diff --git a/index.md b/index.md index 91ff8485..ecdaeb24 100644 --- a/index.md +++ b/index.md @@ -7,86 +7,60 @@ title: MDAnalysis MDAnalysis -**MDAnalysis** is an object-oriented Python library to analyze -trajectories from molecular dynamics (MD) simulations in [many popular -formats]({{site.pypi.docs}}/documentation_pages/coordinates/init.html#id1). It -can write most of these formats, too, together with [atom -selections]({{site.pypi.docs}}/documentation_pages/selections_modules.html#selection-exporters) -suitable for visualization or native analysis tools. - -MDAnalysis allows one to read particle-based trajectories (including -individual coordinate frames such as biomolecules in the PDB format) -and access the atomic coordinates through -[NumPy](https://numpy.org/) arrays. This provides a flexible and -relatively fast framework for complex analysis tasks. In addition, -powerful atom -[selection commands]({{site.pypi.docs}}/documentation_pages/selections.html) -are implemented. Trajectories can also be manipulated (for instance, -fit to a reference structure) and written out. The -[basic example]({{ site.baseurl }}/pages/basic_example) demonstrates some -of these features. - -Read more: - -* [installation quick start]({{ site.baseurl }}/pages/installation_quick_start) -* [learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis) - -Also, check out the [blog]({{ site.baseurl }}/blog) or subscribe to our -[news feed]({{ site.baseurl }}/{{site.feed.path}}) to follow development -updates and events. - -## Availability ## - -MDAnalysis can be [**easily -installed**]({{site.baseurl}}/pages/installation_quick_start/) with -its dependencies using the ``pip`` or ``conda`` package managers; -MDAnalysis is also available in some recent Linux distributions. - -All **source code** is available under the -[GNU General Public License, version 2](https://www.gnu.org/licenses/gpl-2.0.html) -(or any later version at your choice) from -[github.com/MDAnalysis/mdanalysis](https://github.com/MDAnalysis/mdanalysis) -and the Python Package index -[pypi.org/project/MDAnalysis](https://pypi.org/project/MDAnalysis). - -## Participating ## - -Ask **questions** on the [{{ site.mailinglists.discussion.name }} -forum]({{ site.mailinglists.discussion.url }}) and **be part of the -conversation**. You can also join the [{{ site.discord.name }} -Discord Server]({{ site.discord.url }}) to talk with other users and -developers. (In order to join our Discord server, use the invitation link -[{{ site.discord.invite }}]({{ site.discord.invite }}).) - -Please report **bugs** or **enhancement requests** through the [Issue -Tracker]({{ site.github.issues }}). - -MDAnalysis is **open source** and welcomes *your* contributions. [Fork -the repository on -GitHub](https://github.com/MDAnalysis/mdanalysis#fork-destination-box) -and submit a pull request. Participate on the [{{ -site.mailinglists.developer.name }} -forum]({{ site.mailinglists.developer.url }}). - -MDAnalysis regularly takes part in various **mentoring and outreach programs**, such as [Google Summer of Code](https://summerofcode.withgoogle.com/), [Google Season of Docs](https://developers.google.com/season-of-docs), [Outreachy](https://www.outreachy.org/), the [Station1 Frontiers Fellowship](https://www.station1.org/sff), and the [CompChemURG](https://www.bindingsites.co.uk/home) mentorship schemes. Many of the [current core developers](/about/#mdanalysis-core-developers/) joined the project through these mentoring schemes. The project also frequently offers **teaching workshops**, both online and in-person; recordings are often made available on the [MDAnalysis YouTube channel](https://www.youtube.com/@mdanalysis3040). Follow our [blog]({{ site.baseurl }}/blog), [LinkedIn](https://www.linkedin.com/company/mdanalysis/), [Twitter](https://twitter.com/mdanalysis), and [Bluesky](https://bsky.app/profile/mdanalysis.bsky.social) pages for updates on how to participate. - - -## Supporting ## - -If you like MDAnalysis and want to support our mission, please -consider making a donation to support our efforts. + The **MDAnalysis Project** develops open-source tools for the analysis of molecular simulation data, providing researchers with efficient and