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Empowering African Scientists - an Investigation Into a CD-Based Installer for Scubuntu

Empowering African Scientists - an Investigation Into a CD-Based Installer for Scubuntu

Empowering African scientists - an investigation into a CD-based installer for scubuntu

P. VAN ZYL, T. FOGWILL Meraka Institute, PO Box 395, Pretoria, 0001 Email: [email protected] , [email protected]

Abstract One of the key activities in scubuntu is the Open source software (OSS) is software for determination of profiles of scientists, based on which the source code is made available and can their computing and software requirements. be freely modified and redistributed. OSS has These profiles are coupled with a specification been identified in the South African national R&D identifying the OSS scientific tools that are most strategy as a vehicle for fostering local innovation appropriate for that profile. The refinement of and economic development. It promotes these profiles and package collections is an inclusivity by being freely available and allowing ongoing activity that will be driven by the unconstrained customisation and modification. scubuntu user community. The use of OSS for scientific computing can significantly lower the barriers-to-entry for poorly Investigative work was undertaken to determine funded research institutions in developing the suitability of a CD-based installation program countries. At the same time, it can empower for scubuntu. An experimental prototype of such scientists to contribute and collaborate with their an installer was developed, based on the peers globally. standard installer. This prototype installer allows users to select and install scientific is an open source . There software based on their field of study or profile. are scientific tools that run on Linux for almost all The work done to develop this prototype is scientific disciplines. While there are successful presented here. -based projects like SciLab (SciLab 2008), MATLAB (Matlab 2008), and the R programming language for statistics (R 1. Introduction 2008),and despite its significant advantages, scientific computing on Linux is not as The scubuntu project is an initiative to develop an widespread as it could be. To address this Ubuntu-based specifically problem, the Meraka Institute is developing targeted at scientific users and researchers. scubuntu, an Ubuntu-based Linux distribution for This paper highlights the investigative work scientists. The project vision is that scubuntu will undertaken to determine the suitability of a CD- become the premier choice of desktop operating based installation program for scubuntu. An system for researchers and scientists. experimental prototype was developed, based on the standard Ubuntu installer. The prototype A number of challenges are associated with installer allows users to select and install scientific computing on Linux. The scubuntu scientific software based on their field of study or project seeks to address these problems. One of profile. the major challenges is that scientific software is not installed by default in any Linux distribution. This paper also highlights some of the key For most scientists, it is difficult to select, install lessons learned while developing the prototype. and maintain appropriate scientific software on Linux. These tasks require knowledge of the OSS Section 2 provides some background on open applications that are available as well as source software (OSS) and its connection with technical proficiency on Linux. This can be time science, as well some background information on consuming, and the results are usually not scubuntu itself. The scubuntu installer is shared, so effort is unnecessarily duplicated. The discussed in section 3. Sections 4 and 5 scubuntu project seeks to address these summarise, present some conclusions and problems by making scientific packages part of discuss possible future work. the default distribution and providing tools to ease their discovery, installation and management. 2. Background

