BIOCLOUD COMPUTING WORKSHOP (BCW)

• BioSlax Slides PDF (1.7 MBytes)
• Desktop-as-a-Service and BioCloud PPTX (4.5 Mbytes)

Mark de Silva is a Principal Systems Engineer at the National University of Singapore (NUS) and is the IT Manager for the Life Science Institute's (LSI) BioInfomatics Resource Unit. An engineer with quick mind and vast experience, he has been managing the bioinformatics resources in NUS since the early days of 1996. From setting up core infrastructure and implementing protocols, he has played a significant part in progressively building up the centralized bioinformatics resources in NUS to what it is today. His in depth knowledge of programming, IT networking and security and how these can be applied to almost any field, has earned him quite a reputation in NUS and citations in several research papers and posters on top of holding two US patents as one of the co-inventors of the "Multi-Language Domain Name Service". In 2005, he was one of the 2 senior staff invited to teach in the 2nd Training Course on Bioinformatics and Functional Genomics Applied to Insect Vector of Human Diseases and 4th Regional Training Course on Bioinformatics Applied to Tropical Diseases in Southeast Asia and together with staff from the Super Visualisation and Computing Unit of NUS, took second prize in the High Performance Computing Challenge 2005/2006 under the PC Grid Parallel Speedup Category. In 2006, he also created the BioInformatics Live Media, BioSLAX, which is being used by NUS in its Life Science Curriculum. In addition to his role in NUS, he acts as technical consultant to various local and international organisations, including S*Star Alliance for BioInformatics Education and the Asia Pacific BioInformatics Network (APBioNet) where he is the acting chief technical coordinator for Singapore APBioNet BioMirrors Project, a world BioInformatics public service for high speed access to up-to-date DNA & protein biological sequence databanks for which he authored a poster which was presented at the 2nd Asia Pacific International Molecular Biology Network (AP-IMBN) conference held in July 1999 at the Concorde Hotel, Singapore.

Lim Kuan Siong is a Senior Engineer at the National University of Singapore (NUS) and is the Deputy IT Manager for the Life Science Institute's (LSI) BioInfomatics Resource Unit. A technically sound engineer with vast programming and IT knowledge, he has played a very active role in bioinformatics research efforts earning him citations in several research papers and posters including one entitled "Strategies for EBV vaccine design using computational tools" presented at the "International symposium on Human Genetics and Gene Therapy", 5-6 February. 1999, Singapore. This also appeared in the January - March 1999 issue of "Newsletter of the Singapore Society for Microbiology and Biotechnology". In 2005, the Senior Systems Engineer was also invited to teach in the 2nd Training Course on Bioinformatics and Functional Genomics Applied to Insect Vector of Human Diseases and 4th Regional Training Course on Bioinformatics Applied to Tropical Diseases in Southeast Asia and was part of the team that took second prize in the High Performance Computing Challenge 2005/2006 under the PC Grid Parallel Speedup Category. In addition to his role with NUS, he is also a technical consultant to the Asia Pacific BioInformatics Network (APBioNET) and S*Star Alliance for BioInformatics Education.

BioSLAX is a live CD/DVD/USB comprising a suite of more than 30 bioinformatics tools and application suites that has been released by the Bioinformatics Resource Unit of the Life Sciences Institute (LSI), National University of Singapore (NUS). It is bootable from any PC that allows CD/DVD/USB boot option and runs the compressed SLACKWARE flavour of the LINUX Operating System (OS) which is also known as SLAX.

BioSLAX is currently being used by NUS in the teaching of Bioinformatics, under the Life Science Curriculum. It caters to about 200 undergraduate students per semester, where they learn how to make use of the many popular tools available in the Live CD/DVD in their problem-based learning laboratory sessions and class projects, which involves the setup of a bioinformatics node server to present their project research, findings and/or search tools to any databases created (also using tools from BioSLAX) for the project.

There are two parts to the SLAX build, the core system and the individual modules. The core system contains the OS and necessary basic tools for the operation of the live CD/DVD/USB. The core system is also that is referred to as the 'base', while the modules are the individual utilities that a user wants to put on their system. As the modules can be inserted or removed in the creation of the CD/DVD/USB, the system is fully modular and easily customisable. BioSLAX has been used to rapidly create classroom environments for courses on specific applications (eg: R/BioConductor course held in conjuction with AMBIS in 2008), to setting up bioinformatic resource node at Institute of Biotechnology (IBT) Vietnamese Academy of Science and Technology in 2007.

The flexibility of BioSLAX allows many variations which can be customized to an individual's needs. In this workshop, we will teach interested participants to create their own live CD/DVD BioSLAX distribution, from infusing the base with selected modules to creating their own modules. We will also be talking about possibilities of deploying BioSLAX with relevant GRID agent modules, allowing for the rapid creation of a GRID environment through which compute intensive jobs maybe submitted.