Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

biology):

Constructor



(computing):

Containment hierarchy



(computing):

Continuous



(mathematics):

Convolution



(mathematics):

Covalent bond



(chemistry):

Cross product



(mathematics):

Ctrl (computing):

Cursor (computing):

structure, to resist changes during evolution, resulting in similar

forms. Some evolutionary changes are more conservative than

others, e.g. DNA changes that don’t affect protein sequence or

amino acid changes that conserve chemical characteristics.

A function that is part of the definition of an object class, which

is executed whenever a new object of that type is made. Thus a

constructor may be used to set up the initial state of a computer

object. In Python the constructor function is named __init__.

A means of describing the links and relationships between

computational data items, especially in a data model, where one

kind of object belongs to, or is contained by, another, producing

a tree-like system of categorisation.

Where a quantity is modelled in terms of the real numbers

instead of a discrete series, i.e. taking any value, not just whole

numbers.


The modification of one function given another, whereby for

different offsets (sliding one relative to the other) a new

function is created as the summation of the product of the two.

Commonly used in image adjustment where original pixel

values are modified by a convolution matrix that specifies how

pixels of the adjusted image are formed by the weighted

combinations of surrounding pixels.

A strong chemical bond between two atoms that are held

together in a discrete molecule.

In three dimensions, a vector which is orthogonal to both of two

specified vectors, and with length given by the area of the

parallelogram determined by the two vectors.

The control key on the keyboard, usually used in combination

with other keys so the user can issue specific commands. The

equivalent for German keyboards is ‘Strg’.

The point on a computer screen where typed keyboard

characters appear. Often indicated by a graphical marker so the



Cursor (databases):

Database schema



(computing):

Data model



(computing):

Decorator (computing):

Degrees of freedom

(mathematics):

Denormalisation



(computing):

Destructor (computing):

Determinant

(mathematics):

user can see where text will be extended or inserted.

A way of accessing the data records in a relational database via

programming, to process it in terms of its rows.

A way of specifying the layout of the information that will be

stored in a relational database.

Using data object definitions, as formalised in classes, to create

a computational representation of a network of interconnected

concepts. A data model will often, but not always, contain

classes that correspond closely to real-world entities, such as

atoms, molecules or even people. The purpose of the model is to

provide a convenient way of representing data and its

connections. The model itself is an abstract concept, and so does

not contain any specific data. Rather the model is a specification

of how to represent data, which in turn is used to create real

instances of computer objects.

A Python function that is used to wrap and modify another

function (similar to annotations in Java). A modifying decorator

function is declared before the target function it operates on

(using the @ symbol), but is equivalent to calling the modifying

function on the result of the target.

The number of parameters that are free to vary in a

mathematical model; the minimum number of parameters that

are needed to fully specify the state of a system.

The redundant storage of data in a relational database so that

fewer tables are used, i.e. by repeating values.

A function that is part of the definition of an object class, which

is executed whenever an object is deleted, e.g. to perform any

required clean-up.

A number that can be calculated from a matrix that gives the

volume of the region obtained when the matrix is applied as a

transformation to a region with unit volume.




Detailed balance:

Dictionary (computing):

Diffraction pattern


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