From 9220b2fb4af74362f9e9d2cc166af55e7d56ae38 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 13 Mar 2025 11:20:42 +0000 Subject: [PATCH 1/6] Refined About, Mission, Governance, and Funding pages --- about.md | 298 ++++---------------------------------------- pages/funding.md | 129 +++++++++++++++++++ pages/governance.md | 90 +++++++++++++ pages/mission.md | 22 ++++ 4 files changed, 267 insertions(+), 272 deletions(-) create mode 100644 pages/funding.md create mode 100644 pages/governance.md create mode 100644 pages/mission.md diff --git a/about.md b/about.md index 8f71cbc5..bc8bf1ef 100644 --- a/about.md +++ b/about.md @@ -6,294 +6,48 @@ title: About MDAnalysis MDAnalysis -## Mission +MDAnalysis is an open-source Python library for analyzing molecular dynamics simulations and biomolecular structures. It enables 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. +Learn more about our mission on the [Mission]({{ site.baseurl }}/pages/mission/) page. -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. +MDAnalysis is built and maintained by a global community of researchers, developers, and users. There are many ways to participate: +- **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, or community support, get started with our [Contributing Guide]({{ site.baseurl }}/pages/contribute/). +- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/pages/conduct/). +## Team & Leadership -## Community +MDAnalysis is maintained by [Core Developers][] who lead the project and make key decisions regarding its development. Past contributors who stepped back hold the title of Emeritus Core Developer. -**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. +Our governance structure ensures transparency and sustainability. Learn more on our [Team]({{ site.baseurl }}/pages/team/) and [Governance]({{ site.baseurl }}/pages/governance/) pages. -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). +## Funding & Sponsors -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 supported by grants, sponsorships, and community contributions. Organizations such as the **Chan Zuckerberg Initiative, Google, NumFOCUS, and the National Science Foundation** have played key roles in funding our development. -MDAnalysis is used in a variety of [other molecular dynamics tools]({{site.baseurl}}/pages/mdakits/). +For more information on our funding sources and how you can support MDAnalysis, visit our [Funding]({{ site.baseurl }}/pages/funding/) page. +## Open Source & Availability -## Open source +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. -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. +MDAnalysis is: -Installable packages are available through the popular ``pip`` and -``conda`` package managers as well as some Linux distributions. +- **Easy to install** — Available via `pip` and `conda/mamba`. +- **Openly developed** — The [source code]({{ site.github.repo }}) is hosted on GitHub. +- **Regularly updated** — Official releases are distributed via [PyPI][]. +For full installation instructions and setup guides, visit our [Getting Started]({{ site.baseurl }}/pages/getting_started/) page. -## Governance +## Share Your Feedback -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 welcomes feedback for improvement from its users and community. Share your thoughts on MDAnalysis, the community, or events by filling out [this feedback form][]. -### MDAnalysis Core Developers +[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://forms.gle/n8GLe2QsL2hW2QiDA +[Core Developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members -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) - -Chan Zuckerberg Initiative - -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/) - - Google Summer of Code - -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 - - Google Season of Docs - -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/) - - -National Science Foundation - -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][] - -NumFOCUS Sponsored - -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/) - -Outreachy - -The following contributors were sponsored to work on MDAnalysis through the [Outreachy](https://www.outreachy.org/) program. - -- **2024**: @adetutudeborah -- **2022**: @umak1106 - -### [Station1](https://www.station1.org/) - -Station1 Logo - -The following contributors were sponsored to work on MDAnalysis through the [Station1 Frontiers Fellowship](https://www.station1.org/sff) program. - -- **2023**: @jong9559, @KarenBekhazi - -
- -## Feedback - -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/ -[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/ diff --git a/pages/funding.md b/pages/funding.md new file mode 100644 index 00000000..7ead1970 --- /dev/null +++ b/pages/funding.md @@ -0,0 +1,129 @@ +--- +layout: otherpage +title: 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) + +Chan Zuckerberg Initiative + +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/) + + Google Summer of Code + +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 + + Google Season of Docs + +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/) + + +National Science Foundation + +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][] + +NumFOCUS Sponsored + +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/) + +Outreachy + +The following contributors were sponsored to work on MDAnalysis through the [Outreachy](https://www.outreachy.org/) program. + +- **2024**: @adetutudeborah +- **2022**: @umak1106 + +### [Station1](https://www.station1.org/) + +Station1 Logo + +The following contributors were sponsored to work on MDAnalysis through the [Station1 Frontiers Fellowship](https://www.station1.org/sff) program. + +- **2023**: @jong9559, @KarenBekhazi + +
