From 3702dc9512a369b487815254f31f692797d03d52 Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Tue, 4 Feb 2025 17:40:45 +0100 Subject: [PATCH 1/5] Upload coredev blog post --- _posts/2025-02-04-new_coredevs | 56 ++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 _posts/2025-02-04-new_coredevs diff --git a/_posts/2025-02-04-new_coredevs b/_posts/2025-02-04-new_coredevs new file mode 100644 index 00000000..abd16bcb --- /dev/null +++ b/_posts/2025-02-04-new_coredevs @@ -0,0 +1,56 @@ +--- +layout: post +title: Meet our New Core Developers! +--- + +We are thrilled to announce that MDAnalysis has elected three new [Core Developers]({{ site.baseurl }}/pages/about/#mdanalysis-core-developers/) to the project: @BradyAJohnston, @marinegor, and @p-j-smith. We thank each of them for the many contributions they have already made to the MDAnalysis project, and look forward to having them help shape the future direction of the project. Keep reading to [learn more about Brady, Egor, and Paul](#introductions), as well as the [process behind becoming a Core Developer](#becoming-a-core-developer) of MDAnalysis. + +## Introductions +### Brady Johnston (@BradyAJohnston) +Brady Johnston + +I originally did my PhD in structural biology at the University of Western Australia. Starting out doing crystallography, I became interested instead with ways to better visualise molecular data instead of collecting it. I created [Molecular Nodes](https://bradyajohnston.github.io/MolecularNodes) (MN) for cinematic visualisation of molecular data inside of the 3D modelling and animation program [Blender](https://blender.org). Molecular Nodes relies heavily on MDAnalysis for import and handling of molecular dynamics (MD) datasets, with projects going forward also allowing Blender to become a tool for analysing MD trajectories. I have now left academia and do freelance scientific illustration and development full time. You can contact me on on [BlueSky](https://bsky.app/profile/bradyajohnston.bsky.social), [GitHub](https://github.com/bradyajohnston), Discord and [LinkedIn](https://www.linkedin.com/in/bradyajohnston/) as @bradyajohnston, or see my [website](https://bradyajohnston.github.io). I’m always excited to chat about anything related to Blender and data visualisation. + +### Egor Marin (@marinegor) +Egor Marin + +Please write a short (1-2 paragraphs) bio here. Feel free to include your affiliation(s), ways you interface with MDAnalysis, and any other personal and/or professional interests. Please include any contact information you feel comfortable sharing publicly (e.g., GitHub/Discord handle, LinkedIn, website, etc.) + +### Paul Smith (@p-j-smith) +Brady Johnston + +Please write a short (1-2 paragraphs) bio here. Feel free to include your affiliation(s), ways you interface with MDAnalysis, and any other personal and/or professional interests. Please include any contact information you feel comfortable sharing publicly (e.g., GitHub/Discord handle, LinkedIn, website, etc.) + +## Becoming a Core Developer +MDAnalysis is a dynamic, ever-changing [community]({{ site.baseurl }}/pages/about/#community), with many new contributors joining continuously. It is important to us that the leadership of MDAnalysis reflects the community that builds it. Therefore, the MDAnalysis Core Developer team regularly holds elections for new core developers, as described in our [governance section]({{ site.baseurl }}/pages/about/#governance/). While this voting process is conducted in private, we are publishing and formalizing what we consider when voting, in the interests of transparency. + +Firstly, potential Core Developers are identified based on their past contributions to MDAnalysis and potential to move the MDAnalysis project forward. Contributions we account for include both those that are technical in nature, and also less quantifiable ones which add value to the MDAnalysis organization. Examples include: +* Fixing bugs +* Adding features +* Adding or fixing documentation +* Reviewing pull requests (PRs) +* Interacting with the community on [GitHub]({{ site.github.repo }}) or our Discord server ({{ site.discord.url }}) +* Participating in discussions in PRs and issues +* Organizing workshops or events +* Mentoring either in an official capacity (e.g., [Google Summer of Code](https://summerofcode.withgoogle.com/)) or unofficially (e.g., through reviewing PRs) +* Promoting a culture which reflects the core values of MDAnalysis, as detailed in our [Code of Conduct]({{ site.baseurl }}/pages/conduct/) (e.g., promoting diversity and inclusion within our