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295 changes: 25 additions & 270 deletions about.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,294 +6,49 @@ title: About MDAnalysis
<img src="{{ site.baseurl }}/public/mdanalysis-logo_square.png"
style="float: right" alt="MDAnalysis" width="30%"/>

## Mission
MDAnalysis is an open-source project dedicated to advancing molecular dynamics analysis through a robust software library, an active community, and sustainable governance. Our tools enable high-performance, reproducible computational studies supporting researchers across academia and industry.

The MDAnalysis [Community](#community) is interested in all facets of **working
with data in the computational molecular sciences**. We welcome everyone. **We all follow our
[Code of Conduct] and strive to create an environment that is welcoming to
all.** Our primary purpose is to produce software that scientists in academia and
industry will trust to use in their research.
The MDAnalysis Project is committed to open-source, reproducible computational research. Our [Mission]({{ site.baseurl }}/mission/) guides our efforts in developing robust tools, fostering an inclusive community, and supporting scientists worldwide.

We develop and maintain projects related to the broader goal of processing and
analyzing data in the computational molecular sciences. We aim to empower users/developers to
work with our packages following [FAIR principles]. Our central package is the
[MDAnalysis library] for the analysis of computer simulations of many-body
systems at the molecular scale.
## Get Involved

We believe that scientific software should be open to all while using best
practices to maintain high standards of correctness and reproducibility. We
emphasize educating our users to make best use of the tools that we produce, to
enable them to become contributors to our community and code bases.
- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/conduct/) before participating.
- **Join the Community:** Connect with other users, report issues, and contribute through multiple channels. Learn more on our [Community]({{ site.baseurl }}/pages/community/) page.
- **Contribute:** Whether through coding, documentation, community support, or event organization, you can help shape the MDAnalysis ecosystem. Get started with our [Contributing Guide]({{ site.baseurl }}/pages/contribute/) or [join a team]({{ site.baseurl }}/pages/team/) to support specific initiatives.
- **Support MDAnalysis:** MDAnalysis relies on grants, sponsorships, and donations to sustain development and community events. Your support helps fund maintenance, development, UGMs (User Group Meetings), workshops, and more. Learn more on our [Funding]({{ site.baseurl }}/pages/funding/) page.
- **Share your Feedback:** MDAnalysis welcomes feedback for improvement from its users and community. Share your thoughts on MDAnalysis, the community, or events by filling out [this feedback form][].

## Team & Leadership

MDAnalysis is maintained by the [Core Developers]({{ site.baseurl }}/pages/governance/#mdanalysis-core-developers) who lead the project and make key decisions regarding its development. Past contributors who've stepped back become Emeriti Core Developers.

## Community
Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/pages/team/) pages for more details.

**MDAnalysis** is developed and maintained as a freely available, open-source
project by a global community of scientists. The MDAnalysis community adheres
to our [Code of Conduct]({{site.baseurl}}/pages/conduct/) and invites everyone
to [participate]({{site.baseurl}}/#participating) --- be it on GitHub Discussions,
through issue reports, or code contributions.

All *contributors* to the MDAnalysis library and its subprojects are acknowledged
in a file called `AUTHORS` in each source code repository and in the list of
contributions; as examples see the [`AUTHORS` file for
mdanalysis](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/AUTHORS)
and the [contributors for
MDAnalysis/mdanalysis](https://github.com/MDAnalysis/mdanalysis/graphs/contributors).

MDAnalysis and the algorithms implemented in the library and the subprojects are
scientific software that are described in [academic
publications]({{site.baseurl}}/pages/citations/).

MDAnalysis is used in a variety of [other molecular dynamics tools]({{site.baseurl}}/pages/mdakits/).


## Open source

All our [code]({{site.baseurl}}/#availability) and our [teaching
materials]({{site.baseurl}}/pages/learning_MDAnalysis/) are available
under open source licenses from repositories at
[https://github.com/MDAnalysis/](https://github.com/MDAnalysis/). The
MDAnalysis library itself is published under the [GNU General Public
License, version 2](https://www.gnu.org/licenses/gpl-2.0.html); other
supporting libraries are published under the MIT or the BSD-3 clause
licence.

Installable packages are available through the popular ``pip`` and
``conda`` package managers as well as some Linux distributions.


## Governance

Project leadership is provided by a subset of contributors, the
*MDAnalysis Core Developers*
([@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs))
who have produced substantial contributions over extended lengths of
time and who remain active in reviewing issues and discussions on
GitHub Discussions and our Discord server.