+ +## 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 }} + +[Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ +[NumFOCUS]: https://www.numfocus.org + diff --git a/pages/governance.md b/pages/governance.md new file mode 100644 index 00000000..6c5edfe9 --- /dev/null +++ b/pages/governance.md @@ -0,0 +1,90 @@ +--- +layout: otherpage +title: Governance +--- + +Project leadership is provided by a group of contributors, known as the +*MDAnalysis Core Developers* ([@MDAnalysis/coredevs][]) who have produced substantial contributions over an extended period and who actively review issues and participate in discussions on GitHub Discussions and Discord. + +## 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][] 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. + +[simple majority]: https://en.wikipedia.org/wiki/Majority#Majority_vote +[orgrepo]: https://github.com/MDAnalysis +[NumFOCUS]: https://www.numfocus.org +[@MDAnalysis/coredevs]: https://github.com/orgs/MDAnalysis/teams/coredevs/members + diff --git a/pages/mission.md b/pages/mission.md new file mode 100644 index 00000000..e9eb5e53 --- /dev/null +++ b/pages/mission.md @@ -0,0 +1,22 @@ +--- +layout: otherpage +title: Mission +--- + +The MDAnalysis community is dedicated to advancing computational molecular science by developing open-source tools for data processing and analysis. We foster an inclusive, collaborative environment where everyone is welcome. + +We follow our [Code of Conduct]({{site.baseurl}}/pages/conduct/) to ensure a welcoming space for all contributors. Our primary goal is to produce high-quality, trusted software for scientists in academia and industry. + +## What We Do + +- **Develop Open-Source Tools:** We create and maintain projects that support data analysis in computational molecular sciences. +- **Empower Users & Developers:** We help researchers leverage our tools while encouraging them to become contributors. +- **Uphold [FAIR principles][]:** We ensure our tools follow the principles of Findability, Accessibility, Interoperability, and Reusability. +- **Promote Reproducibility & Best Practices:** We prioritize correctness, transparency, and reproducibility in scientific software development. + +Our central package, [MDAnalysis]({{ site.github.repo }}), provides robust tools for analyzing computer simulations of molecular systems. + +We believe that scientific software should be **open, reliable, and accessible** to all. Through documentation, training, and an engaged community, we equip researchers with the skills to use and contribute to our ecosystem. + +[FAIR principles]: https://www.go-fair.org/fair-principles/ + From 0db42dfd74c92ea21227c1345350ae8de9cf8238 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 18 Mar 2025 19:55:28 +0000 Subject: [PATCH 2/6] address PR review comments --- about.md | 30 ++++++++++---------- pages/funding.md | 67 +++++++++++++++++++++------------------------ pages/governance.md | 3 +- pages/mission.md | 33 +++++++++++----------- 4 files changed, 62 insertions(+), 71 deletions(-) diff --git a/about.md b/about.md index bc8bf1ef..3f5bf549 100644 --- a/about.md +++ b/about.md @@ -6,29 +6,31 @@ title: About MDAnalysis MDAnalysis -MDAnalysis is an open-source Python library for analyzing molecular dynamics simulations and biomolecular structures. It enables high-performance, reproducible computational studies, supporting researchers across academia and industry. +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. -Learn more about our mission on the [Mission]({{ site.baseurl }}/pages/mission/) page. +The MDAnalysis Project is committed to open-source, reproducible computational research. Our [Mission]({{ site.baseurl }}/pages/mission/) guides our efforts in developing robust tools, fostering an inclusive community, and supporting scientists worldwide. ## Get Involved -MDAnalysis is built and maintained by a global community of researchers, developers, and users. There are many ways to participate: - +- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/pages/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, or community support, get started with our [Contributing Guide]({{ site.baseurl }}/pages/contribute/). -- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/pages/conduct/). +- **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. You can also help organize or participate in MDAnalysis events, such as User Group Meetings (UGMs) and workshops. +- **Support MDAnalysis:** MDAnalysis relies on grants, sponsorships, and donations to sustain development and community events. Your support helps fund maintenance, development, UGMs, 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 [Core Developers][] who lead the project and make key decisions regarding its development. Past contributors who stepped back hold the title of Emeritus Core Developer. +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. + +Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/pages/team/) pages for more details. -Our governance structure ensures transparency and sustainability. Learn more on