community) +* Involvement in ongoing community projects (e.g., applying for grants) and liaising with other organisations, such as our fiscal sponsor, [NumFOCUS](https://numfocus.org/) + +If a candidate has shown a history of participating in these activities, they are put forward for election. The Core Developer team reviews the candidate and votes on whether or not they wish to elect an individual, following [our standard voting procedures]({{ site.baseurl }}/pages/about/#decision-making-process-and-membership/). + +Finally, being an active Core Developer requires some amount of active participation in meetings, decisions, and other administrative business. As MDAnalysis does not have any guaranteed long-term funding, this work is usually unpaid. Therefore, the final decision to accept or decline the election is left to the developers themselves: do they have the time and willingness to keep contributing? + +If you are interested in becoming a Core Developer, we highly encourage you to [participate]({{ site.baseurl }}/#participating) in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our [MDAnalysis team]({{ site.baseurl }}/pages/team/) page, and reach out to us on our [GitHub discussions forum]({{ site.mailinglists.discussions.url }}) or [Discord server]({{ site.discord.url }}) (join the server using the invitation link, [https://discord.gg/fXTSfDJyxE]({{ site.discord.invite }}). On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer. + +Being a Core Developer is work, but it’s also a fantastic opportunity to work with and for a wonderful and welcoming community. As part of [our mission]({{ site.baseurl }}/about/#mission), we welcome anyone who cares for this community and wants to help it grow. + +— [@MDAnalysis/coredevs](https://github.com/orgs/MDAnalysis/teams/coredevs) From f7649131fa0a62d088da3824bd6ec8b33935998c Mon Sep 17 00:00:00 2001 From: Oliver Beckstein Date: Wed, 5 Feb 2025 09:23:42 -0700 Subject: [PATCH 2/5] add Paul's bio Co-authored-by: Paul Smith --- _posts/2025-02-04-new_coredevs | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/_posts/2025-02-04-new_coredevs b/_posts/2025-02-04-new_coredevs index abd16bcb..adc4f16a 100644 --- a/_posts/2025-02-04-new_coredevs +++ b/_posts/2025-02-04-new_coredevs @@ -28,7 +28,9 @@ src="Picture Here" title="Brady Johnston" alt="Brady Johnston" style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" /> -Please write a short (1-2 paragraphs) bio here. Feel free to include your affiliation(s), ways you interface with MDAnalysis, and any other personal and/or professional interests. Please include any contact information you feel comfortable sharing publicly (e.g., GitHub/Discord handle, LinkedIn, website, etc.) +I did my PhD in computational biophysics at King's College London, using molecular dynamics simulations to study the biophysics of lipid membranes. During my PhD, I began contributing to open-source scientific software, including MDAnalysis. I created [LiPyphilic](https://github.com/p-j-smith/lipyphilic) - an open-source Python package for analysing simulations of lipid membranes, built on top of MDAnalysis. + +I'm now a Research Software Engineer at [University College London](https://www.ucl.ac.uk/advanced-research-computing/), working on projects broadly related to medical imaging. I'm excited to join the Core Developer team, and always happy to chat about biophysics and open-source software. You can get in touch with me on [LinkedIN](https://www.linkedin.com/in/p-j-smith/) or [GitHub](https://github.com/p-j-smith). ## Becoming a Core Developer MDAnalysis is a dynamic, ever-changing [community]({{ site.baseurl }}/pages/about/#community), with many new contributors joining continuously. It is important to us that the leadership of MDAnalysis reflects the community that builds it. Therefore, the MDAnalysis Core Developer team regularly holds elections for new core developers, as described in our [governance section]({{ site.baseurl }}/pages/about/#governance/). While this voting process is conducted in private, we are publishing and formalizing what we consider when voting, in the interests of transparency. From 5edb37533cbef2ca5064a5a26037bce604980d18 Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Fri, 7 Feb 2025 17:53:09 +0100 Subject: [PATCH 3/5] Use variable for discord invite link Co-authored-by: Oliver Beckstein --- _posts/2025-02-04-new_coredevs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-02-04-new_coredevs b/_posts/2025-02-04-new_coredevs index adc4f16a..6dad1e03 100644 --- a/_posts/2025-02-04-new_coredevs +++ b/_posts/2025-02-04-new_coredevs @@ -51,7 +51,7 @@ If a candidate has shown a history of participating in these activities, they ar Finally, being an active Core Developer requires some amount of active participation in meetings, decisions, and other administrative business. As MDAnalysis does not have any guaranteed long-term funding, this work is usually unpaid. Therefore, the final decision to accept or decline the election is left to the developers themselves: do they have the time and willingness to keep contributing? -If you are interested in becoming a Core Developer, we highly encourage you to [participate]({{ site.baseurl }}/#participating) in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our [MDAnalysis team]({{ site.baseurl }}/pages/team/) page, and reach out to us on our [GitHub discussions forum]({{ site.mailinglists.discussions.url }}) or [Discord server]({{ site.discord.url }}) (join the server using the invitation link, [https://discord.gg/fXTSfDJyxE]({{ site.discord.invite }}). On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer. +If you are interested in becoming a Core Developer, we highly encourage you to [participate]({{ site.baseurl }}/#participating) in some of the activities listed above, especially reviewing pull requests and mentoring other developers. Learn more about the many roles MDAnalysis community members take on to move the project forward on our [MDAnalysis team]({{ site.baseurl }}/pages/team/) page, and reach out to us on our [GitHub discussions forum]({{ site.mailinglists.discussions.url }}) or [Discord server]({{ site.discord.url }}) (join the server using the invitation link, [{{ site.discord.invite }}]({{ site.discord.invite }}). On our end, the MDAnalysis Core Developer team will, to the best of its abilities, aim to offer mentorship and other opportunities to people who express an interest in becoming a Core Developer. Being a Core Developer is work, but it’s also a fantastic opportunity to work with and for a wonderful and welcoming community. As part of [our mission]({{ site.baseurl }}/about/#mission), we welcome anyone who cares for this community and wants to help it grow. From 0fe93e6c21f20922f5105de30cc685c91ec7b2d2 Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Fri, 7 Feb 2025 19:19:31 +0100 Subject: [PATCH 4/5] Fix text for Paul's photo ( copy/paste error :) ) --- _posts/2025-02-04-new_coredevs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-02-04-new_coredevs b/_posts/2025-02-04-new_coredevs index 6dad1e03..bed75aa2 100644 --- a/_posts/2025-02-04-new_coredevs +++ b/_posts/2025-02-04-new_coredevs @@ -25,7 +25,7 @@ Please write a short (1-2 paragraphs) bio here. Feel free to include your affili ### Paul Smith (@p-j-smith) Brady Johnston I did my PhD in computational biophysics at King's College London, using molecular dynamics simulations to study the biophysics of lipid membranes. During my PhD, I began contributing to open-source scientific software, including MDAnalysis. I created [LiPyphilic](https://github.com/p-j-smith/lipyphilic) - an open-source Python package for analysing simulations of lipid membranes, built on top of MDAnalysis. From 4b08264e83fde743208a54bb197e3211dd588e7a Mon Sep 17 00:00:00 2001 From: Egor Marin Date: Mon, 10 Feb 2025 01:02:00 +0100 Subject: [PATCH 5/5] Update 2025-02-04-new_coredevs Add information about Egor Marin --- _posts/2025-02-04-new_coredevs | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/_posts/2025-02-04-new_coredevs b/_posts/2025-02-04-new_coredevs index bed75aa2..1741dd1a 100644 --- a/_posts/2025-02-04-new_coredevs +++ b/_posts/2025-02-04-new_coredevs @@ -20,7 +20,9 @@ src="Picture Here" title="Egor Marin" alt="Egor Marin" style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" /> -Please write a short (1-2 paragraphs) bio here. Feel free to include your affiliation(s), ways you interface with MDAnalysis, and any other personal and/or professional interests. Please include any contact information you feel comfortable sharing publicly (e.g., GitHub/Discord handle, LinkedIn, website, etc.) +I started my career as a scientist from macromolecular crystallography, and during my PhD slowly moved towards structural bioinformatics and relevant machine learning methods. +I am currently employed at [ENPICOM B.V.](https://enpicom.com/about-us/) as Machine Learning Scientist, and continue contributing to open-source as much as I can. +You can find me as `@marinegor` almost everywhere, and check out [marinegor.dev](https://marinegor.dev) for some short-form tech posts about my research and open-source work. ### Paul Smith (@p-j-smith)