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Books

2024

Deploying a bare-bones Python webserver 16/Apr

Books Read Over the Years 16/Jan

2023

Bosco Ho 20/Nov

2020

★

Sometimes, Javascript > Python 7/Jun

2018

★

Programming dirty-dive into the Human Genome (in Python) 13/Sep

Slurping data into your webapp 21/Apr

★

Who are the Ho's? 21/Apr

2017

★

Cantonese self-learning guide 18/Mar

2015

Getting Started with Javascript 6 3/Nov

Command-line Utilities for Everybody Else 16/Jul

2014

Notes for Systems Biology 25/Oct

Bioinformatics and Human Origins 8/Jun

Surface Area and Volume Tools for PDB files, written in easy to read Python 26/May

Structural alignment done right 22/May

2013

★

The First Language of Zen is Cantonese 1/Sep

★

Parsing Large XML files, Serially, in Python 28/Jun

Archiving a PHP-based Blog to Markdown text files 12/Jun

Installing TPP 4.6.2 on Mountain Lion Mac OSX 22/Apr

Vector Representation in Structural Biology 21/Jan

Urinal-based Science Supervision 14/Jan

Favorite Books Read 2012 4/Jan

On the need for a canon of Australian literature 1/Jan

2012

Thoughts on Cal Newport's "Too Good to be Ignored" 20/Oct

CSV is my bioinformatic data format of choice 11/Sep

Faking big arrays in matplotlib 18/Jul

Interview with a Rainman 27/May

★

Doing big science: Brian Schmidt and his measurement of the accelerating universe 6/Mar

2011

★

A Fundamental Breakthrough in Protein Folding 27/Dec

★

Magic Numbers and unit conversions in Structural Biology 13/Dec

What I've Done with this Blog 7/Dec

The infidelity of the theoretical protein backbone 15/Nov

Some English pronunciation tips 9/Nov

★

Swimming, Running, Hunting, and Meditating: the Evolutionary Origin of Mystical States 10/Oct

The GPCR-G complex: the canonical structure of Cell Signaling (with interactive guide) 1/Aug

Some Poems I Like 31/Jul

★

Intuition arises out of Mathematical Intractability 18/Jul

The Pain: Installing Matplotlib in Snow Leopard on a Mac 2/Jun

Purity in the atomic force-fields of molecular dynamics simulations 28/May

★

Jargon: The Art of Naming Things 22/May

Towards mastery: deliberative practice, flow and personality traits 9/May

Multiple Widget Embedding for Jolecule 27/Apr

The Shattering Potential of Shepherds in War 11/Apr

WebGL makes inroads into the browser for the foot soldiers of Biochemisty 6/Mar

Solving the Commenting Problem for Science Articles 3/Mar

Three Bus Systems of Lima 27/Feb

Jolecule widgets for your embedding pleasure! 24/Feb

The Reification of Data: from the Printing Press to the Web-centric API 21/Feb

When living lightly, home floats along with you 14/Feb

Stupid tourist played by a Peruvian conman 10/Jan

Enjoyable Reads of 2010 3/Jan

2010

Darwinian Evolution versus Neo-Darwinian Evolution 2/Dec

The Minimal Set of Equipment to do Computational Biology 8/Nov

The End of Natural Evolution 28/Oct

Why Berliners love Punk and Techno so 25/Oct

Jolecule Example: RNase 23/Sep

Heating Water in Molecular Dynamics 11/Sep

HTML5 mojo: JOLECULE, a javascript protein viewer that runs on the web 10/Sep

Modern solo piano, the generation gap 31/Aug

Why bioinformatics !== compstructbio, or why Rosetta is not a glorified SVM 28/Jul

★

The 2 billion dollar protein sequencing error 11/Jul

We should retire the term "Postdoc" 10/Jul

The Theory of Single Domain Allostery 30/May

★

Beautiful arguments: Linus Pauling's triumphal calculation of the chemical bond 27/May

The Religious Enclave in the House of Science 15/Apr

How the hell do I model this thing? 20/Mar

★

A Decade in Computational Structural Biology 4/Jan

2009

You're Just Not that into Science 21/Dec

"The Sound and the Fury": Incomprehensible Gothic 13/Dec

A New Type of Scroll Bar (for PDF files) 15/Nov

The bioinformatic-journal/software hydrid 25/Oct

Heat a residue in a protein, large loops pop out 12/Jul

Final Figure Blues 29/May

Thousands of hours of Molecular Dynamics saves you minutes of a Monte Carlo calculation 23/May

★

Bionostalgia: Notes to an Even Younger Computational Biologist 12/May

The attempt to reduce the Scientific Process to Computation 18/Apr

Bioinformatics in the Near Concurrent Future 4/Mar

★

An Annotated History of Molecular Dynamics 25/Feb

★

Muscle Memory 23/Feb

Favourite Reads of 2008 22/Feb

How efficient is Molecular Dynamics? 9/Feb

The Future of Reading 26/Jan

The Karaoke Nazi 21/Jan

★

Rewatching "Northern Exposure" 19/Jan

2008

The real authentic Zhang Daqian 22/Dec

"Milk" 21/Dec

★

Rainbow color spectrum in 2dplots considered useless 25/Nov

★

The Historical Mix of Tenure, Academic Freedom and Torture 21/Oct

How the Serpin protein traps the digestive powers of the enzyme Serine Protease 13/Oct