### MDAnalysis Core Developers

The **Core Developers** lead the MDAnalysis project and are responsible to
the community and to NumFOCUS, our fiscal sponsor. They **represent
the project publicly** and **vote to make decisions for the project**.

PIs on a grant submitted by MDAnalysis via NumFOCUS must be Core Developers
while co-PIs do not have to be Core Developers.

Core Developers are granted commit rights (write access) to the [GitHub source
code repositories][orgrepo] and thus can approve pull requests for merges.

The current
[@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs/members)
team ("MDAnalysis Core Developers") consists of:

- @BradyAJohnston
- @fiona-naughton
- @hmacdope
- @IAlibay
- @jennaswa
- @lilyminium
- @marinegor
- @micaela-matta
- @orbeckst
- @p-j-smith
- @richardjgowers
- @RMeli
- @tylerjereddy
- @yuxuanzhuang

### MDAnalysis Emeriti Core Developers

**Emerita/Emeritus Core Developers** are former Core Developers who remain
connected to the project but have stepped back from the day-to-day
decision making. Emeriti Core Developers can reinstate themselves to
Core Developer status.

Emeriti Core Developers maintain commit rights (write access) to the
[GitHub source code repositories][orgrepo] and can approve pull requests for
merges.

The current *Emeriti Core Developers* are:

- @dotsdl
- Elizabeth Denning
- @jandom
- @jbarnoud
- @kain88-de
- @mnmelo
- @mtiberti
- @nmichaud
- @PicoCentauri
- @seb-buch
- @zemanj

### Decision Making Process and Membership

1. All decisions are made by *simple majority*[^1] of the [MDAnalysis Core
Developers](#mdanalysis-core-developers).
2. New *Core Developers* are elected with a simple majority of current
MDAnalysis Core Developers.
3. Current Core Developers are polled annually to *opt-in* to remain
a Core Developer; otherwise they transition to [Emerita/Emeritus
Core Developer](#mdanalysis-emeriti-core-developers) status.

[^1]: A [simple majority][] is defined as *more than half the votes
cast*. Abstentions or blanks are excluded in calculating a
majority vote. Totals do not include votes cast by someone not
entitled to vote[^2] or improper multiple votes by a single
member. Illegal votes[^3] are counted as votes cast;
if only two choices (such as a binary "yes"/"no" vote) are
possible, a majority vote is more "yes" than "no" votes.

[^2]: See [MDAnalysis Core Developers](#mdanalysis-core-developers)
for the list of *individuals entitled to vote*.

[^3]: *Illegal votes* are votes that were cast for ineligible choices.

### Code of Conduct

Everyone in the MDAnalysis community adheres to our [Code of
Conduct]({{site.baseurl}}/pages/conduct/). A rotating subset of three
MDAnalysis Core Developers is tasked to respond to and to investigate
[Code of Conduct]({{site.baseurl}}/pages/conduct/) violations.


## Partners

MDAnalysis is a [fiscally sponsored
project]({{site.numfocus.sponsored_project}}) of [NumFOCUS][], a nonprofit
dedicated to supporting the open source scientific computing
community.

If you like MDAnalysis and want to support our mission, please
consider making a [donation]({{site.numfocus.donate}}) to support our
efforts. NumFOCUS 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.

{{ site.numfocus.donate_button }}


## Funding

We are grateful for financial support from the following organizations, which have supported MDAnalysis either through direct funding or indirectly by funding MDAnalysis contributors.

### [Chan Zuckerberg Initiative][] (CZI)

<a href="https://chanzuckerberg.com/"><img
src="{{site.images}}/CZI_Logo.jpg" title="Chan Zuckerberg
Initiative" alt="Chan Zuckerberg Initiative" style="display:
inline; float: right; height: 4em; margin: 0 0.5em" /></a>

MDAnalysis has been supported by the [Essential Open Source for Science](https://chanzuckerberg.com/rfa/essential-open-source-software-for-science/) (EOSS) program from the CZI Donor-Advised Fund (DAF), an advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989)