1 and 'open source governance' are being used 2.1 Open source software (Open Source 2008). In these new fields, the ideas of open source are being applied to create Open source software (OSS) is software for works that cost less and involve more input from which the source code is made available and can outsiders. The following section looks at the be freely modified and redistributed (Open correspondence between these open source Source Software 2008). OSS has been identified concepts and the process of scientific discovery. in the South African national R&D strategy (Government of the Republic of South Africa 2.2 Open source software and science 2002, p. 45) as a vehicle for fostering local innovation and economic development. It There are clear similarities between the concepts promotes inclusivity by being freely available and of open source and the way in which scientific allowing unconstrained customisation and knowledge is generated. These similarities have modification. been discussed by a number of authors. In particular, DiBona et al. (1999) identify the Goldman and Gabriel (2005, p. 6, 29) identify following: several key benefits of open source, including: ● the sharing of information with peers ● that the user and developer communities ● the opportunities for others to take work together to improve the functionality existing ideas further and to apply them and quality of the software in different contexts ● access to high-quality, free software ● the generation of new ideas. ● access to advice and help on software design and development In open source, program code and ideas are ● promoting participation in the openly shared. This allows others to inspect the development of software source code, provide ideas, critique or ● low cost suggestions for improvement, provide fixes or ● engaging with end-users in design and other code contributions, or create new projects testing derived from the original. This is analogous to the ● shorter time to market work of scientists, who generate new knowledge ● harvesting innovation that is based on, or grounded in, existing ● reduced support costs knowledge (Adler 1999). ● improved integration ● avoidance of vendor lock-in The adoption of OSS in industry and academic institutions has increased in recent years. Laird Studies conducted on open source and (2002) mentions that many labs and scientists innovation have shown that open source and are moving away from proprietary scientific open communication can lead to innovative applications and are beginning to use and solutions (Goldman and Gabriel 2005). Efforts improve open source scientific applications. like InnoCentive (InnoCentive Open Innovation Reasons for this include: 2008) and the work of Lakhani et al. (2007) have ● no-cost licensing shown that opening up and asking for input from ● simpler license management a wider audience can provide huge benefit and ● improved large-scale programmability lead to more innovative solutions. This form of and flexibility user participation during the production of ● convenience of development software is a key property of most successful ● better integration OSS projects. ● better performance ● concerns around intellectual propriety The open source ideas of openness, sharing and ● better support collaboration aren't new. Developers have been sharing ideas and collaborating since the early The use of OSS for scientific computing can days of programming and the Internet. significantly lower the barriers-to-entry for poorly funded research institutions in developing The term 'open source' and the ideas and countries. At the same time, it can empower principles behind it are being applied to diverse scientists to contribute and collaborate with their fields. These include art, music, education and peers globally. politics, where new terms like 'open source curricula', 'open source documentary', 'open Linux, as an example of an open source source movie productions', 'open source politics', operating system, offers a good candidate OSS

2 platform for adoption by researchers. There are scientific tools that run on Linux for almost all Goldman and Gabriel (2005) mention that scientific disciplines. Despite its significant 'innovation happens elsewhere' and that 'many advantages, though, scientific computing on advantages accrue when a company adopts the Linux is not as widespread as it could be. A attitude that most innovation happens elsewhere number of challenges are associated with and focuses on choosing the best outside scientific computing on Linux. One of the major innovations and figuring out the right challenges is that scientific software is not distinguishing features to make its products installed by default in any Linux distribution. For competitive'. The scubuntu project adopts such most scientists, it is difficult to select, install and an approach – it is based on a popular and maintain appropriate scientific software on Linux. successful open source Linux distribution called These tasks require knowledge of the OSS Ubuntu. This allows scubuntu to leverage the applications that are available, as well as existing user and developer communities of technical proficiency on Linux. They can be time Ubuntu, while adding value by collaborating with consuming, and the results are usually not the Ubuntu developers to package scientific shared, so effort is unnecessarily duplicated software. Ubuntu, in turn, is based on , (Fogwill 2008). and benefits from the use of Debian's highly regarded package management system (Debian To address these problems, the Meraka Institute 2008). (also known as the African Advanced Institute for ICT) is developing scubuntu, an Ubuntu-based 2.3.2 Collaboration methods (Ubuntu 2008) Linux distribution for scientists. The project vision is that scubuntu will become Open source projects are built around the the premier choice of desktop operating system concept of collaboration. Most collaboration on for researchers and scientists. The scubuntu OSS projects happens via the Internet (Goldman project is discussed further in the following and Gabriel 2005) (DiBona, Ockman and Stone section. 1999). Open source projects typically use a number of Internet resources to collaborate, 2.3 The scubuntu project including: ● on-line source code repositories for code 2.3.1 Overview management and sharing ● on-line mailing lists and internet relay Scubuntu is an OSS project to develop a desktop chat for technical discussions operating system designed specifically for ● on-line issue tracking tools scientists. The scubuntu project seeks to ● on-line documentation address the problems highlighted in the previous section by making scientific packages part of the Goldman and Gabriel (2005, p.8) also stress the default distribution and providing tools to ease importance for OSS projects of building a their discovery, installation and management sufficiently large community of contributing users (Scubuntu 2008) (Fogwill 2008). and developers. A significant part of the scubuntu effort will be to create and sustain such One of the key activities in scubuntu is the a community of developers and scientists that determination of profiles of scientists, based on volunteer and collaborate to continuously their computing and software requirements. improve the platform. These profiles are coupled with a specification Scubuntu uses Internet-based technologies to identifying the open source scientific tools that facilitate collaboration, to develop and share are most appropriate for that profile. The ideas, and to coordinate development. These refinement of these profiles and package technologies include wikis, weblogs, on-line collections is an ongoing activity that will be project collaboration websites tools such as driven by the scubuntu user community. (Launchpad 2008) and source code revision control systems such as Bazaar (Bazaar In addition to the development of profiles and the 2008). identification of high-quality open source software, scubuntu focuses on the packaging, 2.3.3 Community building integration and improvement of existing OSS scientific tools, and on the development of new A key element of the success of the scubuntu tools where no OSS alternatives exist. project is the extent to which it is adopted by a