our [Team]({{ site.baseurl }}/pages/team/) and [Governance]({{ site.baseurl }}/pages/governance/) pages. +Learn more on . ## Funding & Sponsors -MDAnalysis is supported by grants, sponsorships, and community contributions. Organizations such as the **Chan Zuckerberg Initiative, Google, NumFOCUS, and the National Science Foundation** have played key roles in funding our development. +MDAnalysis is supported by grants, sponsorships, and community contributions. As a fiscally-sponsored project of [NumFOCUS][], we receive funding from various organizations that play key roles in supporting our development. -For more information on our funding sources and how you can support MDAnalysis, visit our [Funding]({{ site.baseurl }}/pages/funding/) page. + See our [Funding]({{ site.baseurl }}/pages/funding/) page for more details on our **funding sources and how you can support MDAnalysis**. ## Open Source & Availability @@ -36,18 +38,14 @@ MDAnalysis is released under the [GNU Lesser General Public License, version 2.1 MDAnalysis is: -- **Easy to install** — Available via `pip` and `conda/mamba`. +- **Easy to install** — Available via `pip`, `conda/mamba` and `conda-forge`. - **Openly developed** — The [source code]({{ site.github.repo }}) is hosted on GitHub. - **Regularly updated** — Official releases are distributed via [PyPI][]. For full installation instructions and setup guides, visit our [Getting Started]({{ site.baseurl }}/pages/getting_started/) 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][]. - [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://forms.gle/n8GLe2QsL2hW2QiDA -[Core Developers]: https://github.com/orgs/MDAnalysis/teams/coredevs/members +[NumFOCUS]: https://www.numfocus.org diff --git a/pages/funding.md b/pages/funding.md index 7ead1970..9e50e1c0 100644 --- a/pages/funding.md +++ b/pages/funding.md @@ -3,9 +3,35 @@ layout: otherpage title: 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. +We are grateful for financial support from the following organizations, which have supported MDAnalysis either directly through grants or indirectly by funding MDAnalysis contributors. -### [Chan Zuckerberg Initiative][] (CZI) +## Fiscal Sponsor: [NumFOCUS][] + +NumFOCUS Sponsored + +MDAnalysis is [fiscally sponsored project]({{site.numfocus.sponsored_project}}) of [NumFOCUS][], a nonprofit organization that supports **open-source scientific computing** projects. Their support allows us to sustain our development, infrastructure, and outreach efforts. + +MDAnalysis has also received [Small Development Grants](https://numfocus.org/programs/small-development-grants) (SDG) from NumFOCUS: + +- 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**: @jennaswa, @namiroues, @micaela-matta, @orbeckst, @IAlibay, @lilyminium) +- 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 + +If you like MDAnalysis and want to support our mission, **please consider making a [donation]({{site.numfocus.donate}})** to help sustain our work. + +NumFOCUS is a 501(c)(3) nonprofit in the United States, and donations are tax-deductible where applicable. As with any donation, you should consult with your personal +tax adviser or the IRS about your particular tax situation. + +{{ site.numfocus.donate_button }} + + +## [Chan Zuckerberg Initiative][] (CZI) NumFOCUS Sponsored - -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/) +## [Outreachy](https://www.outreachy.org/) -## 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 }} - [Chan Zuckerberg Initiative]: https://chanzuckerberg.com/ [NumFOCUS]: https://www.numfocus.org diff --git a/pages/governance.md b/pages/governance.md index 6c5edfe9..30f09c52 100644 --- a/pages/governance.md +++ b/pages/governance.md @@ -12,8 +12,7 @@ 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. +Principal Investigators (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. diff --git a/pages/mission.md b/pages/mission.md index e9eb5e53..e45def6b 100644 --- a/pages/mission.md +++ b/pages/mission.md @@ -3,20 +3,19 @@ layout: otherpage title: Mission --- -The MDAnalysis community is dedicated to advancing computational molecular science by developing open-source tools for data processing and analysis. We foster an inclusive, collaborative environment where everyone is welcome. - -We follow our [Code of Conduct]({{site.baseurl}}/pages/conduct/) to ensure a welcoming space for all contributors. Our primary goal is to produce high-quality, trusted software for scientists in academia and industry. - -## What We Do - -- **Develop Open-Source Tools:** We create and maintain projects that support data analysis in computational molecular sciences. -- **Empower Users & Developers:** We help researchers leverage our tools while encouraging them to become contributors. -- **Uphold [FAIR principles][]:** We ensure our tools follow the principles of Findability, Accessibility, Interoperability, and Reusability. -- **Promote Reproducibility & Best Practices:** We prioritize correctness, transparency, and reproducibility in scientific software development. - -Our central package, [MDAnalysis]({{ site.github.repo }}), provides robust tools for analyzing computer simulations of molecular systems. - -We believe that scientific software should be **open, reliable, and accessible** to all. Through documentation, training, and an engaged community, we equip researchers with the skills to use and contribute to our ecosystem. - -[FAIR