Glossary

absolute path

A path that refers to a particular location in a file system. Absolute paths are usually written with respect to the file system’s root directory, and begin with either “/” (on Unix) or “\” (on Microsoft Windows). See also: relative path.

accession

a unique identifier assigned to each sequence or set of sequences

argument

A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.

categorical variable

Variables can be classified as categorical (aka, qualitative) or quantitative (aka, numerical). Categorical variables take on a fixed number of values that are names or labels.

cleaned data

data that has been manipulated post-collection to remove errors or inaccuracies, introduce desired formatting changes, or otherwise prepare the data for analysis

command shell

See shell

command-line interface

A user interface based on typing commands, usually at a REPL. See also: graphical user interface.

conditional formatting

formatting that is applied to a specific cell or range of cells depending on a set of criteria

CSV (comma separated values) format

a plain text file format in which values are separated by commas

current working directory

The directory that relative paths are calculated from; equivalently, the place where files referenced by name only are searched for. Every process has a current working directory. The current working directory is usually referred to using the shorthand notation . (pronounced “dot”).

factor

a variable that takes on a limited number of possible values (i.e. categorical data)

file system

A set of files, directories, and I/O devices (such as keyboards and screens). A file system may be spread across many physical devices, or many file systems may be stored on a single physical device; the operating system manages access.

filename extension

The portion of a file’s name that comes after the final “.” character. By convention this identifies the file’s type: .txt means “text file”, .png means “Portable Network Graphics file”, and so on. These conventions are not enforced by most operating systems: it is perfectly possible (but confusing!) to name an MP3 sound file homepage.html. Since many applications use filename extensions to identify the MIME type of the file, misnaming files may cause those applications to fail.

flag

A terse way to specify an option or setting to a command-line program. By convention Unix applications use a dash followed by a single letter, such as -v, or two dashes followed by a word, such as --verbose, while DOS applications use a slash, such as /V. Depending on the application, a flag may be followed by a single argument, as in -o /tmp/output.txt.

GB

gigabyte of file storage or file size

Gbase

a gigabase represents one billion nucleic acid bases (Gbp may indicate one billion base pairs of nucleic acid)

graphical user interface

A user interface based on selecting items and actions from a graphical display, usually controlled by using a mouse. See also: command-line interface.

headers

names at tops of columns that are descriptive about the column contents (sometimes optional)

home directory

The default directory associated with an account on a computer system. By convention, all of a user’s files are stored in or below their home directory.

metadata

data which describes other data

NGS

common acronym for “Next Generation Sequencing” currently being replaced by “High Throughput Sequencing”

null value

a value used to record observations missing from a dataset

observation

a single measurement or record of the object being recorded (e.g. the weight of a particular mouse)

operating system

Software that manages interactions between users, hardware, and software processes. Common examples are Linux, OS X, and Windows.

parent directory

The directory that “contains” the one in question. Every directory in a file system except the root directory has a parent. A directory’s parent is usually referred to using the shorthand notation .. (pronounced “dot dot”).

path

A description that specifies the location of a file or directory within a file system. See also: absolute path, relative path.

pipe

A connection from the output of one program to the input of another. When two or more programs are connected in this way, they are called a “pipeline”.

plain text

unformatted text

process

A running instance of a program, containing code, variable values, open files and network connections, and so on. Processes are the “actors” that the operating system manages; it typically runs each process for a few milliseconds at a time to give the impression that they are executing simultaneously.

prompt

A character or characters displayed by a REPL to show that it is waiting for its next command.

quality assurance

any process which checks data for validity during entry

quality control

any process which removes problematic data from a dataset

raw data

data that has not been manipulated and represents actual recorded values

read-evaluate-print loop

(REPL): A command-line interface that reads a command from the user, executes it, prints the result, and waits for another command.

redirect

To send a command’s output to a file, or another command, rather than to the screen, or equivalently to read a command’s input from a file.

regular expression

A pattern that specifies a set of character strings. REs are most often used to find sequences of characters in strings.

relative path

A path that specifies the location of a file or directory with respect to the current working directory. Any path that does not begin with a separator character (“/” or “\”) is a relative path. See also: absolute path.

rich text

formatted text (e.g. text that appears bolded, colored or italicized)

root directory

The top-most directory in a file system. Its name is “/” on Unix (including Linux and Mac OS X) and “\” on Microsoft Windows.

shell

A command-line interface such as Bash (the Bourne-Again Shell) or the Microsoft Windows DOS shell that allows a user to interact with the operating system.

shell script

A set of shell commands stored in a file for re-use. A shell script is a program executed by the shell; the name “script” is used for historical reasons.

standard input

A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a pipe, it receives data from the standard output of the preceding process.

standard output

A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a pipe, it is passed to the standard input of the next process.

string

a collection of characters (e.g. “thisisastring”)

sub-directory

A directory contained within another directory.

tab completion

A feature provided by many interactive systems in which pressing the Tab key triggers automatic completion of the current word or command.

TSV (tab separated values) format

a plain text file format in which values are separated by tabs

variable

A name in a program that is associated with a value or a collection of values. Also: a category of data being collected on the object being recorded (e.g. a mouse’s weight)

wildcard

A character used in pattern matching. In the Unix shell, the wildcard * matches zero or more characters, so that *.txt matches all files whose names end in .txt.