Combat Coronavirus By Folding@Home - Part I
This is the first article of series pertaining to Folding@Home (FAH) and the Coronavirus. Part I focuses on what is FAH and how to contribute.
In late February and early March when coronavirus started spreading throughout the world, I began looking for ways I could help fight the pandemic. My initial thought was monetary donation to organizations assisting people in need, hoping the pandemic would end soon. Then the impact of the virus extended beyond my expectation and affected people I know. Some of my friends lost their jobs, a few others had to get quarantined from contracting the virus, which devastated their lives. I started exploring new ways I can contribute to combat the virus. Listening to public health officials and self isolating was a good start, but I wanted to do more. My monetary donations are limited. I wanted to fight the sense of hopelessness that started creeping up. While I am thankful to be safe and healthy, I know many others are not. I wanted to do more to help. Fortunately, a few days later, I found a great way I (and you) can make a real difference.
One of my coworkers at Headstorm introduced me to Folding@Home. It is the perfect way to help for anyone who has a computer. It costs very little (only the cost of keeping your computer powered on and charged), and it takes only a few minutes to set up. I know it has helped me feel better about my contribution to fight COVID-19.
What is Folding@Home?
“Folding@home (FAH or F@h) is a distributed computing project for simulating protein dynamics, including the process of protein folding and the movements of proteins implicated in a variety of diseases [including COVID-19]. It brings together citizen scientists who volunteer to run simulations of protein dynamics on their personal computers. Insights from this data are helping scientists to better understand biology, and providing new opportunities for developing therapeutics.”
Initially the project (founded at Stanford University in 2000) focused on protein folding, but more recently has shifted to more biomedical problems like Coronavirus.
What is Folding@Home Doing to Combat the Virus?
My knowledge in biology is very limited, therefore I can only speak to what I understand. For full details, refer to https://foldingathome.org/covid19/ as FAH discuss their work in more details. To give some context, FAH uses computational power to create simulation of protein structures and their interactions with one another. Better understanding of how the proteins in a virus affect our immune system can help scientists design therapeutics to stop the virus. The following analogy is directly from FAH’s website. It helped me understand their work in more detail.
Using football as an analogy for the experimental situation, it’s as if you could only see the players lined up for the snap (the single arrangement the players spend the most time in) and were blind to the rest of the game.
Seeing a single structure of a protein (left) is like seeing players lined up for the snap in football. Important information, but a lot missing too. The protein structure shows a sphere for each atom (blue) and red arrows highlighting the one drug binding site in this protein.
How To Get Started?
Getting started is fairly straight forward, and the details can be found on FAH’s website. However, I am writing this to shed some light on some of the details that you will encounter as you’re setting it up.
FAH has made it easy for anyone to contribute. They support a variety of operating systems (OS X, Windows, even Docker images) and today I will share with you steps needed to get started:
Installation
MacOS/Windows
Install the designated installer here.
Tip: if you see something like this on your Mac OS X, just right click on the .pkg file and click open.
Docker
I have never done Docker image folding, but the links below take you to Github repos that instruct you on how to get started:
Setup
These setup instructions will be skewed toward helping out COVID-19 research.
MacOS/Windows (via GUI)
The GUI is web-based so in your default browser you will be greeted with a welcome window. This window will open automatically once you download the client.
- Choose Set up an identity and click Start Folding. This will prompt you to the following window
2. Name: Change your identity to your preferred name. Try to make it unique, if you use someone else’s name you too will collide and share credit.
3. Team Number: if you are part of a team or an organization you can enter team number and earn points as a team. You will move up the ranks quickly!
4. Passkey: At the time of this writing, F@H has shut off their Passkey service to dedicate their resources to giant mob of people requesting work units.
5. Press Save
6. Boom! You are now helping researchers defeat this epidemic!
Settings
Power:
- Light — Recommended for laptops:
- Will not notice it while working on the same machine - Medium — PC Tower/NAS
- You may notice it while working on the same machine. Depends on what you’re doing. Uses a bit more electricity.
- Recommend. - Full:
- This is “Make my CPU hurt” mode
- This is basically saying use all available resource to compute as fast as possible. Runs parallel to Bitcoin mining with CPUs & GPUs.
When:
- Pretty self explanatory, I recommend tuning it based on how you’re using your machine. Use your best judgement here.
Useful links:
- News about FAH: https://foldingathome.org/news/
- Team statistics: https://stats.foldingathome.org/teams
I miss the 4 o’clock traffic in Dallas, and I just want life to go back to normal.
