Base System

This document describes the specification of the base desktop for scubuntu (called scubuntu-base-desktop). This base desktop can be installed by installing the metapackage scubuntu-base-desktop.

The scubuntu base desktop comprises a basic scientific desktop that includes applications and libraries that are commonly useful to most researchers and scientists. It does not include any domain-specific packages (see other scubuntu metapackages for those), but rather represents a base scientific system to which additional packages can be added for specific scineitific domains/fields.

Generic desktop

scubuntu-base-desktop is an extension of the basic Ubuntu desktop, with the addition of packages commonly useful to most scientists. Because it extends the basic Ubuntu desktop (ubuntu-desktop), it has a dependency on

• ubuntu-desktop

Documentation

Scubuntu comes with it's own set of documentation in package

• scubuntu-docs

To enable the "About Scubuntu" menu item in the System menu, Scubuntu needs a custom gnome-panel - this is provided in version 2.24.1-0ubuntu2.2~scubuntu1 of the gnome-panel package (for now, until the changes are merged into the main Ubuntu gnome-panel pacakage).

Artwork and Branding

scubuntu-base-desktop includes all the artowrk and branding that visually differentiate scubuntu from a normal Ubuntu system. This includes a package

• scubuntu-wallpaper

containing the scubuntu wallpaper images, a package

• scubuntu-usplash

that contains the scubuntu usplash theme, a package

• gdm-theme-scubuntu

that contains the Scubuntu login screen theme, and more ...

Science libs

scubuntu-base-deskop includes a number of basic scientific libraries that are commonly useful to scientists. These include:

The GNU scientific library (optionally with reference documentation)

• gsl-bin
• (gsl-ref-html)
• (gsl-ref-psdoc)

The scipy set of scientific tools for Python

• python-scipy

Reference Manager

A reference manager is a tool that allows researchers to manage bibliographic databases, and that allows researchers to easily manage references/citations within documents.

Currently, for the scubuntu 8.10 proof-of-concept,

• jabref

is the selected reference manager. It is a graphical frontend to BibTex.

Future versions of scubuntu will consider other options, notably bibus, which provides more functionality and better integration with OpenOffice.org.

Stats

The base scubuntu desktop includes a number of statistical packages that will allow scientists to do basic (and more advanced) data processing and statistical analysis. The tools include

• openoffice.org-rcalc

which provides a plugin to OpenOffice.org Calc, allowing it to use the GNU R system for statisitical tasks.

In additional, the GNU R system itself is included, optionally with documentation:

• r-base #GNU R statistical computing language and environment
• r-recommended #GNU R collection of recommended packages
• (r-base-latex) #GNU R LaTeX docs for statistical computing system functions
• (r-base-html) #GNU R html docs for statistical computing system functions
• (r-doc-html) #GNU R html manuals for statistical computing system
• (r-doc-info) #GNU R info manuals statistical computing system
• (r-doc-pdf) #GNU R pdf manuals for statistical computing system

Maths

The base scubuntu desktop includes some mathematical tools for numerical computation, algebra, and matrix-based computation. These include (with optional documentation, in cases)

• octave

the GNU Octave language for numerical computation,

• maxima
• (maxima-doc)

a computer-based algebra system,

• scilab
• (scilab-doc)

matrix-based scientific software, and

• r-mathlib #GNU R standalone mathematics library

for general-purpose mathematical functionality in the GNU R system.

Other options exist as well, but are not currently included. An example is the freemat mathematical framework (excluded because it requires Qt).

Plotting

scubuntu-base-desktop includes a number of general-purpose plotting tools, allowing scientists to plot and generate graphs and figures from their research data.

These include:

• octplot

a graphical plotting interface for Octave.

In addition, it includes

• gnuplot
• (gnuplot-doc)

a command-line driven plotting program, with optional documentation, a minimal GNOME frontend called

• plotdrop

and the

• python-gnuplot

library for accessing gnuplot programmatically from Python.

It also includes

• grace

a point-and-click XY plotting tool,

Optionally, the scubuntu base system can also iclude

• (quickplot)

a fast, interactive 2D plotter and data viewer.

Latex and writing

For the writing of scientific articles and reports, scubuntu-base-desktop provides a complete LaTeX authoring environment, that includes the LaTeX typesetting packages

• texlive

and

• texlive-science

It also integrates LaTeX and OpenOffice.org Write by including

• writer2latex
• writer2latex-manual
• openoffice.org-writer2latex

For editing LaTeX documents, two editors are also provided, namely

• winefish #LaTeX Editor based on Bluefish
• texmaker #A Cross-Platform LaTeX Editor

TODO: pick between these two

Possibly a better LaTeX editor is kile, but it is excluded because it is Qt-based.

Scubuntu addons

To ease the installation of additional packages (post installation), scubuntu provides its own customised "Add/Remove Applications" application, with configuration allowing for the installation of additional scubuntu/scientific packages. This customised app-install is contained in the following packages

• scubuntu-app-install #app-install modified for scubuntu
• scubuntu-app-install-data #app-install configs for scubuntu packages

In order to customise the environment appropriately for Scubuntu (including simple customisations such as setting the default mode of the GNOME calculator to scientific), the following package is installed:

• scubuntu-defaults

Ensuring the integrity of Scubuntu package repositories

Packages in Ubuntu and Scubuntu are provided via online repositories. To ensure the integrity and validity of packages downloaded and installed from these repositories, and to prevent malicious attacks, it is necessary to cryptographically sign the repositories. The GPG keys used to sign the Scubuntu package repositories are provided in

• scubuntu-keyring