marimo: Python notebooks that are just Python

What marimo is, why I like it, and a live notebook running right in this page

Split-and-combine parallelization for MDAnalysis AnalysisBase subclasses

Parallel AnalysisBase.run() in MDAnalysis with multiprocessing and dask: the outcome of my GSoC 2023 project

Secondary structure analysis with DSSP for MDAnalysis

Built-in, dependency-free secondary structure analysis (DSSP) for MDAnalysis, started at the 2023 UGM hackathon

Regression-based Accelerated Virtual Screening

A lesser formal version of this JCIM paper

MDAnalysis UGM 2023: MDAnalysis Parallelization @ GSOC

Presentation given at the MDAnalysis User Meeting in 2023

GSOC-2023: summary

Summary of the GSOC work on MDAnalysis parallelization

(again bi)weekly GSOC-4: finally about results aggretation

Fourth biweekly GSOC blogpost

(not anymore bi)weekly GSOC-3: writing `ParallelExecutor` class

Third biweekly GSOC blogpost

Biweekly GSOC-2: splitting the work and writing `_setup_bslices`

Second biweekly GSOC blogpost

Biweekly GSOC-1: decomposing `AnalysisBase.run()`

First biweekly GSOC blogpost

GSOC 2023: what will I do?

A project proposal, written for GSOC-2023 at MDAnalysis

Structural basis for receptor selectivity and inverse agonism in S1P5 receptors

A lesser formal version of this Nature Communications paper