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 Ubuntu installer. This prototype installer allows users to select and install scientific Linux is an open source operating system. 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. scientific Linux-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 Linux distribution 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 Debian, (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