Introduction

I have a recurring problem: often my understanding of simple concepts differs from that of other people. Despite the fact that I am never wrong[*], these other people attempt to prove that their opinion is valid by citing some published material, such as a dictionary. This web page is my defensive shield. Now my opinions are also published and therefore are correct.

[*] Including now.

A very amusing Africian animal. Its main purpose is to convert ants into poo.

Alpha Centauri is a star (actually two stars because it is a binary system) which is currently about 4.4 light-years away from my desk. There is nothing wrong with Alpha Centauri, except that a computer game, Sid Meier's Alpha Centauri is set on one of its planets and that game regularly prevents me from getting any sleep.

Bill Gates is a very rich man. He is rich because he managed to convince people that it is a good idea to send Word Documents to everybody else by email. These recipents then need to buy Microsoft Office and Microsoft Windows. Together those two software packages cost more than my entire PC -- that includes both hardware and software. Either I got a very good deal or lots of people have been conned.

Computers are evil electronic, programmable, calculating devices. Many people suffer as a result of having an unwelcome computer in their home. Symptoms include; sleep deprivation, premature baldness, photophobia, diet of pepsi cola and pizza, delusions that other people are interested in IRQs/Java/ultra DMA-66, short-sightedness and a bushy beard. For many people, these syptoms are due to self-inflicted and prolonged contact with computers. These people may be either Nerds or Geeks.

Some trained chemists have the mistaken belief that exposure to computers has fewer long-term side effects than exposure to toxic, mutagenic, chemicals that smell like lightly grilled training shoes. They are wrong. Nevertheless, many of them leave their jobs as synthetic chemists and learn how to program in Fortran. As soon as they know how to implement poorly designed software, they embark on a career as a computational chemist.

Computational Chemistry is the application of modern computational methods to solve chemical problems. This definition is just blurry enough that computational chemists think that they may also do the jobs of trained computational biophysists, quantum chemists, informatiticians and software engineers.

CVS - Concurrent Version System

An open-source, source code maintainance tool. It is designed to enable multiple users to simultaneously work on the same files at the same time. These multiple users check out files from the source tree, make their modifications, and then commit those changes back into the source. When the other users realise that those modifications were dumb, they can be backed out (This is very useful when I'm working on the project).

This is a phrase which is much more amusing to British people than to American people.

"American" English is to "British" English as Microsoft J++ is to Sun's Java. It exists, it is sufficiently different to be incompatiable for no particular reason, and it is fundamentally pointless.

Fuzzy logic is an area of computational/AI research which replaces boolean decisions (i.e. Yes/No or True/False) with a continuous range of values (i.e. 75% True and 25% False). This is a very useful concept. When your computer program is unable to give exact results, you can say that it uses fuzzy logic, and everybody will be really impressed.

A class of optimisation algorithm which borrows the ideas of evolution from the natural world and applies them to computational problems.

Good things:

Bad things:

Most hormones and pharmaceutical compounds invoke their physiological effects by binding to specific proteins, known as receptors. On the basis of molecular structure and mechanisms, there are four classes of receptor; ligand gated ion channels, receptor tyrosine kinases, steriod hormone receptors and G-protein coupled receptors (known as GPCRs). GPCRs are located in the lipid bilayer that forms the membrane around all cells. Their physiological action is caused via an associated protein, a guanine nucleotide binding protein (known as a G-protein). Typically they act as a switch, controlling a membrane bound enzyme or an ion channel. All GPCRs share a similar structure which consists of seven helical domains which sit as a bundle through the cell membrane. The critical ligand binding site is found within this transmembrane portion of the protein. The family of GPCRs bind a wide range of compounds at this site, triggering a wide range of cellular processes. Consequently GPCRs are considered important pharmaceutical targets.

The symptoms that follow an excessive consumption of alcohol. Typical symptoms are nausea, vomiting, headaches, and elevated sensitivity to bright light and loud noises. These are the combined results of dehydration, irritation to the stomach lining and the toxic effects of alcohol metabolic products. Hangovers are nature's primary method to prevent you spending all of your money on alcoholic beverages. The fact that your girlfriend doesn't like you when you are drunk is the other.

An open-source, UNIX-like operating system developed by some Finnish bloke called Linux Torvelds from Finland, and a large worldwide community of developers from around the world. I use linux because it is free (in terms of free speech as well as free beer). It is very very powerful, but that is less important than its price. Bill Gates doesn't like Linux.

A stochastic search algorithm which is typically applied to sample conformational space.

A prediction algorithm which is losely based on the picture of a simplified brain.

A software development and distribution model. It overlaps with Free software in the sense that it deals with the same practical issues but different philosophical issues. Briefly, the main tenet is that everybody should have access to, and the right to modify, the source code to the software they use. Microsoft don't seem to think that this is a good idea.

An operating system (or OS for short) is the software that controls your computer hardware, and possibly provides elements of the software environment. The only OS that most people ever encounter is Microsoft Windows, which is a pity. Many OSes are essentially free, a few of which are listed here: (And people still put up with Microsoft Windows?)

An efficient methematical representation for orientation or rotation. Very useful for both molecular modelling and computer graphics.

See entry for recursion.

Transmembrane proteins (or TM-proteins for short) are the proteins which sit through a biomembrane, typically the lipid bilayer surrounding every cell. Many very important proteins fall into this category, including those which are the targets for 80 out of the top 100 pharmaceuticals. There are two main families of TM-proteins; the helix-bundles and the porins.

UFO is an acronym with a couple of common meanings:

Occassionally, you might witness a UFO landing. I have compiled a page containing useful advice for such a scenario here.

UNIX is a hugely powerful, widely used operating system. It was originally developed in the early 1960s as a set of tools by programmers for programmers. Until recently UNIX was never popular on the desktop or in the home, but was the main operating system for servers and supercompters. There are many varients of UNIX, and nowadays many of those are now beginning to grab a significant portion of the desktop market. Many operating systems are very similar to UNIX but must be called UNIX-like operating systems rather than UNIX-clones for dodgy legal reasons.

The word computer professionals use when they mean "idiot."
-- Dave Barry, "Claw Your Way to the Top".