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followers: 24.0 following: 7.0 repos: 28.0 gists: 16.0

Name: Victoria Lim

Type: User

Company: @implydata

Bio: Tech docs at @implydata. Computational chemistry PhD from UC Irvine with @MobleyLab.

👋 Hi! I'm Victoria

I write docs. Past identities include computational chemistry researcher and patent scientist. My GitHub repos mostly pertain to one of those three categories—tech writing, science, or patents.

📝 Technical writing

docs-topics: (private) natural language processing and topic modeling of internal forums to identify areas for docs improvement (happy to share a redacted version ✉️)
tech-docs: scripts for docs-as-code technical writing, docs infrastructure, and technical exploration notebooks

🔬 Science

plot_potential: visualize functions that comprise molecular mechanics force fields (ideal for presentations)
misc: basic stats and plots (used for publications); configuration for Grace and VMD; OpenEye OEChem utilities
dihedral-scan: determine the potential energy function of a dihedral angle in a molecule using NAMD
benchmarkff: comparison of optimized geometries and energies from various force fields with respect to a QM reference
off_psi4: quantum mechanical analysis of molecular conformers (moved to MobleyLab/quanformer)
permeability: data analysis from NAMD simulations on calculating membrane permeabilities
GLIC: analysis and visualization for cryo-EM density-fitting simluations using GROMACS
Hv1: setup and analysis of free energy perturbation calculations of the Hv1 protein using NAMD
mismatch: web app to find mismatched base pairs between hybridized DNA sequences

🌎 Patents

patfam: web app for analysis of patent families across different jurisdictions (collaborations welcome! 👯)
textsmoosh: web app to process and combine multi-line text into a single line
excel: (private) scripts for Microsoft Excel to automate processing of datasets with thousands of compounds

Victoria Lim's Projects

advent2021

Advent of Code, https://adventofcode.com/

dihedral-scan

Compute dihedral scan in some molecule, such as to compare an MM force field to QM results.

drug-computing

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

druid

Apache Druid: a high performance real-time analytics database.

glic

Scripts for fitting GLIC receptor to cryo-EM densities

hv1

Free energy perturbation calculations for Hv1 protein

misc

Miscellaneous scripts for research and data analysis using Python, OpenEye Python Toolkit, VMD/Tcl, or Grace.

mismatch

Web app to find mismatched base pairs between hybridized DNA sequences.

Quanformer is a Python-based pipeline for generating conformers, preparing quantum mechanical (QM) calculations, and processing QM results for a set of molecules and their conformers. *** This repo has a new location here:

open-forcefield-data

Datasets for open forcefield parameterization and development

patfam

Web app to determine whether patent applications from different jurisdictions (USPTO, EPO, WIPO, etc.) are of the same family.

permeability

Adaptive biasing force (ABF) & umbrella sampling (US) simulations to calculate membrane permeability

plot_potential

Plot individual potential functions that comprise force fields. Ideal for presentations. Includes energy terms for bonds (harmonic), angles (harmonic), proper torsion (periodic cosine), improper torsion (harmonic), van der Waals (Lennard-Jones), electrostatics (Coulomb), and the Morse potential.

vtlim Goto Github PK

👋 Hi! I'm Victoria

📝 Technical writing

🔬 Science

🌎 Patents

Victoria Lim's Projects

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