General Project Proposal Questions + More About Me
Xu Hong Chen
Hi again,
It is nice to see how lively the group has gotten! I have read through the GSoC FAQ a few times and I thought I would ask my general project proposal questions here as others may find them useful too.
1. Where would be the best place to ask individual questions or request more personalized feedback on my proposal before the application opens? Does MDAnalysis prefer those discussions go here or on Discord?
2. Would I share my draft as a Google doc here, on Discord, or through some other means? Or would it be better to wait for the application window to open and discuss there?
3. Do you have any guidelines for how long a good proposal might be, and is there any page limit?
4. Do you have any formatting and content preferences beyond what is on Google’s GSoC Guide and the MDAnalysis GSoC pages on GitHub?
5. Google states that it is permissible to submit up to three proposals, but what is MDAnalysis’ stance on this? I was thinking I might submit a second proposal if I finish my first and feel I have given it my best effort.
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I also read in that FAQ that you might be interested in hearing more about my background, so I wanted to share some details here. As a member of the Spyracopoulos Lab at the University of Alberta, I took charge of the MD side of our research on the molecular mechanism of Hsp90. I constructed 5 atomic models in PyMOL and conducted extensive classical and steered molecular dynamics (MD) simulations using AMBER for 5 protein mutants: apo and ATP-bound Hsp90 S3CYF N-domains, apo and ATP-bound Hsp90 S3CYF/F6D/F8D N-domains, and intact, ATP-bound Hsp90 S3CYF to investigate the energetic cost of strap release. I then validated experimental NMR data by using CPPTRAJ to calculate theoretical NMR parameters from MD data. While these were my personal contributions, everyone involved played a pivotal role in our work as a lab, and one of the undergraduates I trained did much of the work on the ATP-bound Hsp90 S3CYF/F6D/F8D N-domain mutant, while the other did important work on a different intact chaperone mutant for a newer project.
You can find some examples of my work here:
1. Honors Thesis (Not Yet Published, Publication Will Have Updated Data)
2. 64th Canadian Society for Molecular Biosciences (CSMB/SCBM) Conference on Protein Homeostasis Poster (Second Author, Data in the Poster Was Still Preliminary) (Link to Conference Website)
I also presented at the Faculty of Medicine and Dentistry 54th Annual Summer Students’ Research Day. I initially became involved in the computational sciences because I was intrigued by computational research, and in turn, that work inspired me to pursue computer science (CS). I want to learn how to write scientific software like AMBER and MDAnalysis, understand high-performance computing systems and how to optimize them, and implement software for individuals and researchers. I have used Python and C in my introductory CS coursework but I am new to open source. I have been enjoying the process of contributing to MDAnalysis and am looking forward to learning and helping more!
Thank you for taking the time to read through all this!
Sincerely,
Xu Hong (GitHub: xhgchen)
Oliver Beckstein
On Feb 27, 2023, at 6:17 PM, Xu Hong Chen <xhg...@gmail.com> wrote:1. Where would be the best place to ask individual questions or request more personalized feedback on my proposal before the application opens? Does MDAnalysis prefer those discussions go here or on Discord?
2. Would I share my draft as a Google doc here, on Discord, or through some other means? Or would it be better to wait for the application window to open and discuss there?
3. Do you have any guidelines for how long a good proposal might be, and is there any page limit?
4. Do you have any formatting and content preferences beyond what is on Google’s GSoC Guide and the MDAnalysis GSoC pages on GitHub?
5. Google states that it is permissible to submit up to three proposals, but what is MDAnalysis’ stance on this? I was thinking I might submit a second proposal if I finish my first and feel I have given it my best effort.