Folding at Home and how to make a (tiny) contribution to coronavirus therapeutics research

If you want to help fight against coronavirus but don’t know how to contribute…well, read on. It turns out we all can do something (beyond staying at home and washing our hands!): we can give away our computer processing power to research to understand coronavirus better and design therapeutics to address it.

Now, I’m not fooling myself: my minimal computing resources are not going to move the needle… but hey, what else can I do?

Amanda Blevins, Chief Technologist in the VMware Office of the CTO, has been driving an initiative across the VMware community to get people to contribute to the “Folding at Home” programme.

What is “Folding at Home”?

Let me summarize “Folding at Home” in my simple terms:

Folding looks like at how proteins ‘fold’ – in other words, proteins assemble themselves into a specific form to execute a specific function (like antibodies).

From Wikipedia : A protein before and after folding. It starts in an unstable random coil state and finishes in its native state conformation.

Any virus (like the coronavirus) has proteins that they use to suppress immune systems and reproduce themselves.

If we can understand these virus proteins, we can build medicine to stop them.

The problem with protein structures is that they have many moving parts – the best way to understand these moving parts is to simulate them with super computers.

As these calculations are enormous, the Folding at Home project leverages idle distributed computing to run them – the calculations are distributed across any computers across the world that join the project. It turns out that Folding at Home is one of the largest distributing computing network in the world.

The more calculations completed, the quicker we can understand the viral proteins and the quicker we can design therapeutics to stop them.

All these computers in the work simulate potentially druggable protein targets from SARS-CoV-2 virus, and the related SARS-CoV virus.

I am a VMware user – what can I do?

Well, if you have a homelab or spare capacity in a test lab, you can also contribute.

We have a VMware Cloud on AWS EMEA lab for our customers demo and it had some spare capacity. I deployed a Folding VM in our lab a couple of weeks ago and our lab has now completed over 320 calculations (also referred to as ‘workunits’ – a work unit is the protein data that the client is asked to process).

It’s a minuscule contribution compared to the VMware Hands On Labs who are contributing way more resources but it’s a nice feeling to be able to contribute to the research.

TeamVMware is, as I write this, the 98th biggest contributor to the project and growing at rapid pace.

The VMware stats can be found here on the VMware Tanzu Observability portal.

Certificate below is in my name but should read “vmc-emea” 😊

Can I run this on a standard laptop?

What’s interesting is why not stop there. I found an old MacBook Pro in my drawer with decent specs and got it fired. You can download a client:

How do I get started?

Dean Lewis published a great set of instructions on the Fling page, which was built by William Lam. If you’re used to VMware, you will see it’s pretty straight-forward if you are a regular VMware user.

Here are some screenshots to go along with these instructions.

Step 1 – Deploy OVF
Step 2 – Select Compute Resource
Step 3 – Review Details

If you can, select a Large configuration. I’ve found your VM is more likely to find a Work Unit to work on.

Step 4 – Select configuration
Step 5 – Select Storage
Step 6 – Select Network

Finally, you need to specify the details of the VM, such as your ‘Folding at Home’ username (in my case, ‘nvibert-runvmc’). By default, the F@H team ID is the VMware one (52737).

Step 7 – Specify username and team ID

Review and deploy:

Step 8 – Review and deploy

If everything works as expected, you will see a console such as the one below where the VM is actively working on a workunit. The VM below took about 1h20 minutes to complete the workunit calculation.

WU Calculaion

A good sign is when the VM’s CPU usage starts rocketing: it means it’s working hard!

F@H CPU Usage

I hope you can join the initiative. Time to get Folding!

Posted in VMC

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