Python Programming for Biology: Bioinformatics and Beyond



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[Tim J. Stevens, Wayne Boucher] Python Programming

(graphics):

Top object (computing):

Torsion angle

(mathematics):

Training (computing):

Transcribe (molecular

biology):

Transformation



(mathematics):

Transition matrix



(mathematics):

Translation (molecular



biology):

represent the smallest meaningful parts of a computer language.

A graphical object in a user interface that can contain other

graphical items, but which is not itself contained by any other

items. Such objects are typically free-floating windows and

have an iconified representation when fully minimised.

The top of an object hierarchy in a data model, i.e. the class of

object that contains all others.

See dihedral angle above.

With reference to supervised machine learning methods, the

stage where data with known outcome (e.g. there is a known

classification for a given set of input values) is used to adjust

internal parameters so that the method may be used to recognise

patterns and make predictions in a general way on unseen data.

For a neural network training involves setting the connectivity

weights between nodes so that the output signals are close to the

known values for the given input.

The process of converting a DNA sequence into an RNA

sequence, effectively making a copy of the coding DNA strand

by forming a chain that is complementary, following base-

pairing rules, to the template DNA strand.

A function that maps elements from one set to another,

generally preserving any structure that may be present in the

data. When applied to spatial coordinates, transformations

commonly involve scaling, rotation, translation and shearing.

The matrix that specifies how a Markov chain evolves from one

moment in time to the next; the probability of transitioning from

one state to another.

The process of synthesising a protein’s polypeptide chain where

the sequence of amino acids is determined by subsequent groups

of three bases (codon) in a messenger RNA molecule. The

directed polymerisation reaction is catalysed by a large multi-

component particle called the ribosome.



Transmembrane

(molecular biology):

Transpose



(mathematics):

Travelling salesman

problem (computing):

Trypsin (molecular



biology):

Trigger function



(computing):

Tuple (computing):

Two-sample T-test

(mathematics):

Two-tailed test



(mathematics):

Something that resides in and spans the lipid bilayers that form

cellular membranes. Usually used to refer to hydrophobic

protein domains that are embedded in lipids so that the protein

is exposed on both sizes of the membrane, in contrast to a

membrane-associated protein which is only attached on one

side.

A matrix obtained by swapping rows with columns, i.e. flipping



about the diagonal.

A classic example of a computationally hard problem, involving

the determination of the most efficient route for a person to visit

a given set of points on a map, i.e. which order the visits should

be made in.

A protein-cleaving enzyme (a protease), originally isolated from

the pancreas of many animals where it works to digest food.

Artificially synthesised trypsin is a common tool in molecular

biology for cutting up protein chains at predictable locations.

In machine learning, when referring to the nodes of a neural

network, the trigger function is the operation associated with a

node that converts the summation of all the (weighted) input

signals into an output signal. The trigger functions are typically

step-like or S-shaped (e.g. the sigmoidal hyperbolic tangent) so

that only inputs above a threshold cause a significant output and

so that the maximum output is limited.

A data structure containing an ordered collection of items. In

Python a tuple cannot be modified after creation and may

contain any kind of item, including mixtures of different types.

A statistics test which indicates whether two samplings which

are assumed to be normally distributed with the same variance

have the same mean.

A statistical test that determines the probability of an observed

value having at least a given separation from a mean value (in

either direction); for example, the probability that an

observation is separated from the mean by at least one standard




Type (computing):

Type checking




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