Python Programming for Biology: Bioinformatics and Beyond

(molecular biology):

Negative binomial

distribution

(mathematics):

Nested (computing):

Newline character

(computing):

Nodes (computing):

Non-deterministic

polynomial (NP)

(computing):

Normal (mathematics):

Normal distribution

(mathematics):

The properly folded and functional arrangement of a biological

molecule’s structure, which is generally believed to be close to

the lowest-energy form.

A discrete probability distribution that models the number of

successful trials before a specified number of failed trials

occurs, where the probability of success for each trial is

independent of previous successes and independent of the trial

number. A geometric distribution is a special case of the

negative binomial distribution where number of failures sought

is one.

An arrangement of computer code where one control structure is

placed inside the block of another. For example a loop may be

defined, to repeat the execution of a bit of code, and that bit of

code itself may contain another loop, controlling an inner block.

In this case one loop is said to be nested in the other.

A special character, not resulting in a printed symbol, which

causes the flow of text to begin at a new line. On Linux and

Mac OSX systems the newline character was originally a

linefeed command, from the days of typewriters; represented in

Python by the escape code ‘\n’. On Windows systems a new line

is given by a carriage return and a linefeed control character; in

Python ‘\r\n’.

A point of connectivity within a network, which performs a

process and which is associated with input and output data

streams.

A problem whose solution, if given, can be verified in

polynomial time (polynomial in the size of the problem).

A vector that is perpendicular (at right angles) to a plane or

another vector.

Also called the Gaussian distribution, a special continuous

probability distribution with a ‘bell’ shape that is determined by

its mean and standard deviation and that occurs in many

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Null hypothesis

(mathematics):

Object (computing):

Object attribute

(computing):

Object orientation

(computing):

One-tailed test

(mathematics):

Optimisation

(mathematics):

Order (computing,

mathematics):

Orthologues (molecular

biology):

Overtraining

(computing):

applications of statistics.

When assessing a hypothesis, a competing hypothesis that

represents what would be expected to happen given random

chance or in the absence of discriminating information. The null

hypothesis is useful to give an objective baseline to predictive

theories.

A computational data structure, built according to a class

definition, that contains other items of data (as attributes) and

which may have bound functions (methods).

A bound variable that represents a property of an object.

A general method of writing computer programs, representing

the data items as objects, often with interconnectivity.

A statistical test that determines the probability of an observed

value having at least a given separation from mean value, on

one side only. For example, the probability that an observation

is at or above one standard deviation from the mean.

A method to select the best values (or other elements) from a

range of possibilities. Often this means to find the parameters

which give the minimum or maximum value of a function.

How the number of operations required to perform a

computational task scales with the size of the problem.

Entities which are homologous, sharing a common ancestor,

because of the separation that occurs as separate species evolve.

Effectively different versions of the same protein or gene from

different organisms.

Pertaining to the pattern recognition of supervised machine

learning methods, the problem of applying the training data too

much, so that the method is less general and performs sub-

optimally on unseen data.

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Paired-end reads