Good afternoon everyone,
I have a faculty member that is interested in introducing their anatomy and physiology students to supercomputing. They are looking for ideas that could be useful to explore in the classroom or have students start working on as actual research in the lab. I have done a surface Google investigation and found a few ideas, but we would really value the input from our community here.
Thank you for taking the time to read this!
Adam Erck
A BLAST example or exercise is always a good introduction to bioinformatics for students, this is a good exercise using CLI BLAST: http://hpc.ilri.cgiar.org/beca/training/AdvancedBFX2014_2/course/CommandLineBLAST.pdf
Another good application for A&P would be a proteomics exercise such as this, but this might be a bit over the heads of sophomore undergrads unless they’ve already studied mass spec: https://community.asdlib.org/activelearningmaterials/biological-mass-spectrometry-proteomics/
Thank you for the ideas!
Gateways may be a quick way to get some simulations going.
Simvascular Gateway provides cardio vascular modeling. Please let them check out https://gateway.simvascular.org/.
There are others like https://www.nsgportal.org/index.html for neuroscience. I know there are faculty modeling bone structure and mechanics using HPC like Prof Iwona Jasuik at UIUC.
Thanks,
Sudhakar.
Hi, Adam,
The Virtual Soldier Research Program at the University of Iowa “conducts basic and applied research and development in the field of human modeling and simulation. Our research is aimed at creating interactive, intelligent, and predictive human models that operate in virtual, physics-based environments. The product from this research is called Santos, a human simulator that is widely used by the US military and industry partners. It is the only physics-based human simulator”: https://www.ccad.uiowa.edu/vsr/
The Iowa initiative leverages pioneering work by PI Brian Athey (U-Michigan) made possible with a DARPA investment, and several follow-on projects that were funded by NIH, National Library of Medicine, and others. https://medicine.umich.edu/dept/dcmb/brian-d-athey-phd
E
Hello Adam,
Perhaps obvious choices for many people would be HPC applications involving the NIH-supported Human Connectome Project (https://neuroscienceblueprint.nih.gov/human-connectome/connectome-programs) and other connectome work in the US and around the globe, such as the OpenWorm Project (http://openworm.org/) and the Blue Brain Project (https://www.epfl.ch/research/domains/bluebrain/).
Best regards,
Kevin