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75 changes: 23 additions & 52 deletions pages/learning_MDAnalysis.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,66 +4,39 @@ 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.
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.

The resources below should help you to quickly find out to best use
MDAnalysis for your own specific uses.
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

Start with the [{{ site.docs.quickstart.name }}]({{
site.docs.quickstart.url }}) when you are new MDAnalysis.
1. **Install MDAnalysis**
Follow the instructions in [Getting Started]({{ site.baseurl }}/pages/getting_started/) to install 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.
2. **Quickstart Tutorial**
Begin with the [{{ site.docs.quickstart.name }}]({{ site.docs.quickstart.url }}) tutorial to write and run your first MDAnalysis script.

3. **User Guide**
Explore the [{{ site.docs.userguide.name }}]({{ site.docs.userguide.url }}) for detailed tutorials and self-contained examples.

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 }}).
4. **Tutorials Repository**
Browse additional learning resources and code examples in our Tutorials repository.

5. **Full Documentation**
For in-depth technical details, visit the [Documentation]({{ site.baseurl }}/pages/documentation/) page.

## Documentation ##
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.

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!**
## Videos

The [{{ site.docs.mdanalysis.name }}]({{ site.docs.mdanalysis.url }})
contains technical information on how to use MDAnalysis.
The following videos, presented by core developers at conferences, highlight various aspects of MDAnalysis and demonstrate its use in research.

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.

The [FAQ]({{ site.github.wiki }}/FAQ) contains a
growing list of specific (frequently asked) questions and answers.

## GitHub Discussions ##

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 }}).

## 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.

### 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
Expand Down Expand Up @@ -95,9 +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
Expand All @@ -112,7 +83,6 @@ data):
allowfullscreen class="video"></iframe>
</div>


#### BioExcel Webinar: MDAnalysis: Interoperable analysis of biomolecular simulations in Python

In this [BioExcel](https://bioexcel.eu/) webinar, three of the MDAnalysis Core
Expand All @@ -125,3 +95,4 @@ MDAnalysis**, show more advanced ways to **hack MDAnalysis** and outline
allowfullscreen class="video"></iframe>
</div>


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