Blog

DNA and RNA folding with seqfold

5/30/2021

This is a post about a tool I wrote called . if a python utility library that takes in DNA or RNA sequences and predicts their “minimum free energy” — the most likely secondary structure of the DNA/RNA, i.e. how it will fold up on itself. I wrote it at Lattice after getting tired of software like…

The Emperor's Soul

6/14/2020

The Emperor’s Soul is a novella by Brandon Sanderson about a world in which a “Forger” has to recreate the soul of an assassinated emperor. Alive but brain-dead, the senile emperor is a threat to the political positions of his advisors.The protagonist, Shai, is adept at forgery: the magical ability…

Elantris (Elantris, #1)

3/7/2020

Elantris is a fantasy novel about a country on the verge of takeover by an ethnonationalist, religious state. In the shadow of a once powerful city, Elantris, the characters vie for control of a smaller city called Kae.The story tracked three characters. The first was Raoden, a prince afflicted by…

Death's End (Remembrance of Earth’s Past #3)

2/12/2020

Death’s End is the finale of The Remembrance of Earth’s Past. The series begins with humans encountering a belligerent alien species from a neighboring star system, but the scale of humans’ conflict increases exponentially each each book.Liu’s universe is always kinetic. Characters’ decisions cascade through hundreds of years of human…

Labyrinth of Ice

2/1/2020

Labyrinth of Ice is the story of the 1881 Lady Franklin Bay Expedition. Twenty-five explorers, led by first lieutenant Adolphus Greely, spent years in the most remote parts of northeast Canada and northwest Greenland. The expedition’s goals were twofold: science and fame. The scientific purpose of the trip was to…

I, Claudius

11/12/2019

I, Claudius was the third book by Robert Graves and his first with commercial success. It’s an autobiography from the lost perspective of “Tiberius Claudius Caesar Augustus Germanicus.” While Claudius the actual member of Roman royalty did write an actual 8-part autobiography, this is not that. Instead, it’s a humorous…

Matter (Culture, #8)

10/25/2019

Matter was Iain Banks' 8th book of the Culture series and the first after an eight-year break by Banks. Like other Culture series novels, it tracks the happenings of an advanced civilization, the Culture, as their hippy, drugged-out civilians attempt to maintain peace in a violent and chaotic universe.But this…

The Dark Forest (Remembrance of Earth’s Past, #2)

9/30/2019

The Goodreads hivemind is right, the second book is better.Earth is in preparation mode, readying to meet the Trisolaran fleet 350 years in the future. Luo Ji, a could’ve been cosmic sociologist, is elected Wallfacer: a strategist tasked with outwitting the Trisolarians.The book meanders for its first third. Three retired…

The Three-Body Problem (Remembrance of Earth’s Past #1)

9/19/2019

About half way through I thought that The Three-Body Problem was going to affect me the way Dune did. It fell short, but not by much.The pace is relentless. The characters, timelines and format (first person, government documents, interviews) weave in and out. Just when you’re tired of Professor Wang’s…

The Devil in the White City

9/17/2019

While reading it’s easy to feel like the fair was ten years ago rather than over one hundred. Events and opinions are always reinforced with quotes from letters, journals and news articles to the point where it feels like Larson interviewed the characters directly. The characters feel so alive with…

Tribe

9/16/2019

Junger's writing is always clear and concise. This book is enjoyable to read. In it, Junger convincingly argues that, counterintuitively, social cohesion is a positive outcome of war and that this confers positive mental health benefits on those affected. Personally, I found the most vivid parts of the book to…

Tubulin and External Electric Fields

7/13/2019

Paper: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202141 My great-uncle died of Glioblastoma shortly before I started college. I was surprised because I, naively, didn’t think he was the type of person that would die of cancer. He was young, a long distance runner, a Cornell…

