Lean Bulk Kickoff💪
Sunday, November 9
155.5 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (7/6)
I went to yoga, then worked from home all day. Coding agents usually run really ㅈ디, but sometimes they get weirdly dumb, so I have to double-check everything. Even the smallest configuration changes could break it. I probably should have worked somewhere else to focus (not at home), but I kept replaying LoL Worlds and could not concentrate. Still, my team won, which made me happy😊 I will get back on track tomorrow.
Monday, November 10
154.0 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (1/6)
Today I had a 1-on-1 meeting with Bill and shared recent progress on yeast surface display. I got a lot of advice, especially to reach out to other labs that actively use display. If I can connect with someone who has done sequencing after sorting, that would be awesome. I also attended a subgroup meeting and spent the rest of the day studying the principles of diffusion models. I watched a YouTube video, which really helped me grasp how they work.
After work, I did meal prep. I used the Instant Pot’s pressure cook function for the first time with chicken breast, which was incredibly fast and easy. I also tried adding spice to the rice cooker, which improved the aroma and boosted my appetite. I recommend cumin and a bit of chicken stock in the rice cooker! After finishing meal prep and showering, the fire alarm suddenly went off and everyone evacuated😳 It took a while to settle, but fortunately it was a mistaken alarm from a room on the 5th floor. Embarrassing to rush the shower, but I felt safe since the fire station is right next to campus.
Tuesday, November 11
153.7 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (2/6)
Nothing special today. There was no journal club, so I focused on synthesis. The reaction did not go well, so I set up two different conditions to try to get it done. Hopefully tomorrow morning the TLC will look better (it is pretty ugly right now🥲). I am still figuring out the next step for yeast surface display, and I may reach out again to the Wells lab CCB senior who helped me understand YSD a few months ago. After work I went for a run. As always, I felt better afterward. I want to maintain a healthy body so I can exercise regularly for the benefit of my mental health. Recently I have been training calves and tibialis, and my pace is improving comfortably, so running is becoming more fun 🤩
Wednesday, November 12
153.5 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (3/6)
Thankfully, the chemistry wrapped up today. The reaction I set up yesterday went cleanly. The TLC was ambiguous, but LC-MS confirmed it, so I purified the product and delivered it to the postdoc. He will now use these substrates to map the scope of his de novo enzyme. I hope the results are interesting as we thought!
In the morning, we had a DeGrado lab group meeting. The presenter was a third-year CCB student one year ahead of me, and the talk was very engaging! He double-majored in computer science, so he has a deep understanding of deep learning model architecture and is training a new model tailored to his goals. Seeing how strong fundamentals enable you to fully utilize a model and even build new ones was inspiring. I want to ask him many questions and learn more.
In the afternoon I connected with a postdoc in the Wells lab who is actively running yeast surface display, and I will likely shadow him next week👍
Thursday, November 13
154.0 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (4/6)
Today I learned Schrödinger covalent docking (CovDock) from a Shokat lab member. She has been an amazing help, especially in biology, which is her real expertise. She also documented the workflow, making it easy to follow, even on my first attempt. Much appreciated🙂 I might also take on website management after discussing it with her, since it can be done remotely and my current Shokat lab task is only Shrödinger and not heavily used. I will ask Kevan about that plan tomorrow.
In the afternoon I coordinated with a Wells lab postdoc about yeast surface display and then returned to in silico work. Wynton finally came back from downtime, but it feels much slower than before?😨 I also finally understood how to design cloning primers for In-Fusion and Gibson, and I feel confident I can clone any protein I need now. After work, I did a quick indoor run with some intervals and realized I need more training for running (especially for a half-marathon).
Friday, November 14
153.2 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (5/6)
I had a one-on-one with Kevan, and he liked the idea of taking over the lab website maintenance. Currently, every update requires approval from someone else, which is a hassle, and the site is somewhat outdated. It’s built with GitHub Pages and Jekyll, so I’ll learn how to use it. I also requested a consultation with UCSF IT about using UCSF-supported tools to make future handoffs easier. Finally, I obtained a FlowJo license for analyzing flow cytometry data. I’m grateful that funding isn’t a barrier to my research.
I attended my favorite RIPS class and spent a lot of time on computation. I also shared my thesis project theme with a lab member and, surprisingly, got a suggestion that should make my assay more compelling. It realized the value of scientific conversations with as many people as possible. You can get something for sure. After dinner, I had the same tart as yesterday. It was best fresh; after refrigeration the crust lost its crispness, so next time I’ll eat it right away🥲
Saturday, November 15
153.3 lbs (from 152.5 lbs on Oct 26) | 🏃🏻 Done (6/6)
Did a solid leg workout, and went with a friend to Chinatown to get a haircut. We went to the place where we first ate together in Chinatown (Capital, 839 Clay St, San Francisco, CA 94108) and had a great meal. I feel like I have gone around quite a bit now, and in my opinion this is the place I can easily recommend to anyone. I ate very well😊 One nice thing here is that they always give a fortune cookie, and today it said, “Before the beginning of the great brilliance, there must be chaos.” It was a little scary, but I took it positively, as a mindset to endure situations that are too complicated and sometimes feel overwhelming.
After the haircut, I took a nap at home and spent a relaxed time. Since I have jobs running on my laptop and I am doing something anyway, I feel like I get a little loose. And finally, I think I found my maintenance calories! It seems to be around 2400–2450 kcal, and from now on, I will raise it by 100 kcal and from tomorrow enter a full lean bulk phase👍 Since I am setting a body fat limit of 15%, I do not know how long I can go, but I think I can maintain it for a few months. I will make sure that I continue to increase my training intensity from here.
