7. Glossary#

Anaconda#

A free and open-source (Anaconda Individual Edition) Python and R distribution. It includes Conda and more than 250 open-source scientific packages. Additional packages can be installed from Anaconda Cloud repositories.

Website: https://www.anaconda.com/products/individual

Anaconda Cloud#

Repository for Python and R packages and notebooks.

Website: https://anaconda.org

apt#

A command-line program that handles the installation and removal of software on Debian, Ubuntu and other Linux distributions.

Related section:

-> The command-line version (apt)

bioconda#

A channel for Conda package manager with over 7000 packages of bioinformatics software.

Website: https://bioconda.github.io/

build-essential#

A package that installs software build tools like make and compilers like gcc, which are required for building modules written in languages like C.

Bash#

GNU project’s shell program. The name stands for The Bourne-Again Shell. It is the most commonly used shell in Linux distributions.

Website: https://www.gnu.org/software/bash/

Bioconductor#

Tools written in the R programming language for the analysis and comprehension of high-throughput genomic data.

Website: https://www.bioconductor.org/

BiocManager#

An R package to install and update packages from the Bioconductor project repository.

Website: https://cran.r-project.org/package=BiocManager

BioPython#

Python tools for computational molecular biology.

Website: http://biopython.org/

Bio::Phylo#

Perl package for phylogenetic analysis.

Website: https://metacpan.org/pod/Bio::Phylo

Cinnamon#

Default desktop environment in Linux Mint.

Website: https://linuxmint.com/

commands#

Also called as binaries or executables.

Conda#

Conda is a package and environment manager.

As a package manager, it can be used to install software from Anaconda Cloud. Software dependencies will be installed automatically.

As an environment manager, it can be used to create and manage environments containing different sets of packages. You can activate and use these environments as necessary.

cpanminus#

A Perl script to get, build and install modules from CPAN. It provides the cpanm command.

Website: https://metacpan.org/pod/App::cpanminus

cutadapt#

A Python program that finds and removes adapter sequences, primers, poly-A tails and other unwanted sequences from high-throughput sequencing reads.

Website: https://cutadapt.readthedocs.io

CPAN#

Abbreviation for Comprehensive Perl Archive Network. It provides additional Perl modules for installation (196,752 as of Dec 2020).

Website: https://www.cpan.org/

CRAN#

Abbreviation for Comprehensive R Archive Network. A network of FTP and web servers providing up-to-date versions of R, packages and documentation.

Website: https://cran.r-project.org/

Debian#

A Linux distribution made of free and open source software. It is free for anyone to download, use, modify and distribute.

Website: https://www.debian.org/

Debian package#

An archive of executable files, libraries, and documentation of software. It can be installed on Debian Linux and Debian-based systems like Ubuntu and Linux Mint. These files have the .deb file extension.

dependencies#

Additional programs or libraries that are needed for a program to work.

edgeR#

An R package for empirical analysis of digital gene expression data. It is available from the Bioconductor project repository.

Website: https://www.bioconductor.org/packages/edgeR/

FAST#

Abbreviation for FAST Analysis of Sequences Toolbox. A set of utilities written in Perl that extend the UNIX paradigm to bioinformatic sequence records.

Website: https://metacpan.org/pod/FAST

Files#

The default file manager in Linux Mint Cinnamon edition. Its original name is Nemo.

gdebi#

A simple tool to install Debian package files along with their dependencies (if any).

Website: https://launchpad.net/gdebi

GNU#

GNU is a recursive acronym for GNU’s Not Unix. The goal of the project is to offer a Unix-compatible system that would be 100% free software.

Website: https://www.gnu.org/

GUI#

Abbreviation for graphical user interface. On a personal computer, it typically includes application windows with buttons to access their functions, icons for launching applications and widgets for managing devices and services.

IDE#

Abbreviation for integrated development environment. Some examples include PyCharm, RStudio and Eclipse.

local-lib#

A Perl module to create a local directory structure to install modules with their dependencies without requiring administrator privileges.

Website: https://metacpan.org/pod/local::lib

Linux Mint#

A desktop Linux distribution. It is based on Debian and Ubuntu.

Website: https://linuxmint.com/

MEGA#

Software for Molecular Evolutionary Genetics Analysis. Available as GUI and command-line versions.

Website: https://megasoftware.net/

MetaCPAN#

A search engine for Perl packages and modules available on CPAN.

Website: https://metacpan.org/

Miniconda#

A minimal distribution of Conda. It is faster to install and also uses less disk space, when compared to Anaconda — the alternative installer which comes bundled with additional packages.

Website: https://docs.conda.io/en/latest/miniconda.html

Modeller#

A program for comparative protein structure modelling by satisfaction of spatial restraints.

Website: https://salilab.org/modeller/

nano#

A simple command-line based text editor.

Website: https://www.nano-editor.org/

OVA#

A file format for distributing virtual machine images.

pip#

The Python package installer. It can be used to install packages from PyPI and other Python package indexes.

Website: https://pip.pypa.io/

PyMOL#

PyMOL is a molecular visualization system originally developed by Warren L. Delano. It is currently maintained by Schrödinger, Inc.

Website: https://pymol.org/2/

PyPI#

Abbreviation for Python Package Index. Repository for software written in Python (275,161 projects as of Dec 2020).

Website: https://pypi.org/

root#

The primary administrator account on a Linux system.

R#

Programming language and free software environment for statistical computing and graphics.

Website: https://r-project.org

RStudio Desktop#

An IDE for R. It includes an R console, an editor with syntax-highlighting and tools for plotting, debugging and managing R packages. The open-source version can be downloaded for free from the project website.

Website: https://rstudio.com/products/rstudio/download/

Related sections:

-> Installing a Debian package

setuptools#

Python program for building and installing Python packages.

shell#

The shell provides a command-line interface (CLI) to the operating system’s services.

Software Manager#

The default application(GUI), for installing software on Linux Mint.

Applications with similar functionality are available on other Linux distributions. For example:

Ubuntu Software on Ubuntu
Software on Fedora and other GNOME-based distributions
Discover on Kubuntu and other KDE-based distributions.

Related sections:

-> The quick and easy method

Synaptic#

A GUI package manager for systems using apt.

Website: https://www.nongnu.org/synaptic/

text editor#

Program to edit text files.

Examples (GUI) - Text Editor (xed) on Linux Mint, Text Editor (gedit) on Ubuntu, Kwrite on KDE Plasma, Geany etc.,

Examples (command-line) — nano, VIM or vi, GNU Emacs etc.,

Related sections:

-> Text Editor — create and edit text files

-> Editing text files using nano

Ubuntu#

Linux distribution developed by Canonical and community of developers. It is based on Debian.

Website: https://ubuntu.com/

wheel#

Python program for installing packages distributed in Python wheel (.whl) format.