The Effects of Points Per Reception

7/12/2019

Below is a post I submitted to Reddit’s /r/fantasyfootball. I was and am trying to draw attention to my app, a fantasy football draft wizard. This post did mediocre. It got ~170 upvotes but was surpassed by another post warning about Fantasy Football Calculator. Apparently it’s a scam. I don’t like…

Fantasy Football Draft App

8/31/2018

This week I wrapped up my fantasy draft app. It’s the end of my fantasy football project, and it’s done for two reasons. Firstly, I’m running out of useful features to add, and secondly — and more importantly — the draft season is over. Starting next week, the app will be on ice for another 50 weeks…

Fantasy Football Forecasting Pt. II

8/5/2018

This week, on “Diminishing Returns for Models I Could Find Elsewhere”… I update my FF models with information from experts and Madden. In my other post, I showed the expected/actual plots for FF models based on basic player statistics alone. The takeaways were that 1) the best predictors of next…

Fantasy Football Forecasting Pt. I

7/18/2018

In search of a project for R, I’ve started fantasy football forecasting. I binge on FF already — spending hundreds of hours per season on leagues with payouts in the hundreds of dollars. I might as well learn something. My goals are to 1) predict player’s fantasy points for the upcoming season and…

A Serverless Golang House Scraper

5/14/2018

I recently started looking for a house. I started after reading /r/personalfinance and the cult-guru-like Mr Money Mustache. I was hooked by their message which was basically: an increased savings rate leads to freedom. With high savings and low spending, all decisions can be made on personal rather…

An App for Google's Speech API

4/7/2018

I made this site to “demo projects I’ve worked on.” I’ve done no such thing (the “demo-ing,” not the working on projects part). So this is a “demo-post.” I did a thing, and this demoes it. Look at me — not dead yet… Backstory My SO does research with a psychology group at Northeastern. Her group…

T2 FLAIR Quantification for Glioblastoma

11/11/2017

Over the last couple weeks, I’ve been trying to find an efficient way to automatically quantify the volume and intensity of T2 flair in the MRI scans of patients with Glioblastoma multiforme. MRI Overview An MRI is a visual representation of induced changes in the magnetization of the body’s water…

This Website

10/18/2017

I decided to make this site after starting grad applications. All of them had some field saying something like “Link to personal website.” I did not make this just because of those input fields, but it was the impetus. Other reasons for making it were that 1) joshuatimmons.com was available and 2) I…

IHC Stain Quantification

9/30/2017

My lab was doing an analysis of breast cancer patients looking for correlations between cytotoxic T cells and overall survival. Part of this involved investigation of IHC tumor punches and panel of antigens. An area for improvement was in the “stain quantification.” We were judging the stain…

Tubulin with Tails Extended

8/20/2017

I have been doing runs with tubulin heterodimers in the presence of external electric fields (EEFs), over a range of strengths, to see how the dimer’s motion changes in response. In all of them so far, I’ve started with an equilibrated tubulin with tails (C-termini) lying flat along the surface of…

Spinal Cord GBM Survival Analysis

7/27/2017

Publication is available at Ovid or here. In my research group at BIDMC, there was a half-finished literature review of spinal cord Glioblastoma multiforme (scGBM). To finish the review I added recent scGBM patient records and carried out a survival analysis, which was all new to me. The idea was to…

After More Than 50 Years, Dr. Karger is Retiring, But He Isn't

5/11/2016

I wrote the below for Northeastern’s College of Science in 2016. First off, Dr. Karger isn’t retiring. “I’m not going to just go fishing,” said Dr. Barry Karger, director of the Barnett Institute, “and I don’t play golf.” Three American Chemistry Society awards, many international medals, 53 years…

Capturing and Profiling Rare Cells

4/15/2015

Northeastern University researchers have extensively profiled the proteins of rare cells in blood, a feat that was previously impossible. By successfully isolating and characterizing rare cells that make up just 0.001 percent or less of the total cells present in blood, Northeastern’s Barry Karger…