MDAnalysis/MolSSI Workshop at Arizona State University 2024

Materials for the June 24-25, 2024 MDAnalysis/MolSSI workshop at Arizona State University (ASU).

Instructors

Irfan Alibay - @IAlibay
Oliver Beckstein - @orbeckst
Sam Ellis - @sjayellis
Mike Henry - @mikemhenry
Ian Kenney - @ianmkenney
Fiona Naughton - @fiona-naughton
Ashley Ringer-Macdonald - @armcdona
Yuxuan Zhuang - @yuxuanzhuang

Location

Workshop Lectures and Tutorials:

Room PSF 186, Physical Sciences F Building
Department of Physics
Arizona State University
550 E Tyler Mall, PSF 186
Tempe, AZ 85287
USA

Schedule

Day 1, June 24th

Time (MST)	Session	Materials
08:00-09:00	Breakfast and Check-In/Registration
09:00-09:15	Introduction	Introduction Slides
09:15-10:05	Introduction to MDAnalysis: The Universe	Lecture 1, Tutorial 1
10:05-11:00	Introduction to MDAnalysis: File I/O	Lecture 2, Tutorial 2
11:00-11:15	Break
11:15-12:05	MDAnalysis: Analysis	Lecture 3, Tutorial 3
12:05-12:45	MDAnalysis: Advanced Tips and Tricks	Lecture 4, Tutorial 4
12:45-12:55	Introduction to MDAKits	MDAKits intro lecture
12:55-13:05	Group Photo
13:05-14:00	Lunch
14:00-14:30	Introduction to the Bash Shell	Software Carpentry Tutorial, MolSSI Command Line Basics Lesson
14:30-16:00	Python Packaging	MolSSI Python Package Set-Up Lesson
16:00-16:15	Break
16:15-18:15	Version Control	MolSSI git and GitHub Lessons

Day 2, June 25th

Time (MST)	Session	Materials
08:00-09:00	Breakfast and Check-In/Registration
09:00-10:45	Testing and pytest	MolSSI Testing Lessons
10:45-11:00	Break
11:00-12:30	Documentation	MolSSI Documentation Lessons
12:30-13:30	Lunch
13:30-13:40	Hackathon Introduction	Hackathon Intro Slides
13:40-15:30	Hackathon	Hackathon Directory
15:30-15:45	Break
15:45-17:15	Hackathon	Hackathon Directory
17:15-17:45	Hackathon Wrap-Up and Showcase
17:45-18:00	Closing Remarks

Hackathon

The hackathon will be held on the second day of the workshop. We encourage you to start thinking about what you want to work on early. More information and ideas can be found in the hackathon directory.

