When you’re in the business of saving lives, speed is everything. That’s why scientists at the Centre of Informatics Science (CIS) at Nile University worked with Microsoft to migrate their open-source applications for bioinformatics to Windows® HPC Server 2008. With a user-friendly interface and advanced job-scheduling and deployment features, CIS researchers have succeeded in developing their applications 50 per cent faster than previously, and now enjoy easy-to-use tools that improve research speed.
Finding treatments and vaccinations for illnesses such as influenza, hepatitis C, and cancer are a top priority for governments and research institutions worldwide. In the Middle East, Nile University in Egypt is integral to much of this groundbreaking work. The life-science researchers at CIS need to analyse huge amounts of biological data to compare genomic sequences. Using conventional computers this would not be possible, so high-performance computing (HPC) is vital to their success.
In 2004, Dr. Mohamed Abouelhoda, the Assistant Professor of Bioinformatics at Nile University and leader of the bioinformatics group at CIS, developed a prototype that can be used to compare and examine large amounts of genetic data. This prototype was eventually evolved into an application called the Computational Comparative geNomics Utility Toolkit (CoCoNUT) and is used for comparing complete genomic sequences. To conduct his research, Abouelhoda also used other programs:
- BLAST—which searches databases for the same biological sequences.
- An in-house implementation of the Standard Sequence Alignment Algorithm—which is used for comparing small strings of genetic sequences.
The tools were created using open-source software running on a Linux operating system. Linux uses a complex user interface, and Abouelhoda became aware that other scientists around the world might have difficulty using the tools.
“Linux-based software is operated through a sophisticated command-line interface. Many scientists find this difficult to use, which limits their potential to analyse genetic strings,” says Abouelhoda. “As a result, scientists would often send their work to specialist developers who could operate the applications. This occasionally affected the accuracy of the results and had the potential to breach data security.”
||There’s no question that Windows HPC Server 2008 users are more productive, which ultimately improves research.
||Dr. Mohamed Abouelhoda
Assistant Professor of Bioinformatics,
Abouelhoda wanted to redevelop the tools so that they could be used by all researchers regardless of their technical expertise. He also wanted to make sure that the tools could be easily downloaded and used on different operating systems, so that other institutions could benefit from them.
In June 2008, Abouelhoda worked with both Microsoft Egypt and the Cairo Microsoft Innovation Center (CMIC) to migrate his open-source bioinformatics tools from Linux to operate on a Windows HPC Server 2008 cluster.
He discovered that Windows HPC Server 2008 could not only offer comparative performance to that of the Linux system but could significantly improve manageability and usability. Abouelhoda says: “The Windows operating system is one of the most popular on the market and most scientists are familiar with its graphical user interface and components. Also, Microsoft experts operate throughout the world so we knew that great technical support would be available wherever it was needed.”
To redevelop the applications, CMIC and Abouelhoda used Microsoft Visual Studio® 2008 Professional Edition development system. Abouelhoda says: “The debugging and compiling capabilities of Visual Studio 2008 are very impressive, which speeds up the development of new applications. Visual Studio also supports fast development of parallel algorithms, helping researchers to generate results more quickly.”
Integrated tools included in Windows HPC Server 2008 also make it easy to set up jobs. Abouelhoda says: “From one Administration Console we can set up and configure every aspect of node and cluster management. We also make great use of the Job Scheduler, which simplifies the execution of tasks and automatically allocates resources to specific jobs.”
The project took just nine months to complete. Now, employees at the CMIC and Microsoft Egypt provide all the technical support needed to keep the HPC cluster operational, while researchers need less training on the system. “With data analysis and application development available in a familiar Windows interface, we can now provide HPC to more researchers and scientists than ever,” says Abouelhoda.
Windows HPC Server 2008 has revolutionised the way applications scientists from all over the world perform complex research using the comparative genomics tools developed by Nile University. The user-friendly development environment means that researchers don’t require specialist technical skills to create sophisticated algorithms, freeing them up to focus solely on data analysis. Abouelhoda says: “We had about 40 downloads just two weeks after posting the tool on the Internet, which reflects the need for such tools. There’s no question that Windows HPC Server 2008 users are more productive, which improves research.”
- Enhances researchers’ productivity. Scientists use a Windows graphical user interface to operate the tools developed by Abouelhoda. Sophisticated command lines are no longer necessary, helping scientists without any technical experience conduct more research and obtain results of experiments faster.
- Increases potential for collaboration. Now that the applications operate on a Windows environment, researchers can download the tools and results of research from the Internet. They also come with comprehensive installation features and informative user documentation for simple deployment.
- Accelerates application development. With Visual Studio 2008 Professional Edition, it’s simple for developers to build parallel programs. Abouelhoda says: “Visual Studio supports the Microsoft Message Passing Interface, which makes it easy to compile and run programs, reducing development time by 50 per cent.”
- Increases user recruitment and retention. Features included with Windows HPC Server 2008 reduce the complexity of managing the system. Scientists can concentrate on analysing their biological data, increasing their satisfaction and boosting recruitment and retention rates.
- Encourages research. The collaborative effort between the CMIC, Nile University, and Microsoft Egypt has demonstrated that with Windows HPC Server 2008, scientists can spend less time on computing and more time on research. Abouelhoda hopes that this will encourage other institutions to use the Windows tools to support their research projects.
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