The research portfolio of KAUST’s Computational Bioscience Research Center (CBRC) encompasses computational biology and bioinformatics with applications in life sciences
Through excellence in computational biosciences CBRC creates new ways in which life sciences perform their quest for improving the quality of life.
CBRC develops novel enabling bioinformatics methods and applies them in life science research. The activities of the Center are both in research and development of methods and algorithms for computational biology and bioinformatics, their implementation on high performance computing platforms, and, their application in systems biology, microbiology, biotechnology and related fields. The focus of the research is modeling the key processes in the living cell so as to be able to explore the way cells react to different challenges. Computational bioscience research at CBRC is therefore combined with CBRC’s internal and collaboratively conducted experimental work that helps refine and validate in silico-derived hypotheses potentially useful for various applications.
CBRC Research Focus
The focus of our research is modeling the key processes in the living cell so as to be able to explore the way cell reacts to different challenges, for example, being able to explore and simulate the effects of chemicals on different cellular processes. The solutions in this domain are generic and could find applications in single cell, as well as complex multi-cellular organisms.
From a perspective of computational science, development of computational methods and their application in biology are key areas for generating high impact results and discoveries. This is primarily driven by the recent developments in systems approaches to biological research using a variety of high throughput techniques (genomics, transcriptomics, proteomics and other 'omics' approaches) that provide large quantity of data but do not provide direct answers to important biological questions. The output of these activities has several distinctive characteristics such as:
- Size: the resulting experimental data is often enormous in size of the order of gigabytes to terabytes
- Complexity: available data points to a network of extremely complex interactions between entities encapsulated within data
- Dependency: available information is typically strongly context-dependent, further frustrating analysis of biologically relevant relationships.
Direct application of traditional computational methodologies is not able to adequately address the three challenges mentioned above due to their computational intractability. For that reason, a considerable part of the CBRC's activity is related to addressing this particular problem. These remedies are largely focused in two complementary approaches:
- Development and application of methods resulting in new algorithms that can address computational intractability by providing acceptable solutions.
- Development of new and modification of the existing algorithms in a way that makes it possible for efficient execution on HPC systems. This involves, among other, code optimization and parallelization that allows for properly harnessing the unique advantages offered by KAUST's leading edge HPC and other computer resources within an academic environment.
Thus, these features define the main research focus of the Center: Development of algorithms, methods, systems and platforms for efficient knowledge extraction from massive biological datasets based on the use of HPC systems. Particular biological applications of these are in specific domains of expertise of senior staff of CBRC.
The ability to analyze large and complex data sets facilitates the Center's research in a broad scope of biological problems. These include, for example, mapping and modeling of biological networks; genomics of regionally important plant, animal or even human pathogens; construction of in silico genetic and metabolic cellular models; modeling and metabolic engineering of heterotrophic and photosynthetic microbial cell factories for renewable chemicals and fuels.
Impact of Center's work within the Kingdom of Saudi Arabia
Activities in the Center are congruent with the wider goals of KAUST and its role in research, education and innovation in the Kingdom and the region. As a result, a considerable research effort is directed toward analysis of unique biological issues important to the Arabian Peninsula. Additional key objectives aimed at development of practical bioinformatics resources and skill development within the Kingdom of Saudi Arabia are:
- Support of the Kingdom's biotechnology, environmental protection and specific industrial applications
- Education and bioinformatics expertise development of Saudi students
- Providing regional leadership in bioinformatics, biotechnology and genomics-driven research
The Center will meet these objectives through:
- Cultivating interest in bioinformatics and genomics in young Saudi researchers and students by actively co-opting them in selected areas of ongoing research in the Center
- Collaboration and sharing resources with other Saudi universities, research institutes, etc.
- Industrial collaboration with leading Saudi companies that share specific common interests with the Center, resulting in synergistic approaches in addressing their needs.
Review of the Center's Activities
The main activities in the Center can be summarized as follows:
- Research and publications
- Education and training
- Technology, software, prototype, and patent development
- In-KAUST collaboration and research support/guidance/consulting
- Academic collaboration, both within and outside of the Kingdom
- Industrial collaboration, both within and outside of the Kingdom