MDAnalysis/MolSSI Workshop at Arizona State University (June 24/25, 2024)

14 May 2024

MDAnalysis, in conjunction with the Molecular Sciences Software Institute (MolSSI) and with the support of the Chan Zuckerberg Initiative and the Center for Biological Physics, is holding a free, 2-day workshop on June 24th-25th 2024 at Arizona State University in Tempe, Arizona, USA.

This two-day workshop is intended to transform attendees from users to developers and will cover an introduction to MDAnalysis, software best practices, and guide participants through the creation of their own MDAKit.

This workshop is suitable for students and researchers in the broad area of computational (bio)chemistry, materials science and chemical engineering. It is designed for those who have familiarity with MDAnalysis and are comfortable working with Python and Jupyter Notebooks. 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”. Workshop participants should also already have a working conda or mamba installation of MDAnalysis (mamba preferred), as well as an editor of their choice for editing files.

Workshop Overview

MDAnalysis developers and experienced MolSSI instructors will teach participants how to build their own MDAnalysis-based Python packages by guiding them through the development of their own MDAKits. Specifically, the workshop will include 3 modules: (1) an introduction to using and writing custom analyses in MDAnalysis; (2) an overview of software development and maintenance best practices; and (3) an interactive hackathon session where participants write their own MDAKits.

The program will run from the morning of Monday, June 24th until the early evening of Tuesday June 25th. Breakfast and lunch will be provided together with tea/coffee during breaks.

Parts of the workshop will be held in a hybrid mode for those unable to attend in-person. Registration for the hybrid components is required. Recordings of hybrid sessions will be made available after the workshop.

Registration

Attendance at this workshop will be free but the in-person part of the workshop will be limited to 40 participants. The workshop will be delivered to a small group to allow interactive discussions, questions, and participant engagement.

A number of bursaries will be available to assist with travel and accommodation costs for participants from outside the greater Phoenix area. Bursaries (up to $600 in costs for US domestic travel) and up to 3 nights of hotel accommodation (single room within 5 minutes of the workshop venue) will be awarded and you can apply for them as part of the registration process.

Register by May 27, 2024 (midnight anywhere on Earth):

Register

Bursaries for in-person attendance

We especially welcome your application if you consider yourself being part of an underrepresented demographic in the computational molecular sciences.

Bursaries are reserved to enable the attendance of participants from outside the greater Phoenix area.

Note that airfare for travel awardees will have to be booked by June 3 through our travel agency, so as an awardee you will have to be able to respond to our communications (via email) immediately and act quickly.

Bursary recipients will be notified on May 29 or earlier.

Online participants

Part of the workshop will be taught in hybrid mode and if you are not able to attend in person, please register for the online portion using the same registration link above.

Travel

Tempe is part of the “Valley of the Sun” metropolitan area, which encompasses Phoenix, the 5th most populous city in the US. Today the area is home to more than 4.8 million people and encompasses the ancient lands of the Akimel O’odham (Pima), Maricopa, and Tohono O’odham tribes.

Airport

Phoenix Sky Harbor PHX airport has direct connections to all major hubs in the US.

PHX airport is 5.5 miles (10 minutes by car/rideshare) from the workshop venue.

Public transport (Light Rail)

The Valley Metro Light Rail connects the airport to Tempe along a West-East axis. If your destination is near a Light Rail stop then public transport works well:

1. Take the free PHX Sky Train from the terminal to the 44th St/Washington Metro Rail stop.
2. Walk from the Sky Train stop to the Light Rail stop (all inside the 44th St Sky Train structure)
3. Buy a ticket at the ticket machine near the exit escalators to the Light Rail stop.
4. At the 44th St/Washington stop (Stop #10018) take the east-bound Light Rail (direction Mesa, Gilbert Rd/Main St).
5. The stop closest to the Hyatt Place Hotel and the workshop venue is University Dr/Rural Rd (Stop #10023). If you want to get off closer to downtown Tempe get off one stop earlier at Veterans Way/College Ave (Stop #10025)
6. Walk to your destination.

Car/rideshare

To get from the airport to anywhere in Tempe either take a cab (traditional or self-driving Waymo) or rideshare (Lyft, Uber).

Workshop Venue

The workshop will be held in the Student Success Center in the Department of Physics at Arizona State University (room PSF 186 in the Physical Sciences F building). The address is

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

Paid parking is available in the Tyler Street Parking Structure and other on-campus parking structures.

Accommodation

The closest hotel (5 min by foot) is the Hyatt Place Tempe.

Other hotels are available in Tempe within walking distance.

Weather

Arizona is hot during June. Temperatures in excess of 110ºF (43.3ºC) are not rare, so it is important that you bring a hat/sunscreen for sun protection and carry enough water with you.

Avoid hiking in the desert during the hot portion of the day (10am - 6pm), as it can be deadly.

Workshop materials

All materials are made available in the https://github.com/MDAnalysis/MDAnalysisMolSSIWorkshop-Intermediate2Day repository.

• Schedule with links to Google Colab notebooks for individual lessons.
• Set-up and installation instructions for how to prepare your environment so that you can follow along on your own computer.

Who to Contact

If you have any questions or special requests related to this workshop, you may contact the organizing committee.

• @fiona-naughton @IAlibay @jennaswa @orbeckst (the workshop team at MDAnalysis) and @armcdona (MolSSI)