Python Programming for Biology: Bioinformatics and Beyond

biology):

Maximum likelihood

(mathematics):

Mean (mathematics):

Memoization

(computing):

Memory allocation

(computing):

Meoisis (biology):

Method (computing):

Microarray (biology):

A two-dimensional, rectangular array of numbers, i.e. arranged

into rows and columns.

Inert, solid material that is used to support or attach a

component of interest.

The estimate of parameters of a probability distribution which

maximises the probability that the data is observed given the

hypothesized distribution.

The average value of a collection of data.

The process by which a function remembers the results from

previous executions, so that a cached result may be returned if

an operation is repeated for the same input data, thus

eliminating the need to perform the entire operation again. This

often improves program speed, at the expense of using more

memory.

The allocation of a specific chunk of memory for use by a

program, which some (typically older) programming languages

usually have to do explicitly.

The separation of chromosomes within the nuclei of eukaryotic

cells (i.e. not bacteria) into two sets, each containing half of the

chromosomes. After cell division this results in daughter cells

which have only one copy of each kind of homologous

chromosome. For example the original cell will have two copies

of chromosome 1, but after divisions the cells have one copy

each.

A function that belongs to a computational object, and which is

generally specified in the object’s class definition.

A kind of multiplexed experiment, where many miniature

experiments, which are of the same type but use different

reagents, are performed at the same time within a rectangular

array on a solid support.

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Mitosis (biology):

Model (bioinformatics):

Model (computing):

Module (computing):

Monte Carlo method

(computing):

Motif (molecular

biology):

Multiple inheritance

(computing):

Multiple-sequence

alignment

(bioinformatics):

Mutable (computing):

The reproduction and separation of chromosomes within the

nuclei of eukaryotic cells (i.e. not bacteria) that results in two

identical sets of chromosomes. Mitosis is usually followed by

cell division, i.e. to create two copies of the original cell.

In relation to three-dimensional structures, a conformation (see

above) that is consistent with the known data.

An abbreviation of data model.

A discrete unit of computer code that is stored as a separate file,

but which may have its functionality imported into the program

code represented in other files.

A means of solving a problem by using random numbers to

create test points or solutions. The Monte Carlo method is used

as an unbiased way of getting a representative picture of a

problem without having to have any innate understanding of the

underlying mechanics and while only considering a small

proportion of possible values.

A small, recurring feature within biological molecules, such as a

group of closely related sequences or sub-structures, that can be

related to a particular biological function. For example a protein

may bind to a given DNA sequence motif to activate a number

of different genes.

When considering object orientation and the construction of

class definitions, the process by which one class is based on two

or more parent super-classes and thus inherits properties from

all of them.

An alignment (see above) where there are more than two

macromolecule sequences. Sequence elements are arranged, by

placing gaps, to maximise the similarity between residues in

each column.

The ability to manipulate a data item so that its value or

contents changes internally, but leaving the handle (reference) to

the data item unaffected.

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Native conformation