From 82da757fb00f353affaf587ad54237adb02a06a0 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 10 Mar 2025 16:23:32 +0000 Subject: [PATCH 1/3] refine 'learning MDAnalysis' page --- pages/learning_MDAnalysis.md | 53 ++++++------------------------------ 1 file changed, 8 insertions(+), 45 deletions(-) diff --git a/pages/learning_MDAnalysis.md b/pages/learning_MDAnalysis.md index 23a52a27..6bb4ec60 100644 --- a/pages/learning_MDAnalysis.md +++ b/pages/learning_MDAnalysis.md @@ -4,60 +4,23 @@ title: Learning MDAnalysis order: 3 --- -Once you had a look at the -[basic example]({{ site.baseurl }}/pages/basic_example) -you might want to learn more about how to use -MDAnalysis. MDAnalysis is primarily a library that helps you to build -your own tools but it also works very well for **interactive data -exploration** of MD data in [IPython](http://ipython.org/), in -particular within [Jupyter notebooks](https://jupyter.org/) and in -conjunction with [pandas](http://pandas.pydata.org/). MDAnalysis is -well suited for a *rapid development* approach. - -The resources below should help you to quickly find out to best use -MDAnalysis for your own specific uses. +MDAnalysis is a powerful Python library for analyzing MD simulations. While primarily designed to help you build custom analysis tools, it also supports interactive data exploration in environments like [IPython](http://ipython.org/) and [Jupyter notebooks](https://jupyter.org/), especially when combined with [pandas](http://pandas.pydata.org/). This makes MDAnalysis an excellent choice for rapid prototyping and exploratory analysis. +Whether you're new to MDAnalysis or looking to deepen your expertise, this page will guide you through our learning resources. ## Tutorials ## -Start with the [{{ site.docs.quickstart.name }}]({{ -site.docs.quickstart.url }}) when you are new MDAnalysis. - -Then browse the [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}), which contains detailed documentation for all the important parts of MDAnalysis and many self-contained tutorials. - - -There are a number of [older tutorials]({{site.github.wiki}}/Tutorials) available, too, although we recommend new users start with [{{ site.docs.quickstart.name }}]({{ -site.docs.quickstart.url }}) and then start reading the [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}). - - -## Documentation ## - -The [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}) -contains installation instructions, the [{{ site.docs.quickstart.name -}}]({{ site.docs.quickstart.url }}), and comprehensive description of -the functionality of MDAnalysis from a user's perspective. **New users -should start here!** - -The [{{ site.docs.mdanalysis.name }}]({{ site.docs.mdanalysis.url }}) -contains technical information on how to use MDAnalysis. - -The [paper on MDAnalysis]({{ site.baseurl -}}/pages/citations#Gowers2016) contains a high-level description of -the structure and philosophy of the library together with examples of -its use. +If you are new to MDAnalysis, start with: -The [FAQ]({{ site.github.wiki }}/FAQ) contains a -growing list of specific (frequently asked) questions and answers. +- [{{ site.docs.quickstart.name }}]({{ site.docs.quickstart.url }}) – A quick introduction to MDAnalysis. +- [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}) – Detailed documentation with in-depth tutorials. -## GitHub Discussions ## +For full documentation, visit the [Documentation page]({{ site.docs.url }}). You can ask for advice or help on [{{ site.mailinglists.discussion.name }}]({{ -site.mailinglists.discussion.url }}). If you find *bugs* or -want to *request enhancements* please [file a report]({{ -site.github.wiki }}/ReportingProblems) in the [Issue Tracker]({{ -sitemap.github.issues }}). +site.mailinglists.discussion.url }}). If you find *bugs* or want to *request enhancements* please [file a report]({{site.github.wiki }}/ReportingProblems) in the [Issue Tracker]({{sitemap.github.issues }}). -## Videos ## +## Learning through Videos ## The videos listed below were given by core developers at conferences. They highlight various aspects of MDAnalysis and show how From dfcec08ff8d2e39eb2cad5ca072faa85bdde0678 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Mon, 10 Mar 2025 17:49:34 +0000 Subject: [PATCH 2/3] address PR review comments --- pages/learning_MDAnalysis.