3 community of users and researchers. The There are other efforts in the Linux community scubuntu project aims to develop, grow and that seek to address the problems of scientific sustain such a community by: computing on OSS. These include: ● strongly aligning the scubuntu project ● Scientific Linux (Scientific Linux 2008) is with Ubuntu, to leverage the large a rebuild (from source code) of Red Hat community of existing scientific users Enterprise Linux (Red Hat 2008). that Ubuntu already has Scientific Linux focuses on providing a ● raising awareness of scubuntu through framework for the development of publication and exhibition at conferences customised versions of Linux for use in and in journals laboratories. ● inviting the participation of scientific ● Poseidon Linux (Poseidon Linux 2008) is users by posting on mailing lists and based on Ubuntu and previously on other online fora Kurumin Linux (Kurumin Linux 2008). It is ● formal and informal discussions with similar to scubuntu, but does not provide research organisations and individual the same flexibility (it does not provide a researchers to promote the use of way for users to select which scubuntu packages/profiles they wish to install). ● handing out CDs and promotional ● Scibuntu (Scibuntu 2008) is based on material at universities, Linux user group Ubuntu. Scibuntu is not a Linux meetings and conferences distribution but a script that is run to ● providing good information and install scientific applications on an documentation (including information on existing Ubuntu installation. profiles) on the project website ● Other bioinformatics-focused Linux ● publishing information about scubuntu on distributions such as Bioknoppix sites such as freshmeat.net and (Bioknoppix 2008) and Vlinux (VLinux slashdot.org 2008), both of which are based on ● responding in a timeous, friendly and (Knoppix 2008). These helpful manner to users who interact with distributions focus exclusively on the team to obtain advice, assistance or bioinformatics. information ● (Edubuntu 2008), which is based on Ubuntu, is focused on 2.3.4 Licensing of scientific packages educational usage but also provides some scientific packages. Edubuntu Goldman and Gabriel (2005, p.7) highlight that does not allow package selection at licenses grant the right to distribute and make install time – instead, base packages are changes to source code, but that they can also installed and then extra packages can be restrict what developers and users are allowed to selected after the base installation. do. Understanding the issues around licensing and choosing appropriate licenses are thus Ubuntu has been shown by DistroWatch critically important for open source projects. (DistroWatch 2008) to be the most popular desktop Linux distribution. As such, the scubuntu For scubuntu, the process of selecting suitable team chose Ubuntu as the base for their scientific software to include in the distribution distribution. Scubuntu clearly differentiates itself needs to consider the license under which that from the other Ubuntu-based projects above by: software is released. Some software packages ● focusing on the development of a have licenses that are 'viral', forcing derived community of users and developers works to be released under the same license, ● focusing on the development of profiles while other software packages have licenses that ● performing all work in the open and may be incompatible with those of existing contributing back to Ubuntu packages in the distribution. These license issues ● packaging the appropriate tools into the must be carefully investigated and documented core distribution to ease their installation, before any package can be added to the without compromising the users' ability to scubuntu distribution. select their own preferred packages.