How to Compute Chemistry, Conference Report 24/Sep

How to avoid some pain at working at a desk for hours and hours 25/Aug

Travel Report: the iPhone 24/Aug

My Sore Right Shoulder 9/Jul

★

Longevity in science 14/Jun

★

On The Tacit Process of (Scientific) Discovery 4/Apr

★

How to build a cathedral door out of 456 proteins 13/Mar

On the Visualization of Huge Chunks of Data 21/Feb

How to avoid futility: a guide to parameterizing non-standard amino acids in AMBER 7/Feb

Retracing the ghost of Research Past 17/Jan

2007

Beauty in the Eye of the Programmer 2/Dec

★

The Catholic Trinity: The Fortuitous Construction of the Tri-partate God 18/Nov

★

This is Meister Eckhart from whom God hid Nothing 5/Nov

The Hipster Rite of Passage: organizing your very own Kitchen Show Party 31/Oct

Have a care for the compiler writer 26/Oct

★

Some reflections on programming in D, and why it kicks serious ass over C++, leaving it dead and broken on the sidewalk 23/Oct

★

Calculating the Solvent Accessible Surface-Area 19/Oct

The Plasticity of the Human Face 15/Oct

How the Scientific Publishing Industry Began to Eat Itself 14/Oct

Overthinking, the curse of the rank beginner 9/Oct

★

Parsing PDB files: sometimes you really should reinvent the wheel 1/Oct

A Most Ugly Hack: translating from CHARMM to AMBER trajectories 12/Aug

Fetching PDB files remotely in pure Python code 10/Aug

Quick and dirty minimization 20/Jul

The Romans Stomping on the Jews 18/Jul

Recruiting on Airplanes 25/Jun

Health care in this country is really fucked up 24/May

Wet Holes in the Membrane 9/May

★

The Schrodinger Equation in Action 9/May

Seeing a carbon-monoxide molecule escaping from the clutches of the Myoglobin protein 8/May

★

The Many Layers of the Mystical Mind Cake 6/May

Our Parallel future: an introduction to functional programming 1/May

★

Why I think Python is good (as in granola) for the scientist who programs. 31/Mar

★

A Sign, a Flipped Structure, and a Scientific Flameout of Epic Proportions 21/Mar

Config Files in Python, with a splash of dynamic programming 20/Mar

How to do Great Science, by the great Richard Hamming 16/Mar

Poems I Wrote 14/Mar

★

Notes to a young computational biologist 13/Mar

Heating up a Protein, One residue at a time 11/Feb

Story: The Lighthouse keeper 5/Feb

2006

★

Come together, electrostatically, as one 31/Dec

Looking at the surface of a membrane 30/Dec

Talking in (another) tongue 23/Nov

Sculptor in Conversation 12/Nov

Structural features of the Beta-sheet 23/Sep

Self-referential promotion letter 19/Sep

Randomly Entertaining Science Articles 16/Sep

Jürgen Habermas 16/Aug

Painting: The Three Belgians 15/Aug

COMIC: A Horoscope for the Incurably Pessimistic 12/Aug

★

The Mysterious Regions of the Ramachandran Plot 7/Aug

COMIC: The Adventures of @gendaman 5/Aug

Comic: The Socratic Society T-Shirt Design 2/Aug

Comic: Members of the Dill Lab 2/Aug

Comic: Maxwell's Demon 2/Aug

COMIC: The Amazing Adventures of Infiniteman! 1/Aug

butoh in the dark 5/Jul

A Rose by any other Name 5/Jun

★

Of culture, nature, and flying carpets in the American Museum of Natural History 3/Jun

notes on filming tv 19/May

He Got Game 5/Apr

2005

Of proteins, clusters and musical chairs 5/Oct

Transcription as Compilation 24/Sep

I Can See Clearly Now, the Pain is Gone 23/Jul

★

RMSD: Root Mean Square Deviation 1/Jul

Guitar Etiquette 30/May

Farewell HuaFeng Xu 27/May

Story: The History of David McKowski 27/May

It's official, Australia is Asian 30/Mar

What You'all think about the second person plural in English? 11/Jan

2004

We can fold it for you wholesale 12/Jun

We're Number Two 20/May

★

The Ten Commandments of Protein Folding 10/May

Straight Guy Dancing in a Gay Bar 10/May

What happened to me at the Baltimore airport 20/Feb

★

The Golden Hostel Experience 20/Feb

2003

Story: The Critic 13/Sep

2002

Cinema in Paris 19/Dec

Bread 11/Jul

Life in Brussels 12/Mar

Dublin 4/Mar

A Shorter History of Belgium 11/Feb

Hanover 26/Jan

★

theory vs experiment 15/Jan

Snow 1/Jan

Noel en La Charmee 1/Jan

2001

The Pantheon 19/Dec

Gaudi Gaudi Gaudi 19/Dec

★

I.A. Richards' Theory of Literary Criticism 21/Nov

Flying tips 7/Nov

Taxonomy of Exam Papers 4/Aug

1996

★

The Mr Tompkins Quantum Mechanics Assignment 15/Mar