Recent content on Everyday Is A School Day
Textbooks say LOOCV has the lowest bias but highest variance compared to 10 and 5-fold. Coded a K-Fold CV from scratch for learning to test that on simulated data 🔍📊 — and at n=1000 it holds up. At n=100? Not so much. 🤔 The above image was generated via chatGPT. Uploaded all the text of this blog post and asked it to generate a cartoon. Very impressive! It used to be spelling error and…
🧬 Back to basics! Learning non-polar amino acids, what zwitterions actually are, and dipping into the applied math — Rodrigues rotation and Lennard-Jones potential. Slowly building toward optimal phi/psi! Motivations We’ve explored quite a bit lately in molecular dynamic simulation and then protein-protein docking as well the last time. There is still so much to learn. I’ve decided to go back to…
Exploring the CovR/S two-component system in Group A Strep 🧫 — from genome annotation with Bakta & BaktFold, to AlphaFold confidence metrics, and a first attempt at protein docking with Haddock3. Learning as we go! 🙌 Motivations Since the last ampC adventure , I’m really curious about the mechanism of some of these bacterial virulence. Remember how chromosomal ampC organisms use ampG,…
A note to myself on survival analysis — KM curves, log-rank tests & Cox models 🧮 If I wrote it the way I understood it, maybe I’ll actually remember it 🤞 Motivations We see survival analysis or more generally called time-to-event analysis almost all the time when we review journals articles on NEJM etc. Even though we understand the heuristic in interpreting some of the simpler result, I…
Dipping my toes into quantum computing 🌊 — circuits, gates, superposition. Still very much a beginner, but hands-on experiments with qiskit + R’s reticulate made it click a little more. Baby steps! Motivations Alright, we’ve done molecular dynamic simulation and then the post-processing part where we used PBSA/GBSA. I was told that quantum mechanics can more accurately estimate the…
🦠 Made up my own memory tricks — Gatekeeper, Dumpster, Repressor — to understand AmpC mechanics. Discovered Serratia has 2 recyclers (AmpD + AmiD2) making derepression harder, and E. coli lacks AmpR so AmpC stays silent! Probably not textbook, but it helped me learn 🙌 AmpC beta-lactamase of Enterobacter cloacae generated by AlphaFold and ChimeraX Motivations We’ve learnt about ESBL and CRE…
📊 Dipping my toes into financial statements — income, balance sheet & cash flow. Still don’t fully get it, but slowly piecing together the story these numbers tell. Warren Buffett makes it look easy 😅 Baby steps! 🌱 Motivations I’ve always wanted to learn financial statement, what it means, what it tells us, what Warren Buffett sees in them. Following the book Warren Buffett and the…
Exploring pip/tazo PTA for Pseudomonas using popPK simulation. Key finds: 30-min infusions fall short of 90% PTA at MIC 16; prolonged infusion helps, but neutropenic fever population sees the biggest drop in PTA. ~46% of susceptible PsA isolates carry blaOXA-2 — tazobactam matters more than I thought Motivations We’ve learnt a bit of PK/PD last time, here . Let’s apply that on Pip/tazo…
🧪 Diving into PK/PD for the first time — simulating ceftriaxone with mrgsolve in R. Free drug levels were… surprisingly high? Even pushed it to q48h dosing out of curiosity and the results left me with more questions than answers 🤔📈 Motivations Learning pharmacokinetics (PK) and pharmocodynamics (PD) have always been an interest of mine. It’s always challenging to read through…
Learnt major carbapenemase genes (KPC, NDM, OXA) using NCBI isolate data and molecular dynamics. Includes gene frequency trends, co-resistance patterns, and MM/PBSA binding comparisons of avibactam with KPC vs NDM to illustrate mechanistic differences 🧬 Motivations: We’ve previously learnt about ESBL genes and took a peek under the hood of the nucleotides and explore NCBI library and assess…