2.3.5 Comparison to other initiatives 3. The scubuntu installer

Scubuntu is based on the Ubuntu “live CD” and a modified version of , the Ubuntu

4 installation program. Ubiquity is a simple ● copies an entire mirror of the content of graphical installation program that runs from a the live CD onto the selected disk live CD and is designed to integrate well with partition – this essentially installs the Debian- and Ubuntu-based systems. It is written base Ubuntu system, largely in Python and uses the Debian Installer ● reboots the system into the newly (d-i) as a back-end for many of its functions installed Ubuntu desktop. (Ubiquity 2008) (Debian Installer 2008) (Ubuntu Installer Development 2008). The following section discusses the various alternatives that exist for allowing users to select The following sections discuss how Ubiquity was the packages to be installed. modified to provide the features required by scubuntu. 3.2 Package selection methods

3.1 Ubiquity overview There are a number of approaches to allowing the users to select and install packages. This The scubuntu team decided to investigate the section discusses these approaches and use of CD/DVD-based installer for scubuntu, with describes the method adopted by scubuntu. all the scientific applications already on the CD. This approach could work well for the markets in , another “flavour” of Ubuntu, adds developing countries, where the lack of good additional screens to Ubiquity. These screens connectivity is a constraint preventing the use of allow the user to select custom packages for network-based installers. This section describes installation. The Mythbuntu screens provide a how this CD-based installer operates. hard-coded, preselected list of extra packages to install from. Ubuntu is distributed on a live CD called the Ubuntu desktop CD. The Ubuntu desktop CD is a Older versions of Edubuntu used the normal bootable CD and contains a complete operating ubiquity screens but with a modified Phase 2 that system that runs completely from the CD. It installed a predefined set of additional includes a Gnome (Gnome 2008) graphical educational and scientific packages. The current . After the CD boots up and version of Edubuntu no longer has its own starts a Gnome graphical session, the Ubiquity installer – it is installed simply as an “add-on” to a installer can be executed from the user's desktop normal Ubuntu system. to install Ubuntu onto the selected hard drive. Scibuntu does not provide a CD-based installer. Ubiquity supports a number of alternative It rather provides scripts that are run on a normal Graphical User Interfaces (GUIs), besides the Ubuntu system (post installation) to install default Gnome/GTK+ based one. These include: additional packages. a base version, a KDE/ (KDE 2008) based front-end, a front-end customised for Mythbuntu (Mythbuntu 2008), and a non-interactive version The scubuntu installer will follow a similar for unattended installations. strategy to Mythbuntu by providing an additional selection page where users can select scientific For the interactive versions, the Ubiquity GUI packages from a list. The difference will be that provides screens where users can for example the list of available packages will be created ● select their language, country and dynamically and will be grouped using scientific keyboard layout profiles. These profiles and their associated ● select the disk partition on which to install packages will be read from an XML file to create Ubuntu a tree-based package selection screen. Each ● configure the network new release of scubuntu will provide a new and ● create user accounts and passwords updated XML file describing the packages and It also provides a final screen (before the actual profiles. installation commences) displaying a summary of what was entered and selected by the user. 3.3 Profiles

This initial phase of user input is called Phase 1. Scubuntu employs the concept of profiles. Phase 2 follows Phase 1 and Profiles represent categories of packages or ● formats the selected hard disk scientific domains (i.e. fields of study). Profiles partition(s), are associated with lists of individual application

5 packages. In addition, they can also be For the first prototype of scubuntu, only two associated with sub-profiles. More specific scientific fields are included - biosciences (or profiles can thus be nested within more general biological sciences) and geographic information profiles to form a hierarchical structure. For systems (GIS). These fields were selected example, Figure 1 describes the situation where because of the availability of expert researchers scubuntu has a top-level profile called Biology in these fields within the CSIR who were willing to with sub-profiles Biochemistry and Molecular assist the scubuntu team in designing Biology. Each of these sub-profiles then contain appropriate profiles. lists of software packages appropriate for Bio- Chemists and Molecular Biologists, respectively.

