Tools & Tutorials

In this page is a subject-classified directory of tutorials, essays, and tools on digital art, chemistry, LaTeX typesetting, music, magic, teaching, balloon twisting and more.

Digital Art

Mostly relating to vector illustrations using Adobe Illustrator, the tools and tutorials here nonetheless makes occasional excursions to 3D (mostly Blender), raster, and algorithmic methods of graphic preparation.

Drawing a Population of Molecules (Tedious Vector Style)

This tutorial shows you step-by-step instructions to draw a large number of molecules in vector, using a combination of ChemDoodle, Avogadro, and Adobe Illustrator.

Using 3D Shapes in Adobe Illustrator

A beginner tutorial shows how 3D shapes can be used to create an instructional illustration.

Rich Shading in Adobe Illustrator

An intermediate tutorial showing how to use the shapebuilder tool, custom graphic styles, and layers to create and manage rich shadows and highlights.

Quirks of Brush Style/Settings in Illustrator CS5

Systematic findings of how various path profile/brush appearance/creation method interact with other tools.

Education

A Letter to New Grad Student Teachers

Distilling what I’ve learnt about teaching over 2004-2010.  Written for and reprinted from the UVic Learning and Teaching Center Newsletter.

A Happy Illustrated Guide to a PhD

There are different takes to what a PhD means; this is my optimistic take, written in response to Might’s Illustrated Guide to a PhD.

Popular Science

How does Smartshade Cosmetics Work?

A cosmetic that “changes color to match your skin” — just how does it work?  An illustrated guide.

Science, Lemons, and Press Releases

Discussing the stretching press releases in popular science websites, and their effects on science perception, using the framework of what economists call “the Market of Lemons”.

Silly Scientific Articles

Daring Chemists 1, Eagle Eyed Editors 0

What Calvin (of Calvin cycle fame) hid in his JACS paper.

The Silliest (and Most Awesome) Science Technique

I won’t spoil the surprise.

The quickest read

It is a serious problem…

Science

Membranes & Channels

Synthetic Ion Channels: Interactive Bibliography

An interactive timeline for exploring the field of synthetic ion channels.  Use filters to locate authors and topics of interest, and use the direct links to publishers to track down articles.  Database last updated mid-2011.

Pretty Picture of Messy Membranes

Presenting molecular mechanics data in an infographic to show the scales and dynamic distribution of atoms in lipid membranes.

Practical

Mass Spectroscopy: Online Calculator for Multiply Charged Ion Adducts

An online calculator that, given a molecular mass and possible ions, predicts all possible combinations of adducts.

Writing in the lab: Lab-book and Sample Annotations

Some practical tips (incl. what pens to use!) about writing lab-book and samples, tailored for the synthetic chemist.

Code & Software

ClampFit in OSX

How to run Molecular Devices’ ClampFit suite of software in OSX, using WineBottler as the bridge.

Scientific Visualization: Learning Enthought Traits

Part 1, 2, and 3.  A tutorial series describing how to program interactive visualization software using the Enthought Traits framework.

3D Bar Histogram in Python

Tutorial showing how to prepare 3D Bar Histograms using the Python Matplotlib library.

LaTeX Typesetting

Writing LaTeX for Chemistry

Parts 1, 2, and 3.  A tutorial series describing the motivation and techniques in using LaTeX to write chemistry manuscripts.  Automatic compound numbering with chemscheme is described.  Exercise files supplied.

Embedding python in LaTeX

A tutorial about embedding python in LaTeX to prepare articles that is dynamically sourced.

Spell-checking LaTeX in OSX

A Subdued Color Scheme for TeXShop

Writing with LaTeX

A generic tutorial about how and why to write in LaTeX, a flexible, free, and nerdy typesetting system.

Part 1: Advantages of writing with LaTeX

Part 2: Installation & Resources.

General Interests

“Compassionate Voices” by Hub Meeker

Hub Meeker summarizes the role and experiences of decades as a crisis line volunteer.  Hub and I both served on the NEED Crisis and Information Lines in Victoria BC.

The Best Hangman Word

What is the best hangman word you can choose?  I explored this question by writing code to systematically evaluate the possibilities… answer provided.

Love, Marriage, and Monte Carlo

A mythical story made the analogy for love and marriage as searching for the best grain of wheat in a field – but where one have no knowledge of the future and can only pick once.  Given these conditions, how does one go about finding that “best grain of wheat”?  I approached this problem with a Monte Carlo simulation.

Part 1: Establishing the problem.

Music

Vivaldi & Bach’s Magnificat

Recordings of performances by the UVic Prima Choir in 2010 (while I was singing with them).  Conducted by Noble and Aloni.

Parts for Rubank Advanced Flute Duets

Flute recordings of the separate voices; I made these recordings so I could play duets with myself =)

Magic, Entertainment, and Mnemonics

The Pivot Switch

The Pivot Switch is a card sleight I developed, based on prior work by Marlo and Jones.  It is an angle-friendly one-handed multiple top-change.  The method is described in an detailed, illustrated 4 page manuscript.

The “Shapely” Mnemonics System

 I developed the “shapely” mnemonics system to remember numbers of arbitrary length.  This mnemonics system is currently supported by a decoder (see article), and an encoder is in the works.