JD Russo @quasifrodo@qoto.org
- GitHub
- https://github.com/jdrusso
PhD candidate in #ComputationalBiophysics. I work on weighted ensemble enhanced sampling and Markov analysis of molecular dynamics simulations. Passionate about bringing good software development practices into the research world.
In my free time, I'm a #hardware and #software #DIY-er, into #3DPrinting, and a #smarthome + #homelab enthusiast.
He/him
Joined Nov 2022
:AddBiophysicist
JD Russo
boosted
My advice if you're trying to start your own #mastodon isntance: USE CLOUD STORAGE! I'm specifically using #s3, but there are other options. If you end up federated with a lot of other servers you're going to be downloading a lot of media, and that will fill up your local storage quickly. S3 is pretty cheap, and a better form of #contentdelivery anyway. #advice #gettingstarted #twittermigration #selfhosted
JD Russo
boosted
Now #biophysics is a thing on #ScienceMastodon !
Following the idea of sociologists (https://social.tchncs.de/@perspektivbrocken/109257556102307689, thx to them!) I offer that we help newcomers find who to connect with by listing ourselves at https://jocelynetienne.github.io/Mastodon-Biophysicists/
@biophysicists
JD Russo
boosted
Time for an #introduction
I'm a computational (bio)physicisct and have mostly worked with MD simulations of lipid membranes and membrane proteins but also some experience in machine learning and free energy calculations.
Currently I work as a senior scientist at Schrödinger in New York City, after doing a postdoc at Stanford University and a PhD at the Max Planck Institute of Biophysics.
Besides work, I'm an avid amateur photographer and I like reading about science, history, and languages.
Today's accomplishment: I have an analysis pipeline with a few parallelizable steps. I typically run my analysis in parallel on my desktop, but I've both been needing more oomph and have been running out of drive space nonstop.
My #homeserver (40 cores/80 threads with quad E4870s) is running ZFS on a RAID0 array, currently just with two 10k SAS drives. By mounting this as an NFS share on my desktop, I can put all my generated simulation data directly on that larger filesystem.
Additionally, my server is running #proxmox, and has a "science" container. I can also mount that NFS share in the science container, giving it direct access to my simulation data, and run it as a #Ray cluster head node. Now, I can do simulations on my desktop, run the single-core tasks on that machine, and farm out the parallel analysis to workers on the server, putting all 80 cores to work!
Time for an #introduction! I'm a PhD candidate in #computational #biophysics working on Markov analysis of molecular dynamics #simulations. I also work on weighted ensemble enhanced sampling, and am a core maintainer of the WESTPA project. I do a lot of work with #HPC and #supercomputing clusters as well.
I'm really passionate about bringing best practices from the software development world into computational research!
I love playing with software, and I like playing with #selfhosting a number of services on my #homelab servers, from . Current setup is a Thinkpad laptop that runs the essential services, and a Supermicro quad-socket server with 4x E7-4870s for the fun stuff.
Also really into DIY, including #3Dprinting, #smarthome stuff and #homeassistant -- I spent a couple months designing and building a smart thermostat with a wireless remote thermometer from scratch because my WFH desk was close to a window and got too cold.
#science #computationalchemistry #simulation #selfhost #DIY #linux #supercomputers #technology
- GitHub
- https://github.com/jdrusso
PhD candidate in #ComputationalBiophysics. I work on weighted ensemble enhanced sampling and Markov analysis of molecular dynamics simulations. Passionate about bringing good software development practices into the research world.
In my free time, I'm a #hardware and #software #DIY-er, into #3DPrinting, and a #smarthome + #homelab enthusiast.
He/him
Joined Nov 2022