Profiles and sub-profiles will be implemented as Debian meta-packages in scubuntu. Meta- packages are packages that group together a set of other applications. Meta-packages do not themselves contain any application files or data, but rather specify a list of package dependencies. Selecting the meta-package for installation automatically selects all its dependencies for installation as well. Meta-packages thus provide a mechanism for simplifying the task of installing sets of related packages (Tille 2007). In Figure 1, biology, molecular-biology, biochemistry and base-plotting-tools would all be meta-packages, while the remaining nodes would be real application packages.

Figure 1: An example of a profile with meta- packages

The hierarchy of profiles, sub-profiles and packages is stored in an XML file. The scubuntu installer reads the XML file and creates a tree component representing this hierarchy. Each profile, sub-profile and package has a checkbox. Users can mark these checkboxes to select the profiles and/or packages they wish to have installed. The scubuntu package and profile selection screen is shown in Figure 2.

6 The installation process starts by displaying the Gnome/GTK+ input screens to the user. The additional scubuntu page, which allows for the selection of scientific packages, is also displayed. On this screen, packages are displayed as a package tree, which is created from the package.xml file. The ScubuntuGUICreator class in scubuntu_ui.py is responsible for reading the XML package file and creating the package tree and selection screen. Nodes in the tree can be selected or deselected. If a parent node (i.e. a profile or sub-profile) is selected, its children are all selected automatically as well. If a parent Figure 2: Scubuntu's scientific package select node is deselected, then its child nodes will also be deselected. If a child node of a previously screen selected parent node is deselected, the parent Installer prototype node must be deselected as well to indicate that all its children are no longer selected. The UML collaboration diagram in Figure 3 shows the Python classes and scripts that

Figure 3: Ubiquity collaboration diagram Ubiquity uses during the installation process. It As the user selects or deselects packages, also shows where code changes have been events are fired. These events result in the made for scubuntu. invocation of methods to add or remove the

7 selected packages from a list. This list is then automatically installed. For this initial prototype, iterated and its contents are stored in the the focus was limited to two scientific fields. Debconf database for use in the second phase when the actual packages are installed. 5. Conclusions and future work

'Debconf is a configuration management system Despite the many potential benefits for scientists for Debian packages' (Hess 2007). Debconf is of using Linux as their desktop operating system, used to request user input during the installation a number of challenges make this problematic: ● of packages - the user is requested to answer Few people are aware of Ubuntu as certain configuration questions and these platform for scientific computing ● answers are stored in Debconf's database Finding and choosing best scientific tools (Debconf 2008). Ubiquity uses Debconf to track on Ubuntu is difficult ● the user’s installation preferences, while OSS scientific tools are not integrated in scubuntu merely uses Debconf to record the cohesive suites ● packages the user selected for installation. Some OSS scientific tools provide only limited functionality ● In the second phase, the standard Ubuntu OSS tools are not available for certain scientific tasks packages are copied from the installation CD to ● the disk. The installation script, install.py, was Ubuntu is not certified to run all proprietary scientific software modified to read the additional scubuntu package ● list from package_list.txt and iterate over this list Software maintenance requires technical to check whether the package is marked for proficiency installation in the Debconf database. The resultant list is later passed to APT (Advanced The approach taken by scubuntu addresses some of these problems by: Packaging Tool), which performs the actual ● installation of the packages. Making all work publicly available ● Formal and informal collaboration ● The creation of user and developer An alternative approach to that of using Debconf communities would have been to store only the selected ● Integrating scientific OSS into cohesive packages in the package_list.txt file. However, suites of packages this alternative was not considered as Debconf ● Centralising technical management and provides a richer configuration environment maintenance of packages (Debconf 2008) that could be used in more sophisticated ways later by scubuntu. In addition, the work on the installation program presented in this paper further addresses these Currently, the modifications that were made to difficulties by: Ubiquity are being incorporated into a locally built ● Pre-selecting the best-of-breed scientific scubuntu live CD/DVD and will be tested by open source software and grouping scientific users. After testing and additional these packages into profiles improvement (if required), the changes will be ● Predefining profiles for supported incorporated into the main (upstream) Ubiquity scientific domains source tree. ● Providing a user-friendly way for scientists to select these profiles and install the associated package sets. 4. Summary The scubuntu prototype presented here will be This paper discussed the ongoing effort tested by scientists in a number of scientific undertaken by the scubuntu team to create an fields, to determine its suitability, usability and the open source Linux distribution that provides extent to which it can be expected to be adopted researchers and scientists with better package by scientists. Future work will include the selection and installation features. To achieve development of new profiles to cover additional this goal, the scubuntu team modified the scientific fields, the refinement of existing profiles, standard Ubuntu live CD installer (Ubiquity), to and the investigation of additional options for the include a package/profile selection screen. This installer program. In particular, it is thought that selection screen provides a list of scientific the current design may not be optimal, as it is profiles (and associated packages) for users to severely restricted by the amount of data that can choose from. The selected packages are then be placed on a CD/DVD. There may be

