Latest Posts

Why are 20nt primers sufficiently unique in the human genome? (28 Dec 2023) [notes] [biology]

Combinatorics and Shannon Entropy

Eichmann in Jerusalem by Hannah Arendt (26 Dec 2023) [notes]

Arendt's disputes with the Israeli court

Custom elisp function to jump to analysis folders (02 Oct 2023) [emacs] [org-mode]

An outcome of having a systematic nomenclature of projects

A note on fractional dilution (09 May 2023) [notes]

A neat counter intuitive result, and the resulting rabbit hole

Shadi Hamid's The Problem with Democracy (23 Feb 2023) [notes]

Notes, ideas and quotations from the book

I'll be presenting a poster at ASCB 2022 (30 Nov 2022) [research]

See you in DC!

Fall in Massachusetts (23 Oct 2022) [photo]

Visited Otter River State Forest

SLURM notes (31 May 2022) [python] [emacs]

I've been treating the HMS cluster like my local machine. Nope.

Introducing biomodels.el (27 Feb 2022) [emacs] [model]

An emacs interface to interacting with the BioModels API

Perspective test (09 Oct 2021) [python] [art]

Underestimated the number of carbdoard boxes I recycle everyday at work

Karl Deisseroth's 'Projections' (16 Aug 2021) [notes]

Notes, ideas and quotations from the book

Red chair (30 May 2021) [art]

Mixed media, with Ameya

Saba Mahmood's Religious difference in a Secular Age (29 May 2021) [notes]

Notes, ideas and quotations from the book

Writing a slackbot for org-capture (10 May 2021) [emacs] [python]

Or how I learned to appreciate ngrok and my raspberry pi

Lines 1 (17 Apr 2021) [art] [javascript]

p5js playground

Creating super-personalized dashboards with org-mode and some elisp (31 Dec 2020) [emacs]

Using emacs to solve inconveniences

Quantifying my pandemic year (25 Dec 2020) [quantifiedself]

Quantified self

A timeline of the studies investigating stochastic gene expression (22 Dec 2020) [biology]

Mostly theory, with some experiments thrown in

Rammohun Roy's 'Against Hindoo idolatory' (1820) (05 Sep 2020) [review]

Book review

Thoughts on E.O. Wilson's On Human Nature (23 Aug 2020) [biology] [review]

Book review

Parsing webpages to build a collection of Qawwali performances (18 Jul 2020) [python] [music]

Attempting to parse webpages

Mechanisms in biology (02 Jul 2020) [biology]

Notes from Nicholson 2012

Landing page evolution of my site (11 Jun 2020) [me]

Git history makes it worth the effort!

A Boolean expression to polynomial generator (17 Apr 2020) [python]

Useful for bulk converting Boolean rules

Utility function to control the tags vocabulary in a bibtex file (07 Mar 2020) [emacs]

Messing around with elisp again!

Beeline: Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data (06 Jan 2020) [biology] [simulation]

Our paper is out in Nature Methods!

Multithreading in Python is a pain (02 Dec 2019) [python]

Or how I learned about the GIL

Testing SWIG: Using C modules in python (19 Nov 2019) [python]

faster functions in C, maybe.

Diced Circles (06 Oct 2019) [python] [art]

Badly drawn pie charts

Traffic (04 Oct 2019) [python] [art]

Early morning traffic on Mount Road

Bubbles (03 Oct 2019) [python] [art]

Coffee stains turned to bubbles?

Tiling - 1 (02 Oct 2019) [python] [art]

Euler Map to create tilings

Contaminated plates (01 Oct 2019) [python] [art]

Procedurally generated hexagons

Introducing deqn-mode.el (02 Sep 2019) [emacs] [ODE]

A common emacs interface to define differential equations

Procedural art: Clouds (18 Jul 2019) [python] [art]

Using matplotlib to procedurally generate pink sunsets!

Procedural art: Rangolis (02 Mar 2019) [python] [art]

Generating rangolli patterns with a minimal set of rules

My first elisp function: Create an analysis template (09 Feb 2019) [emacs] [modeling]

A function to populate an org file with boilerplate containing python headers and org-export descriptions.

Towards constructing relationship graphs between raags (01 Dec 2018) [music] [kala]

A post capturing the discussion on relationships between raags from this week's kala meeting

Exploring the relationships between thaats in Hindustani Music (24 Nov 2018) [music] [kala]

Creating a graph based on shared notes between thaats

A poor man's twitter using org-capture (05 Sep 2018) [emacs]

A rough ssh-based pipeline to "capture" a tweet-like text and push to a remote web server

a YASnippet Template for an org-mode notebook (21 Apr 2018) [python] [emacs] [research]

A yasnippet to define a template for a generic computational analysis "experiment"

Fun with Mandelbrot sets (04 Mar 2018) [python]

Visualizing the Mandelbrot set using matplotib

Scripts to generate graphic summaries of weekly org-reports (16 Nov 2017) [emacs] [org-mode] [python]

An alternative to toggl for pretty summaries of org-clock info

The Two-Hit Hypothesis: Insight from statistics (16 Aug 2017) [biology]

What I learned about Knudson's two-hit hypothesis

Compartmental model of cytoskeletal polarization during chemotaxis (27 Apr 2017) [python] [biology] [non-linear-systems]

Some interesting results from our model of cytoskeletal polarization using Watts-Strogatz randomization to mimic disruption of the cytoskeleton

What is the relationship between model size and number of parameters? (04 Mar 2017) [python]

Nutrient Signaling in budding yeast (01 Jan 2017) [biology]

An overview of my research project

A script to study Kuramoto Oscillators (01 Dec 2016) [python] [biology] [non-linear-systems]

Animating a coupled oscillator system using matplotlib

Agent Based Simulation of a chronic Influenza infection (30 Nov 2016) [python] [biology] [simulation]

An animation from our Mod and Sim class showing the spread of infection using an agent-based model