accessible solutions for studying molecular structures and dynamics. -{{ site.numfocus.donate_button }} + MDAnalysis is a fiscally sponsored project of [NumFOCUS][], a nonprofit that promotes open practices in research, data, and scientific computing. + +At the core of the project is *MDAnalysis*, **an open-source Python library** for analyzing molecular dynamics (MD) trajectories across [multiple formats]({{ site.docs.userguide.url }}/formats/index.html#formats). *MDAnalysis* enables seamless reading and writing of simulation data, allowing users to efficiently analyze molecular structures and dynamics, including particle-based trajectories and individual coordinate frames (e.g., biomolecules in the [PDB format][]). + +With *MDAnalysis*, you can access atomic coordinates as [NumPy][] arrays, providing a flexible and efficient framework for complex analysis tasks. The library includes powerful [atom selection commands]({{ site.docs.userguide.url }}/selections.html) for extracting subsets of structures and supports trajectory transformations (e.g., fitting to a reference structure). + +Learn more about our **mission, development, team, and governance** on the [About MDAnalysis]({{ site.baseurl }}/about/) page. + +## Get Started + +If you're new to *MDAnalysis*, explore the following resources to install the `MDAnalysis` package, access tutorials, and dive into the documentation: + +- [Getting Started]({{ site.baseurl }}/pages/getting_started/) +- [Learning MDAnalysis]({{ site.baseurl }}/pages/learning_MDAnalysis) +- [Documentation]({{ site.baseurl }}/pages/documentation) + +## Community + +MDAnalysis is driven by an active **community of users and contributors**. Stay updated and get involved through the following pages: + + +- [Community]({{ site.baseurl }}/pages/community/) — Get involved, ask questions, and collaborate. +- [Blog]({{ site.baseurl }}/blog) — Stay updated with development news and community highlights. +- [Events]({{ site.baseurl }}/pages/events/) — Join workshops, conferences, and mentoring programs. + +## Contributing + +Want to contribute to MDAnalysis? Here’s how: -(Donations are made through [our fiscal sponsor][], [NumFOCUS][], which is -a 501(c)(3) non-profit charity in the United States; as such, -donations to NumFOCUS are tax-deductible as allowed by law. As with -any donation, you should consult with your personal tax adviser or the -IRS about your particular tax situation.) +- [Contribute]({{ site.baseurl }}/pages/contribute/) — Learn how to help improve MDAnalysis through coding, documentation, or discussions. +- [MDAKits and MDA-based tools]({{ site.baseurl }}/pages/mdakits/) — Build and extend MDAnalysis with MDAKits. +- [Support MDAnalysis financially](#funding--support) — Donate via NumFOCUS to sustain the project. + + +## Citing MDAnalysis + +If you use MDAnalysis in your research, please cite it appropriately and consider displaying our MDAnalysis badge in your projects. All citation formats and badge instructions are available in our [Citation guidelines]({{ site.baseurl }}/pages/citations/). + +Additionally, consider displaying our badge in your projects that use MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis). [![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org) -Additionally, consider displaying our badge in your projects that use -MDAnalysis. We provide several [embedding markup examples]({{ site.baseurl }}/pages/citations/#powered-by-mdanalysis). + +## Funding & Support + +If you find MDAnalysis useful and would like to support its continued development, please consider making a donation. You can learn more about out Sponsors in our [Funding]({{ site.baseurl }}/pages/funding/) page. + +{{ site.numfocus.donate_button }} + + + Donations are made through [our fiscal sponsor][], [NumFOCUS][], which is a 501(c)(3) non-profit charity in the United States; as such, donations to NumFOCUS are tax-deductible as allowed by law. As with any donation, you should consult with your personal tax adviser or the IRS about your particular tax situation. + - [NumFOCUS]: https://www.numfocus.org [our fiscal sponsor]: {{site.baseurl}}/about#partners +[NumPy]: https://numpy.org/ +[PDB format]: https://www.wwpdb.org/documentation/file-format