My name is Lucía María Moya Sans. I am a bachelor student in Biomedical and Informatics engineering. I am working on computational neuroscience data at Dr. Ana Solodkin’s lab with @ylwang. As he said some posts ago, we are trying to use the virtual brain (TVB) to do individualized large-scale brain modeling and brain dynamics modeling.
Experience on HPC:
I have worked with HPC for other projects on convolutional neural networks and also I am taking some courses in HPC and parallelization this semester
My workflow:
For data analysis, I use Python and Matlab both in Windows and in Linux, normally locally.
Challenge:
The amount of data that we need to process for Neuroimaging is too much for doing it locally without the help of a HPC
That’s fantastic that you are able to work with Dr. Solodkin during your undergrad. My work experience as an undergrad in a lab was much more educational than (most) classes I took.
I’m familiar with the TVB workflow from the web portal and from the jupyter notebook side but I haven’t seen how you guys plan to drive python with TVB directly.
Do you or @ylwang have any examples running or is the workflow still a work in progress? I’d be happy to sit down with the two of you and discuss how to go about optimizing.
From my experience, I can just use TVB directly on python.
I attached a link from my github about how to use the python TVB package to generate the local field potential signals and find out the hopf bifurcation point in different brain states. All I need to do is to import TVB packages in my python script.
from tvb.simulator.lab import *
from tvb.simulator.models.stefanescu_jirsa import ReducedSetHindmarshRose
import tvb.simulator.plot.timeseries_interactive as ts_int
I think I will ask TVB staffs more about how to deploy TVB on HPC on next week. I will let you know if they have better idea than directly using python packages~
I think one of the first things we should do is show you guys how to run High Throughput jobs efficiently. I’m going to take a few questions / topics from there introductory posts and put together a training.
I’ll aim to have the first training after finals but before Xmas break. That way, you’ll have a bunch of new skills to learn and develop over the holiday.
That sounds perfect!! Looking forward to the training!! I will invite all the lab members who will need to use TVB in their projects to join us at that time. Thanks so much Dr. Simmons!