From 1333452cb59dbf8ad094ee5b811c7e17d56f845b Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Wed, 29 May 2024 16:07:24 +0200 Subject: [PATCH] Upload skeleton blog post for GSoC and Outreachy intros (#378) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Upload skeleton intro post for gsoc/outreachy * Update 2024-05-03-gsoc-outreachy-students.md * Lawson Post (#22) * Lawson Post * Update _posts/2024-05-03-gsoc-outreachy-students.md * Update _posts/2024-05-03-gsoc-outreachy-students.md --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * GSOC2024 Valerij Post (#23) * Update 2024-05-03-gsoc-outreachy-students.md Added Picture and project description * Update 2024-05-03-gsoc-outreachy-students.md Added Background an social * Update 2024-05-03-gsoc-outreachy-students.md * Change GSOC to GSoC and link to Jupyter Notebook docs * Grammatical edits and fix link to Wolber lab --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * Update 2024-05-03-gsoc-outreachy-students.md (#26) * Add GSoC and Outreachy logos * Luna post (#27) * MDA/MolSSI workshop page with registration (#379) * draft for MDA/MolSSI workshop page * Apply suggestions from code review Co-authored-by: Rocco Meli * ASU workshop edits - moved public transport before rideshare - add May 29 as deadline for informing bursary applicants * placeholder for registration button * reST fixes * Apply suggestions from code review Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * ASU workshop - single registration deadline May 27 - add paragraph on intended audience and skill level (from reg form) - changed header indentation levels - clarified in-person vs online * add @armcdona to the org team for MolSSI * changed "by May 29" to "on May 29 or earlier" * spell-checked * Remove extra 'will' --------- Co-authored-by: Rocco Meli Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * update actions * Update UGM event page (#387) * Add registration form link * Add draft agenda link * Upload draft UGM agenda * Add MGMS logo to sponsors * Upload MGMS logo * Fix links for agenda and MGMS logo * Add KCL summer accommodations as hotel option * Update ugm2024.md small edits * Update ugm2024.md highlighted registration vs abstracts * Move registration section further up * Add full venue address * Update Francesca's affiliation Uploading new speaker announcement card (from blog post, https://www.mdanalysis.org/2024/03/14/ugm2024-updates) to reflect the rebranding of Sosei Heptares --> Nxera Pharma (since we will be advertising the keynotes when we send out registration advertisements) --------- Co-authored-by: Micaela Matta <31009265+micaela-matta@users.noreply.github.com> * Update UGM agenda (add Racquel's surname) * Fix typo in Raquel's name * Several updates to UGM page (#389) * Add UGM 2024 logo * Add link to abstracts book * Upload updated agenda and abstracts book * Add food suggestions * Add additional transportation details * Add TYC logo * Change 'verbal' to 'oral' in abstracts book * Change 'Lisbon' to 'London' * Add UGM 2024 logo * Fix link to UGM 2024 logo * Add links to restaurant websites * Line breaks between sponsor images and switch NF logo (previous was poor resolution) * Try putting images on new lines with

* Switch

to
and add hyperlinks to sponsor logos * Remove
tags * Point to MolSSI python lesson (#390) Closes https://github.com/MDAnalysis/MDAnalysis.github.io/issues/386 as discussed during the last workshop planning meeting * Upload skeleton intro post for gsoc/outreachy * Update 2024-05-03-gsoc-outreachy-students.md * Lawson Post (#22) * Lawson Post * Update _posts/2024-05-03-gsoc-outreachy-students.md * Update _posts/2024-05-03-gsoc-outreachy-students.md --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * GSOC2024 Valerij Post (#23) * Update 2024-05-03-gsoc-outreachy-students.md Added Picture and project description * Update 2024-05-03-gsoc-outreachy-students.md Added Background an social * Update 2024-05-03-gsoc-outreachy-students.md * Change GSOC to GSoC and link to Jupyter Notebook docs * Grammatical edits and fix link to Wolber lab --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * Update 2024-05-03-gsoc-outreachy-students.md (#26) * Add GSoC and Outreachy logos * Luna post --------- Co-authored-by: Oliver Beckstein Co-authored-by: Rocco Meli Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Co-authored-by: Micaela Matta <31009265+micaela-matta@users.noreply.github.com> Co-authored-by: ljwoods2 <145226270+ljwoods2@users.noreply.github.com> Co-authored-by: Valerij Talagayev <82884038+talagayev@users.noreply.github.com> Co-authored-by: Adetutu Oluwasanmi * Update date for blog post * Incorporate Cedric's suggested text for Valerij's project Co-authored-by: Cédric Bouysset * Streamline code by removing GH profile links * Update to SSL links (where not already) * Edit OpenBabel sentence --------- Co-authored-by: ljwoods2 <145226270+ljwoods2@users.noreply.github.com> Co-authored-by: Valerij Talagayev <82884038+talagayev@users.noreply.github.com> Co-authored-by: Adetutu Oluwasanmi Co-authored-by: Luna Morrow <159094759+lunamorrow@users.noreply.github.com> Co-authored-by: Oliver Beckstein Co-authored-by: Rocco Meli Co-authored-by: Micaela Matta <31009265+micaela-matta@users.noreply.github.com> Co-authored-by: Cédric Bouysset --- _posts/2024-05-27-gsoc-outreachy-students.md | 86 ++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 _posts/2024-05-27-gsoc-outreachy-students.md diff --git a/_posts/2024-05-27-gsoc-outreachy-students.md b/_posts/2024-05-27-gsoc-outreachy-students.md new file mode 100644 index 00000000..542a50fa --- /dev/null +++ b/_posts/2024-05-27-gsoc-outreachy-students.md @@ -0,0 +1,86 @@ +--- +layout: post +title: Google Summer of Code and Outreachy Students 2024 +--- + +We are happy to announce that MDAnalysis is hosting three [Google Summer of Code][gsoc] (GSoC) contributors - @ljwoods2, @talagayev and @lunamorrow - and an [Outreachy][outreachy] intern - @adetutudeborah. MDAnalysis has been accepted as its own [organization with GSoC][mda-gsoc] for the fifth year running, and we are excited to be hosting our second-ever [MDAnalysis Outreachy internship][mda-outreachy]. We are grateful to Google and Outreachy for granting us the opportunity to get started on _four_ very exciting projects! + +# GSoC + + Google Summer of Code + +## Lawson Woods: [Enhancing the Interoperability and Efficiency of the Zarrtraj MDAKit](https://summerofcode.withgoogle.com/programs/2024/projects/BYYAE9MR) + +Lawson Woods + +Streaming trajectory data directly from cloud storage will allow researchers to share their trajectories more easily than ever before, however, rewriting existing trajectory file readers for cloud-streaming would be a slow and complex process. [zarrtraj](https://github.com/Becksteinlab/zarrtraj), a trajectory file format based on [Zarr](https://zarr.readthedocs.io/en/stable/) storage, presents an alternative which natively supports AWS S3, Google Cloud Buckets, and Azure Blob Storage in addition to reading from a local directory without much added complexity. Lawson's GSoC 2024 project will be to continue enhancing the ease-of-use, robustness, and efficiency of this format. + +Lawson is a computer science student at Arizona State University (ASU) graduating in December 2024. You can find Lawson on GitHub as @ljwoods2 and on [LinkedIn](https://www.linkedin.com/in/lawson-woods/). To see updates on the `zarrtraj` project as well as his other projects you can check out [his blog](https://ljwoods2.github.io/). + +## Valerij Talagayev: [2D Visualization for Small Molecules](https://summerofcode.withgoogle.com/programs/2024/projects/sfy3kuqc) + +Valerij Talagayev + +The main objective of Valerij's GSoC project will revolve around the visualization of small molecules in 2D through the application of the MDAnalysis RDKit converter, which allows converting MDAnalysis atomgroups into RDKit objects and benefit from its powerful drawing code to display small molecules. These can then be annotated at the atom level with information associated with the MDAnalysis Universe or arbitrary data in an easy to use interactive display in [Jupyter Notebooks](https://jupyter-notebook.readthedocs.io/en/stable/). + +Valerij