||
| - family-names: Fuchs | ||
| given-names: Patrick F. J. | ||
| - family-names: Garcia-Fandino | ||
| given-names: Rebeca | ||
| - family-names: Gushchin | ||
| given-names: Ivan | ||
| - family-names: Kav | ||
| given-names: Batuhan | ||
| - family-names: Kučerka | ||
| given-names: Norbert | ||
| - family-names: Kula | ||
| given-names: Patrik | ||
| - family-names: Kurki | ||
| given-names: Milla | ||
| - family-names: Kuzmin | ||
| given-names: Alexander | ||
| - family-names: Lalitha | ||
| given-names: Anusha | ||
| - family-names: Lolicato | ||
| given-names: Fabio | ||
| - family-names: Madsen | ||
| given-names: Jesper J. | ||
| - family-names: Miettinen | ||
| given-names: Markus S. | ||
| - family-names: Mingham | ||
| given-names: Cedric | ||
| - family-names: Monticelli | ||
| given-names: Luca | ||
| - family-names: Nencini | ||
| given-names: Ricky | ||
| - family-names: Nesterenko | ||
| given-names: Alexey M. | ||
| - family-names: Piggot | ||
| given-names: Thomas J. | ||
| - family-names: Piñeiro | ||
| given-names: Ángel | ||
| - family-names: Reuter | ||
| given-names: Nathalie | ||
| - family-names: Samantray | ||
| given-names: Suman | ||
| - family-names: Suárez-Lestón | ||
| given-names: Fabián | ||
| - family-names: Talandashti | ||
| given-names: Reza | ||
| - family-names: Ollila | ||
| given-names: O. H. Samuli | ||
| title: Overlay Databank Unlocks Data-Driven Analyses of Biomolecules for All | ||
| journal: Nature Communications | ||
| volume: 15 | ||
| issue: 1 | ||
| pages: 1136 | ||
| year: 2024 | ||
| month: 2 | ||
| issn: 2041-1723 | ||
| doi: 10.1038/s41467-024-45189-z | ||
| abstract: >- | ||
| Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank—a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution. | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Please sync with
AUTHORS.md. Add an instruction that a contributor should add himselv to this file (modifyCONTRIBUTION.md).There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
updated.