principles]: https://www.go-fair.org/fair-principles/ - +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 }}/pages/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/ \ No newline at end of file From 01a520336c7a477fd824a23a54c8aec424e42ed3 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Thu, 20 Mar 2025 17:33:07 +0000 Subject: [PATCH 3/6] address PR review comments --- about.md | 15 ++++++++++----- pages/conduct.md => conduct.md | 3 +-- pages/mission.md => mission.md | 2 +- 3 files changed, 12 insertions(+), 8 deletions(-) rename pages/conduct.md => conduct.md (99%) rename pages/mission.md => mission.md (79%) diff --git a/about.md b/about.md index 3f5bf549..519a8edc 100644 --- a/about.md +++ b/about.md @@ -8,14 +8,14 @@ style="float: right" alt="MDAnalysis" width="30%"/> 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 Project is committed to open-source, reproducible computational research. Our [Mission]({{ site.baseurl }}/pages/mission/) guides our efforts in developing robust tools, fostering an inclusive community, and supporting scientists worldwide. +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. ## Get Involved -- **Follow Our Code of Conduct:** We foster a welcoming, inclusive environment. Read our [Code of Conduct]({{ site.baseurl }}/pages/conduct/) before participating. +- **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. You can also help organize or participate in MDAnalysis events, such as User Group Meetings (UGMs) and workshops. -- **Support MDAnalysis:** MDAnalysis relies on grants, sponsorships, and donations to sustain development and community events. Your support helps fund maintenance, development, UGMs, workshops, and more. Learn more on our [Funding]({{ site.baseurl }}/pages/funding/) 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 @@ -28,6 +28,11 @@ Learn more on . ## Funding & Sponsors +NumFOCUS Sponsored + MDAnalysis is supported by grants, sponsorships, and community contributions. As a fiscally-sponsored project of [NumFOCUS][], we receive funding from various organizations that play key roles in supporting our development. See our [Funding]({{ site.baseurl }}/pages/funding/) page for more details on our **funding sources and how you can support MDAnalysis**. @@ -46,6 +51,6 @@ For full installation instructions and setup guides, visit our [Getting Started] [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://forms.gle/n8GLe2QsL2hW2QiDA +[this feedback form]: https://docs.google.com/forms/d/e/1FAIpQLScAjjI730i63LbyVkk_tuZ1-FCXUkg6xFugw_gmcsqUvBUtnw/viewform?usp=sf_link [NumFOCUS]: https://www.numfocus.org diff --git a/pages/conduct.md b/conduct.md similarity index 99% rename from pages/conduct.md rename to conduct.md index 68c0b6a6..2e1ec244 100644 --- a/pages/conduct.md +++ b/conduct.md @@ -1,7 +1,6 @@ --- -layout: page +layout: otherpage title: Code of Conduct -order: 0 --- diff --git a/pages/mission.md b/mission.md similarity index 79% rename from pages/mission.md rename to mission.md index e45def6b..316a36dd 100644 --- a/pages/mission.md +++ b/mission.md @@ -5,7 +5,7 @@ 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 }}/pages/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. +[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 From 7cf48dbf7cb71ea656ba126d7a256549eae14d76 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 21 Mar 2025 17:22:39 +0000 Subject: [PATCH 4/6] address PR review comment --- about.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/about.md b/about.md index 519a8edc..c8c05f21 100644 --- a/about.md +++ b/about.md @@ -33,7 +33,7 @@ Learn more on . sponsored project" alt="NumFOCUS Sponsored" style="display: inline; float: right; height: 4em; margin: 0 0.5em" /> -MDAnalysis is supported by grants, sponsorships, and community contributions. As a fiscally-sponsored project of [NumFOCUS][], we receive funding from various organizations that play key roles in supporting our development. +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. See our [Funding]({{ site.baseurl }}/pages/funding/) page for more details on our **funding sources and how you can support MDAnalysis**. From 831387c21dcf6218bde949d00381b04916dca34b Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Fri, 21 Mar 2025 19:16:12 +0000 Subject: [PATCH 5/6] minor fix - remove extra / --- about.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/about.md b/about.md index c8c05f21..615fedb5 100644 --- a/about.md +++ b/about.md @@ -20,7 +20,7 @@ The MDAnalysis Project is committed to open-source, reproducible computational r ## 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. +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. Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/pages/team/) pages for more details. From 5dd5e330834ee7f2d4877b18cdd1479c3c2a5af5 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Tue, 25 Mar 2025 19:31:27 +0000 Subject: [PATCH 6/6] remove redundant line-reference --- about.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/about.md b/about.md index 615fedb5..54b5ad6c 100644 --- a/about.md +++ b/about.md @@ -24,8 +24,6 @@ MDAnalysis is maintained by the [Core Developers]({{ site.baseurl }}/pages/gover Our governance structure ensures transparency and sustainability. See our [Governance]({{ site.baseurl }}/pages/governance/) and [Team]({{ site.baseurl }}/pages/team/) pages for more details. -Learn more on . - ## Funding & Sponsors