- EOSS5, 2022-253062 (**2022**): [MDAnalysis: Outreach and Project Manager](https://chanzuckerberg.com/eoss/proposals/mdanalysis-outreach-and-project-manager/) (**Personnel**: @IAlibay, @jennaswa, @micaela-matta, @orbeckst, @richardjgowers (*PI*))
- EOSS4, DAF2021-237663, DOI [https://doi.org/10.37921/426590wiobus](https://doi.org/10.37921/426590wiobus) (**2021**): [MDAnalysis: Faster, Extensible Molecular Analysis for Reproducible Science](https://chanzuckerberg.com/eoss/proposals/mdanalysis-faster-extensible-molecular-analysis-for-reproducible-science/) (**Personnel**: @fiona-naughton, @hmacdope, @IAlibay, @ianmkenney, @lilyminium, @orbeckst (*PI*), @richardjgowers)

### [Google](https://opensource.google/)

<a href="https://summerofcode.withgoogle.com/"> <img
src="https://developers.google.com/open-source/gsoc/images/gsoc2016-sun-373x373.png"
title="Google Summer of Code" alt="Google Summer of Code"
style="display: inline; float: right; height: 4em; margin: 0
0.5em" /></a>

The following contributors were sponsored to work on MDAnalysis through the [Google Summer of Code](https://summerofcode.withgoogle.com/) program.

- **2024**: @ljwoods2, @lunamorrow, @talagayev
- **2023**: @marinegor, @xhgchen
- **2022**: @aya9aladdin, @BFedder
- **2021**: @ojeda-e, @orionarcher
- **2020**: @cbouy, @hmacdope, @yuxuanzhuang
- **2019**: @NinadBhat
- **2018**: @ayushsuhane, @davidercruz
- **2017**: @utkbansal
- **2016**: @fiona-naughton, @jdetle

<a href="https://developers.google.com/season-of-docs"> <img
src="https://developers.google.com/season-of-docs/images/SeasonofDocs_Icon_Grey_300ppi_trimmed.png"
title="Google Season of Docs" alt="Google Season of Docs"
style="display: inline; float: right; height: 4em; margin: 0 0.5em" /></a>

The following technical writers were sponsored to work on MDAnalysis through the [Google Season of Docs](https://developers.google.com/season-of-docs) program.

- **2019**: @lilyminium

### [National Science Foundation](https://www.nsf.gov/)

<a href="https://nsf.gov/">
<img src="{{site.images}}/nsf.jpg" title="National Science
Foundation" alt="National Science Foundation" style="display:
inline; float: right; height: 4em; margin: 0 0.5em" /></a>

Earlier work was partially supported by the NSF (as part of award ACI-1443054).

- NSF DIBBS award, ACI-1443054 (**2014**): [CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1443054) (**MDAnalysis Personnel**: @orbeckst)

The following students were sponsored to work on MDAnalysis through the [NSF Research Experience for Undergraduates](https://www.nsf.gov/crssprgm/reu/) (REU) program.

- **2021**: @ALescoulie, @edisj
- **2020**: @edisj
- **2019**: @nawtrey
- **2018**: @hfmull
- **2017**: @kaceyaurum
- **2016**: @rbrtdlgd
- **2015**: @ianmkenney

### [NumFOCUS][]
## Funding & Sponsors

<a href="{{site.numfocus.sponsored_project}}"><img
src="{{site.images}}/numfocus-sponsored.png" title="NumFOCUS
sponsored project" alt="NumFOCUS Sponsored" style="display:
inline; float: right; height: 4em; margin: 0 0.5em" /></a>

MDAnalysis thanks NumFOCUS for its continued support as our fiscal sponsor, as well as through its [Small Development Grants](https://numfocus.org/programs/small-development-grants) (SDG) program.

- SDG Round 3 (**2024**): Customizable and automated scientific molecular rendering with Molecular Nodes (**Personnel**: @yuxuanzhuang, @BradyAJohnston)
- SDG Round 2 (**2023**): Unified and comprehensive documentation and learning resources for MDAnalysis (**Personnel**: @IAlibay, @jennaswa, @lilyminium, @micaela-matta, @orbeckst)
- SDG Round 2 (**2022**): Improving the organization and content of MDAnalysis teaching materials (**Personnel**: @micaela-matta, @pgbarletta)
- SDG Round 1 (**2020**): Periodic boundary handling and on the fly transformations
- SDG Round 2 (**2018**): MDAnalysis tutorial and hackathon
- SDG Round 1 (**2017**): Widening platform availability for MDAnalysis: Full Python 3 Support

### [Outreachy](https://www.outreachy.org/)

<a href="https://www.outreachy.org/"><img
src="{{ site.baseurl }}{{ site.images }}/Outreachy-logo.svg"
title="Outreachy" alt="Outreachy"
style="display: inline; float: right; height: 4em; margin: 0 0.5em" /></a>

The following contributors were sponsored to work on MDAnalysis through the [Outreachy](https://www.outreachy.org/) program.