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/pages/learning_MDAnalysis.md b/pages/learning_MDAnalysis.md index 6bb4ec60..b6b9e2cd 100644 --- a/pages/learning_MDAnalysis.md +++ b/pages/learning_MDAnalysis.md @@ -20,11 +20,11 @@ For full documentation, visit the [Documentation page]({{ site.docs.url }}). You can ask for advice or help on [{{ site.mailinglists.discussion.name }}]({{ site.mailinglists.discussion.url }}). If you find *bugs* or want to *request enhancements* please [file a report]({{site.github.wiki }}/ReportingProblems) in the [Issue Tracker]({{sitemap.github.issues }}). -## Learning through Videos ## +## Videos ## -The videos listed below were given by core developers at -conferences. They highlight various aspects of MDAnalysis and show how -to use it in a research context. +The following videos, presented by core developers at conferences, highlight various aspects of MDAnalysis and demonstrate its use in research. + +In addition to conference talks, we have recorded and published a number of MDAnalysis workshop sessions on our [YouTube channel](https://www.youtube.com/channel/UC3TCuK-z_bJNdwWCvsH9D3Q), which cover hands-on tutorials and more in-depth discussions of the library's features. ### Introductory ### @@ -88,3 +88,4 @@ MDAnalysis**, show more advanced ways to **hack MDAnalysis** and outline allowfullscreen class="video"> + From b3ca08de74264c70de1552e4bf668eed285c0929 Mon Sep 17 00:00:00 2001 From: Namir Oues Date: Wed, 12 Mar 2025 15:42:37 +0000 Subject: [PATCH 3/3] address PR review comments and restructure page --- pages/learning_MDAnalysis.md | 37 +++++++++++++++++++++--------------- 1 file changed, 22 insertions(+), 15 deletions(-) diff --git a/pages/learning_MDAnalysis.md b/pages/learning_MDAnalysis.md index b6b9e2cd..073c5974 100644 --- a/pages/learning_MDAnalysis.md +++ b/pages/learning_MDAnalysis.md @@ -6,27 +6,37 @@ order: 3 MDAnalysis is a powerful Python library for analyzing MD simulations. While primarily designed to help you build custom analysis tools, it also supports interactive data exploration in environments like [IPython](http://ipython.org/) and [Jupyter notebooks](https://jupyter.org/), especially when combined with [pandas](http://pandas.pydata.org/). This makes MDAnalysis an excellent choice for rapid prototyping and exploratory analysis. +MDAnalysis is an academic software package, and if you use it in your research, please cite the relevant publications. For details on how to cite MDAnalysis, visit our [Citations]({{ site.baseurl }}/pages/citations/) page. + Whether you're new to MDAnalysis or looking to deepen your expertise, this page will guide you through our learning resources. -## Tutorials ## +## Step-by-Step Guide to Learning MDAnalysis -If you are new to MDAnalysis, start with: +1. **Install MDAnalysis** + Follow the instructions in [Getting Started]({{ site.baseurl }}/pages/getting_started/) to install MDAnalysis. -- [{{ site.docs.quickstart.name }}]({{ site.docs.quickstart.url }}) – A quick introduction to MDAnalysis. -- [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}) – Detailed documentation with in-depth tutorials. +2. **Quickstart Tutorial** + Begin with the [{{ site.docs.quickstart.name }}]({{ site.docs.quickstart.url }}) tutorial to write and run your first MDAnalysis script. -For full documentation, visit the [Documentation page]({{ site.docs.url }}). +3. **User Guide** + Explore the [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}) for detailed tutorials and self-contained examples. -You can ask for advice or help on [{{ site.mailinglists.discussion.name }}]({{ -site.mailinglists.discussion.url }}). If you find *bugs* or want to *request enhancements* please [file a report]({{site.github.wiki }}/ReportingProblems) in the [Issue Tracker]({{sitemap.github.issues }}). +4. **Tutorials Repository** + Browse additional learning resources and code examples in our Tutorials repository. -## Videos ## +5. **Full Documentation** + For in-depth technical details, visit the [Documentation]({{ site.baseurl }}/pages/documentation/) page. -The following videos, presented by core developers at conferences, highlight various aspects of MDAnalysis and demonstrate its use in research. +6. **Watch MDAnalysis videos** + Learn from conference talks, workshops, and webinars presented by core developers. Explore the [Videos](#videos) section below and our [YouTube channel](https://www.youtube.com/channel/UC3TCuK-z_bJNdwWCvsH9D3Q). + +If you need help, check out our [Community]({{ site.baseurl }}/pages/community/) page. -In addition to conference talks, we have recorded and published a number of MDAnalysis workshop sessions on our [YouTube channel](https://www.youtube.com/channel/UC3TCuK-z_bJNdwWCvsH9D3Q), which cover hands-on tutorials and more in-depth discussions of the library's features. +## Videos + +The following videos, presented by core developers at conferences, highlight various aspects of MDAnalysis and demonstrate its use in research. -### Introductory ### +### Introductory #### The universe as balls and springs: molecular dynamics in Python @lilyminium's talk at [PyCon AU 2019](https://2019.pycon-au.org/) *The universe as balls and @@ -58,9 +68,7 @@ analysis of molecular dynamics simulations](http://conference.scipy.org/proceedings/scipy2016/oliver_beckstein.html) which adds detail to the concepts outlined in this talk. - - -### Intermediate ### +### Intermediate #### Looking at molecules using Python @jbarnoud presented at the PyGrunn 2017 conference _Looking at @@ -75,7 +83,6 @@ data): allowfullscreen class="video"> - #### BioExcel Webinar: MDAnalysis: Interoperable analysis of biomolecular simulations in Python In this [BioExcel](https://bioexcel.eu/) webinar, three of the MDAnalysis Core