is a pharmacy student who graduated from the University of Marburg, where he worked at the [Kolb Lab](https://www.uni-marburg.de/en/fb16/ipc/kolb-group). Valerij is currently a PhD student at the Free University of Berlin in the [Wolber Lab](https://www.bcp.fu-berlin.de/en/pharmazie/faecher/pharmazeutische_chemie/wolber/index.html) with his research revolving around Toll-like receptor antagonists with addition to method development such as [OpenMMDL](https://github.com/wolberlab/OpenMMDL). + +You can find Valerij on Github as @talagayev and on [LinkedIn](https://www.linkedin.com/in/valerij-talagayev-260bb820b). To see the updates on the 2D visualization of small molecules project follow his [blog](https://talagayev.github.io/). + +## Luna Morrow: [Extend MDAnalysis Interoperability with OpenBabel](https://summerofcode.withgoogle.com/programs/2024/projects/yLzX6MjS) + +Luna Morrow + +Direct interoperability between molecular dynamics software is critical for enabling collaboration, data transfer and easy use by scientists. [OpenBabel](https://openbabel.org/) is a popular toolbox for chemical molecular modelling as it allows conversion, searching, filtering and analysis of chemical data. The ability to interconvert between OpenBabel OBMols and MDAnalysis AtomGroups will enable input and writing of over 100 chemical data file formats. + +Luna is a Bachelor of Advanced Science (Honours) student at the University of Queensland (Australia), studying biochemistry, computational sciences and software engineering. Luna currently works as a research assistant in Megan O'Mara's group at the Australian Institute of Bioengineering and Nanotechnology, where her role involves code creation, maintenance and improvement. She is pursuing a career as a research software engineer. In her down time around university and work, Luna enjoys hiking, going to the gym, reading, buying plants, cuddling her cat Eddie and spending time with her partner and friends. + +You can find Luna on GitHub as @lunamorrow and on [LinkedIn](https://www.linkedin.com/in/luna-morrow-b2b027232/). To keep up to date with the `Extend MDAnalysis Interoperability with OpenBabel` project, check out her [blog](https://lunamorrow.github.io). + +# Outreachy + +Outreachy + +## Adetutu Oluwasanmi: [Develop a Communications Strategy for a Growing MDAnalysis User and Contributor Base][mda-outreachy] + +Adetutu Oluwasanmi + + +MDAnalysis aims to establish clear communication channels to effectively disseminate information, engage the community, and encourage participation. The main objective of Adetutu's [Outreachy](https://www.outreachy.org/) project is to develop a social media and communications strategy for MDAnalysis to grow its user and contributor base. + +Adetutu will conduct surveys to understand the communication preferences of MDAnalysis developers and users. Based on the survey data, she will recommend the best platforms for discussions and increasing engagement. +Additionally, she will set up an email newsletter to keep the community updated on MDAnalysis news, announcements, and events. + +Adetutu Oluwasanmi is a First-Class Microbiology graduate from Lagos State University. She recently completed a 1-year diploma in software engineering at AltSchool Africa, where she gained coding and software development skills. +Her previous roles include social media manager, communications intern, and freelance science writer, giving her a diverse skill set that she brings to her current project. + +Adetutu is on GitHub as @adetutudeborah, and on Twitter as [@adetutuoluwa2](https://twitter.com/adetutuoluwa2). + +She will be documenting her internship journey on her [Medium blog](https://medium.com/@adetutuoluwasanmi). Feel free to check it out for updates on her experience! + + +— @BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins) + +[gsoc]: https://summerofcode.withgoogle.com +[outreachy]: https://www.outreachy.org/ +[mda-gsoc]: https://summerofcode.withgoogle.com/programs/2024/organizations/mdanalysis +[mda-outreachy]: https://www.outreachy.org/alums/2024-05/