- **2024**: @adetutudeborah
- **2022**: @umak1106
MDAnalysis is a fiscally-sponsored project of [NumFOCUS][]. We are also supported by grants, sponsorships, and community contributions that play key roles in supporting our development.

### [Station1](https://www.station1.org/)
See our [Funding]({{ site.baseurl }}/pages/funding/) page for more details on our **funding sources and how you can support MDAnalysis**.

<a href="https://www.station1.org/"><img
src="/public/images/station1_condensed_logo.png"
title="Station1 Logo" alt="Station1 Logo"
style="display: inline; float: right; height: 4em; margin: 0 0.5em " /></a>
## Open Source & Availability

The following contributors were sponsored to work on MDAnalysis through the [Station1 Frontiers Fellowship](https://www.station1.org/sff) program.
MDAnalysis is released under the [GNU Lesser General Public License, version 2.1 or later (LGPLv2.1+)][]. This ensures that our tools remain accessible, transparent, and reproducible for molecular dynamics research. Some supporting libraries use the MIT or BSD-3 licenses.
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Is there still a line somewhere about teaching materials being open source (I think most are probably cc-by licenses)? As with Oliver's comment about the mission statement, it is our goal to be open as a project, not just related specifically to the library.


- **2023**: @jong9559, @KarenBekhazi
MDAnalysis is:

<div style="clear: both"></div>
- **Easy to install** &mdash; Available via `pip`, `conda/mamba` and `conda-forge`.
- **Openly developed** &mdash; The [source code]({{ site.github.repo }}) is hosted on GitHub.
- **Regularly updated** &mdash; Official releases are distributed via [PyPI][].

## Feedback
For full installation instructions and setup guides, visit our [Getting Started]({{ site.baseurl }}/pages/getting_started/) page.

MDAnalysis welcomes feedback for improvement from its users and community. If you have any general feedback or comments to make about MDAnalysis, the community, events, or other aspects, please [let us know in this form here](https://forms.gle/n8GLe2QsL2hW2QiDA)!

------

[Code of Conduct]: {{ site.baseurl }}/pages/conduct/
[MDAnalysis library]: {{ site.github.repo }}
[FAIR principles]: https://www.go-fair.org/fair-principles/
[GNU Lesser General Public License, version 2.1 or later (LGPLv2.1+)]: https://www.gnu.org/licenses/lgpl-2.1.html
[PyPI]: https://pypi.org/project/MDAnalysis/
[this feedback form]: https://docs.google.com/forms/d/e/1FAIpQLScAjjI730i63LbyVkk_tuZ1-FCXUkg6xFugw_gmcsqUvBUtnw/viewform?usp=sf_link
[NumFOCUS]: https://www.numfocus.org
[simple majority]: https://en.wikipedia.org/wiki/Majority#Majority_vote
[orgrepo]: https://github.com/MDAnalysis
[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/

3 changes: 1 addition & 2 deletions pages/conduct.md → conduct.md
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@@ -1,7 +1,6 @@
---
layout: page
layout: otherpage
title: Code of Conduct
order: 0
---

<!-- DON'T CHANGE THIS. ALWAYS COPY FROM THE MAIN CODE REPOSITORY -->
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---
layout: otherpage
title: Mission
---

The MDAnalysis community is interested in all facets of **working
with data in the computational molecular sciences**. We welcome everyone. **We all follow our
[Code of Conduct]({{ site.baseurl }}/conduct/) and strive to create an environment that is welcoming to all.** Our primary purpose is to produce software that scientists in academia and industry will trust to use in their research.

We develop and maintain projects related to the broader goal of processing and
analyzing data in the computational molecular sciences. We aim to empower users/developers to
work with our packages following [FAIR principles][]. Our central package is the
[MDAnalysis library]({{ site.github.repo }}) for the analysis of computer simulations of many-body
systems at the molecular scale.

We believe that scientific software should be open to all while using best
practices to maintain high standards of correctness and reproducibility. We
emphasize educating our users to make best use of the tools that we produce, to
enable them to become contributors to our community and code bases.

[FAIR principles]: https://www.go-fair.org/fair-principles/
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