Python for Bioinformatics

adventures in bioinformatics

Saturday, June 7, 2025

Python to draw geometry

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Over the last couple of weeks I've been working on a library of geometry utilities in Python, code to work with matplotlib to draw figur...
Thursday, November 16, 2023

Ratio boxes

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I worked up a short new chapter for my Geometry book. It's about a device I'm calling ratio boxes, for want of a better word. When...
Tuesday, November 7, 2023

Napoleon's Theorem

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Napoleon's Theorem is a theorem some attribute (naturally enough) to Napoleon. It says that if you take any triangle and draw equilat...
Friday, September 1, 2023

Newton's series for the exponential

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I've been reading the first chapter of Dunham's Calculus Gallery again (available here ). It starts with a discussion of Newton re...
Monday, August 7, 2023

Archimedes and the Broken chord

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The theorem of the "broken chord" is ascribed to Archimedes, although his original work has been lost. It was analyzed by the Ara...
Thursday, June 22, 2023

Killing geometry

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I think it's fair to say that math is not my granddaughter's favorite subject. The whole debate about whether some people are inher...
Tuesday, June 20, 2023

Acheson's Geometry

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One of my favorite books is David Acheson's The Wonder Book of Geometry (Amazon here ). I especially enjoyed the proof that similar ...
Monday, June 19, 2023

Exploring Hawaii

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Continuing from the previous post , I thought I would summarize how to drill down to individual polygons in a GeoDataFrame containing the...
Sunday, June 18, 2023

Geopandas and maps

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Recently I've been exploring maps again, using GeoPandas in Python. I found it confusing at first, but that was mainly because I did...
Saturday, September 17, 2022

Pizza theorem

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In Acheson's The Wonder Book of Geometry , I came across the " pizza theorem ." The basic form of the problem says to take an...
Monday, February 28, 2022

Comments

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I've had to turn comments off for the blog. Nothing but spam anymore. The intrepid reader will be able to find me. Hint: +"9...
Wednesday, September 15, 2021

Sum of angles: Ptolemy

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 The "sum of angles" theorems are incredibly useful in calculus.  These are formulas for the sine (or cosine) of the sum (or diffe...
Wednesday, August 25, 2021

Calculating continued fractions

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 I've been playing with continued fractions.  The golden ratio is one of the simplest examples. Substituting the whole right-hand side f...
Friday, July 16, 2021

Pentagons, again

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 It's been some years , but I took another look at pentagons.  It is fun to see the connection between φ,  the "golden ratio",...
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About Me

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telliott99
I'm retired, but I used to teach and do research in microbiology and bacterial genetics. This blog started as a record of my adventures learning bioinformatics and using Python. As bbum says, it's so "google can organize my head." The programs here are developed on macOS using Python plus other software as noted. YMMV. I've had to turn comments off for the blog, since there is nothing but spam anymore. The intrepid reader will be able to find me. Hint: +"9" and I use gmail. Please do contact me about missing links, or if you want more info about a topic. Like a lot of sites many old links are broken due to files having moved around, being renamed, etc. If a link doesn't work, let me know.
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