8 significant benefit to taking a hybrid approach, Gnome 2008, viewed 1 September 2008, combining elements of the current design with http://www.gnome.org/ elements of the Edubuntu approach where extra meta-packages are provided as “add-ons” after Goldman, R., Gabriel, R. P. 2005, Innovation installation. This could result in scubuntu Happens Elsewhere: Open Source as business comprising of a number of CD/DVDs. The first strategy, Morgan Kaufmann Publishers Inc., San CD would be a modified Ubuntu live CD that Francisco, CA includes (in additional to normal packages) a set of packages commonly useful to all scientists, Government of the Republic of South Africa regardless of their field of study. Additional “add- 2002, South Africa's National Research and on” CDs could be generated for each supported Development Strategy, The Government of the scientific field – these CDs would include the Republic of South Africa, Pretoria, South Africa. domain-specific packages for that particular field Available from: of study http://www.info.gov.za/view/DownloadFileAction? id=70261 6. References Hess, J. 21 October 2007, Debconf, viewed 1 Adler, S. 1999, Open source/open science, Linux September 2008, J., page 10. http://kitenet.net/~joey/code/debconf/

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9 Open Source Initiative 2008, viewed 1 September 2008, http://opensource.org scubuntu 2008, viewed 1 September 2008, http://scubuntu.meraka.org.za/wiki/ Open Source Software 2008, viewed 1 September 2008, Tille, A. 15 October 2007, Custom Debian http://en.wikipedia.org/wiki/Open- Distributions, viewed 1 September 2008, source_software http://doc.mdcc.cx:8080/doc/cdd-doc/debian- cdd.en.pdf Open Source 2008, viewed 1 September 2008, http://en.wikipedia.org/wiki/Open_source Ubiquity 2008, viewed 1 September 2008, https://wiki.ubuntu.com/Ubiquity OpenWetWare 2008, viewed 1 September 2008, http://openwetware.org/wiki/Main_Page Ubuntu 2008, viewed 1 September 2008, http://www.ubuntu.com/ Poseidon Linux, viewed 1 September 2008, https://sites.google.com/site/poseidonlinux/ Ubuntu Installer Development 2008, https://wiki.ubuntu.com/InstallerDevelopment R 2008, viewed 20 October 2008, http://www.r-project.org/ Vlinux 2008, viewed 1 September 2008, http://www.bioinformatics.org/vlinux/ Red Hat 2008, viewed 1 September 2008, http://www.redhat.com/ 7 .Endnote Scibuntu 2008, viewed 1 September 2008, http://scibuntu.sourceforge.net/ Contribution to the paper was almost equally distributed between the authors, although Pieter Scientific Linux 2008, viewed 1 September 2008, van Zyl did the bulk of the background reading. https://www.scientificlinux.org/ He also did most of the technical development and investigation required to develop the SciLab 2008, viewed 20 October 2008, prototype installer. http://www.scilab.org/

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