Python Programming for Biology: Bioinformatics and Beyond

1

http://www.r-project.org/

.

2

http://rpy.sourceforge.net/

; code was tested on versions 2.0.8 and 2.2.7.

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Absolute path

(computing):

Absolute value

(mathematics):

Acid dissociation

constant (chemistry):

Acidic group

(chemistry):

Active site (molecular

biology):

Affine transformation

(mathematics):

Aliased (signal

processing):

Glossary

This is a simple English glossary to aid understanding. These are not formal definitions,

but rather where you can turn if a particular term makes no sense.

The full specification of a file or directory location within a

computer’s hierarchical file system, starting from the highest

level that contains all files. On Linux and OSX systems this

starts with the root file system ‘/’ and in Windows systems with

a drive letter e.g. ‘C:\’.

The magnitude of a number, irrespective of sign. Calculating an

absolute value effectively means to give the positive version of

the number.

A physical constant which describes the affinity of a chemical

group for hydrogen ions in aqueous solutions, and thus the

strength of an acid. By definition this number is the

concentration of free component times the concentration of

hydrogen ions divided by the concentration of hydrogen-bound

component: [A

−

][H

+

]/[HA].

A chemical group which gives up hydrogen ions, H

+

, in water

(aqueous solution).

The part of a biological molecule’s structure that catalyses a

chemical reaction by binding the reacting substances in a

specific conformation.

A mathematical operation that transforms vectors (e.g.

coordinates) by using a linear transformation (such as a rotation,

scale or shear) and then a translation (movement). For example

this may be used to change the orientation and position of a

shape.

Where the measured frequency of a signal is different from its

actual frequency because the range of measured frequencies is

limited and frequencies outside that range are mapped, in a

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Alignment

(bioinformatics):

Alpha-globin (molecular

biology):

Alpha channel

(graphics):

Alternative hypothesis

(mathematics):

Annealing schedule

(computing):

Argument (computing):

Array (computing):

Asynchronous

(computing):

periodic fashion, into that range.

The placement of macromolecule sequences (codes for different

kinds of component chemicals in a chain) next to one another so

that equivalent residues within the sequences line up. Usually an

alignment is constructed to maximise the similarity between

residues by placing gaps in the sequences.

One of the protein components of the haemoglobin particle

which carries oxygen in blood. Each haemoglobin particle

contains two copies of alpha-globin and two copies of the

similar beta-globin. Each goblin protein binds a red haem

compound which in turn binds oxygen.

The component of an image or pixel that describes transparency.

Usually a maximum alpha value means fully opaque, where no

background shows through, and zero means fully transparent.

In statistics, the opposite of the null hypothesis, i.e. where there

is a non-random relationship between data.

The specification of a series of temperature values that control

the range of search space explored in a simulated annealing

protocol (see below). Typically a schedule starts with a high

temperature, corresponding to a wide initial search, which then

diminishes to a narrow but precise search at the end.

A value that is passed into a function or subroutine. An

argument is represented by a variable inside a general function

definition, but will represent a specific value when the function

is used.

A collection of data items, of the same data type, arranged in a

linear manner, i.e. in order with a first and last position.

Where events occur independently of one another and the main

thread of a program. In parallel processing this means new jobs

may start before previous jobs have finished.

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Artificial intelligence

(computing):

Artificial neural network

(computing):

Attribute (computing):

Back propagation

(machine learning):

Bandlimited (signal

processing)::

Base (molecular

biology):

Base (chemistry):

Basic (chemistry):

Beta-globin

(biochemistry):

The concept of using computers to mimic or approximate the

actions of a person, albeit usually for a specific task. For

example an artificial intelligence (AI) software system can be

used to represent non-human players in a computer game. AI

methods are often involved in pattern recognition.

A computer program that consists of a network of

interconnected data nodes that are capable of machine learning,

commonly used to perform data classification and as substitutes

for analytical functions. Learning occurs when a network is

trained, by changing the strength of connections between nodes.

A named variable that belongs to a computer object of a given

type.

A means of training an artificial neural network in a supervised

way. A known, correct result is used to adjust the layers of the

network in a retrograde manner, from output to input, so that the

output of the network better matches the known result.

The recording of a signal where only a finite range of

frequencies is measured. In practice all signal recordings are

bandlimited because recording devices cannot detect and

represent all possible frequencies.

In reference to nucleic acids like DNA or RNA, the part of a

nucleotide that contains nitrogenous aromatic rings.

A chemical group which accepts hydrogen ions, H

+

, in water

(aqueous solution); the opposite of an acid.

The characteristic of being a chemical base (as above), the

opposite of acidic.

One of the protein components of the haemoglobin particle

which carries oxygen in blood. Each haemoglobin particle

contains two copies of beta-globin. Each goblin protein binds a

red haeme compound which in turn binds oxygen.

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Bias node (computing):

Bilayer (molecular

biology):

Binary number

(mathematics):

Binomial distribution

(mathematics):

Binomial test

(mathematics):

Bit (computing):

Bitwise (computing):

Block (computing):

With reference to machine learning, an extra node in an

artificial neural network which is in the same layer as regular

nodes but which receives no variable input; it usually has a

fixed signal strength of 1.0. The strengths of a bias node’s

connections are trained in the usual way and serve to introduce

signal offsets to the next layer of nodes. In practical terms the

bias connections set a baseline signal that the other, input-

responsive signals adjust.

A double layer of fatty lipid molecules that form cell

membranes. Bilayers are arranged in continuous sheets, with

oily, hydrophobic groups facing the interior and hydrophilic

groups facing the exterior. Lipid bilayers form a barrier that

surrounds and defines cells and sub-cellular compartments.

Representing numbers using base-2, i.e. using only zeros and

ones. In computing such ones and zeros are represented by the

presence or absence of an electrical signal.

A discrete probability distribution that models the number of

successes in a specified number of trials, where the probability

of success for each trial is independent of previous successes

and independent of the trial number.

A statistical test that determines whether the number of

observations of some property follows a binomial distribution

with a specified parameter.

One part of a number represented in binary form, either taking

the value zero or one.

To perform an operation on the binary representation of a

number where each 0 or 1 digit position is considered

separately. For example a bitwise operation 101000 OR 100110

gives 101110, where the answer gives a 1 if either of the input

numbers have a 1 at the same position.

A discrete part of a computer program where commands form

an ordered group that ise executed together. Blocks occur

naturally when using program flow control statements, such as

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Boilerplate code