Setting up your Python Environment Before the Workshop

Instructions for setting up your environment to run this workshop locally are provided in [`INSTALL.md`](INSTALL.md). A full list of the required Python packages can be seen inside [`environment.yml`](environment.yml). As downloading and installing everything will take a little while, ideally you should follow these steps before the workshop starts. If you encounter any issues during installation, we can help! **Note:** Materials may change between now and the time of the workshop, so while we ask you to install ahead of time, also make sure to `git pull` just prior to the start of the workshop. ## Google Colab If for any reason you cannot set up a local environment with all required packages, you can use Google Colab to run all workshop notebooks directly from your browser, no installation required. | Tutorial | Materials | |-------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------| | **Tutorial 1:** Loading and Manipulating your Molecular Simulation Data | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day/blob/jun24-ws/notebooks/Tutorial1_System_Manipulation.ipynb) | | **Tutorial 2:** Positions, Distances and Trajectories | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day/blob/jun24-ws/notebooks/Tutorial2_Trajectories.ipynb) | | **Tutorial 3:** Analysis Tools | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day/blob/jun24-ws/notebooks/Tutorial3_Analysis.ipynb) | | **Tutorial 4:** Advanced Universe Creation and Attributes | [](https://colab.research.google.com/github/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day/blob/jun24-ws/notebooks/Tutorial4_Advanced.ipynb) | ## Asking Questions *Before and During the Workshop* The primary communication channel for asking questions and having relevant discussions for this workshop will be the [MDAnalysis Discord server](https://discord.com/channels/807348386012987462/). To join the server, use the invitation link, [https://discord.gg/dMQWjNcZmh](https://discord.gg/dMQWjNcZmh). If you are new to Discord, [here are some resources](https://support.discord.com/hc/en-us/categories/115000217151) to help you get started. Once you join the server, you will see a “ASU WORKSHOP 2024” category. Start exploring the specific channels and read their descriptions to get used to the organization. You are welcome to introduce yourself in the `#general` channel and start asking any workshop-related questions in the `#questions` forum. Unfortunately Discord is limited in its ability to collapse the post titles posted in the `#questions` and `#hackathon` forums, so a workaround is to mute these channels (a post should show again if someone updates it). ## Connecting to the Wireless Network/Wifi * The **asu guest** wireless network is *available to all participants* but limited in capabilities. * The **eduroam** network is available to anyone whose institution participates in [eduroam](https://eduroam.org/). If you need to set up anything, talk to your institution's IT support *before* coming to ASU. * The **asu** network is only available to members of Arizona State University. ### "asu guest" network Full instructions for connecting to the **asu guest** wireless network can be found in [`connecting-to-the-asu-wifi.pdf`](https://github.com/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day/blob/jun24-ws/connecting-to-the-asu-wifi.pdf). You will need a means to read email or receive text messages because as part of the registration process, a code will be sent to you. *The "asu guest" network is bandwidth-limited. Make sure that you [install the workshop environment](INSTALL.md) before coming to ASU.* ### eduroam Provide your institution credentials. See https://eduroam.org/ and your institution's documentation for how to set up. ## Workshop Pre-Requisites The workshop assumes that attendees have a working knowledge of [Jupyter notebooks][1] and Python (especially the [NumPy library][2]). For a better idea of things participants should be comfortable doing in Python or to freshen up on your skills, please have a look at the MolSSI lesson, “[Python Scripting for Computational Molecular Science](https://education.molssi.org/python_scripting_cms/)”. ## Code of Conduct All members of the MDAnalysis community and participants in MDAnalysis workshops are expected to abide by the MDAnalysis [Code of Conduct](https://www.mdanalysis.org/pages/conduct/). If at any point you experience harassment or witness a violation of our Code of Conduct, please [report it](https://www.mdanalysis.org/pages/conduct/#reporting). If you just need to talk to someone, maybe you are unsure about something or something just doesn't quite feel right, please see the [list of ombudspersons with contact details](REPORTING.md) ## Health and Safety We are committed to providing a safe, comfortable, and healthy environment for the workshop and have looked to local and international entities and other organizations in the open source community to develop onsite safety measures for workshop attendees. ### Testing A limited number of rapid self-tests will be made available at check-in for those who would like to test themselves for COVID-19 during the meeting. **Testing Positive for COVID-19** *Individuals who are COVID-positive should not attend the workshop.* If you receive a positive COVID-19 test result during the workshop, please [notify the workshop organizing committee][workshop_email] and do not return to the event while you are still COVID-positive. * We will treat any information about your testing status as confidential. (If you want to notify any of your contacts you may, of course, do so yourself.) * We will announce to attendees if we are made aware of anyone testing positive for SARS-Cov-2 so that all attendees and instructors are put in a position to make choices that are right for them and their exposure risk level. ### Face Coverings Face coverings are not required, but are welcomed. We view face coverings as a personal choice and will support attendees in their choice to wear or not to wear a face covering. ### Fire Safety Follow the instructions given at the workshop. ## License Written materials are provided under the [CC-BY-4.0 SA license](LICENSE.md). ## Acknowledgements Please see [`AUTHORS.md`](AUTHORS.md) for a list of contributors to the workshop materials. We would like to give a special thanks to our partner and primary sponsor for this workshop, the [Molecular Sciences Software Institute](https://molssi.org/) (MolSSI). This workshop has been made possible in part by grants ([EOSS4](https://chanzuckerberg.com/eoss/proposals/mdanalysis-faster-extensible-molecular-analysis-for-reproducible-science/) and [EOSS5](https://chanzuckerberg.com/eoss/proposals/mdanalysis-outreach-and-project-manager/)) from the [Chan Zuckerberg Initiative](https://chanzuckerberg.com) (CZI) DAF, a donor advised fund of Silicon Valley Community Foundation (funder DOI 10.13039/100014989) and through the support of the [Center for Biological Physics](https://cbp.asu.edu/) at Arizona State University. MDAnalysis also thanks NumFOCUS for its continued support as our fiscal sponsor. ## [1]: https://jupyter-notebook.readthedocs.io/en/stable/ [2]: https://numpy.org/ [workshop_email]: mailto:workshops@mdanalysis.org