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Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data,especially when the data sets are large and complex. Bioinformatics uses biology,chemistry,physics,computer science,computer programming,information engineering,mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
Computational biology refers to the use of data analysis,mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science,biology,and big data,the field also has foundations in applied mathematics,chemistry,and genetics. It differs from biological computing,a subfield of computer science and engineering which uses bioengineering to build computers.
Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems,using a holistic approach to biological research.
The School of Informatics is an academic unit of the University of Edinburgh,in Scotland,responsible for research,teaching,outreach and commercialisation in informatics. It was created in 1998 from the former department of artificial intelligence,the Centre for Cognitive Science and the department of computer science,along with the Artificial Intelligence Applications Institute (AIAI) and the Human Communication Research Centre.
Computational science,also known as scientific computing,technical computing or scientific computation (SC),is a division of science that uses advanced computing capabilities to understand and solve complex physical problems. This includes
Modelling biological systems is a significant task of systems biology and mathematical biology. Computational systems biology aims to develop and use efficient algorithms,data structures,visualization and communication tools with the goal of computer modelling of biological systems. It involves the use of computer simulations of biological systems,including cellular subsystems,to both analyze and visualize the complex connections of these cellular processes.
Metabolic network modelling,also known as metabolic network reconstruction or metabolic pathway analysis,allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular,these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes,and analyzes them within the perspective of the entire network. In simplified terms,a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield,resource distribution,network robustness,and gene essentiality. This knowledge can then be applied to create novel biotechnology.
The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of e-laboratories and have been used in domains as diverse as systems biology,social science,music,astronomy,multimedia and chemistry.
Fluxomics describes the various approaches that seek to determine the rates of metabolic reactions within a biological entity. While metabolomics can provide instantaneous information on the metabolites in a biological sample,metabolism is a dynamic process. The significance of fluxomics is that metabolic fluxes determine the cellular phenotype. It has the added advantage of being based on the metabolome which has fewer components than the genome or proteome.
Gajendra Pal Singh Raghava is an Indian bio-informatician and head of computational biology at the Indraprastha Institute of Information Technology.
Biology data visualization is a branch of bioinformatics concerned with the application of computer graphics,scientific visualization,and information visualization to different areas of the life sciences. This includes visualization of sequences,genomes,alignments,phylogenies,macromolecular structures,systems biology,microscopy,and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple,standalone programs to complex,integrated systems.
Natural computing,also called natural computation,is a terminology introduced to encompass three classes of methods:1) those that take inspiration from nature for the development of novel problem-solving techniques;2) those that are based on the use of computers to synthesize natural phenomena;and 3) those that employ natural materials to compute. The main fields of research that compose these three branches are artificial neural networks,evolutionary algorithms,swarm intelligence,artificial immune systems,fractal geometry,artificial life,DNA computing,and quantum computing,among others.
Complex and Adaptive Systems Laboratory (CASL) is an interdisciplinary research institute in University College Dublin. It is formed around four research clusters. The institute houses research groups from a number of Schools within UCD,notably computer science. It is located in the Belfield Business Park at the northern end of the main UCD campus. The institute is involved in all aspects of research into complex systems from atomistic models,through to societal modelling.
Virtual Cell (VCell) is an open-source software platform for modeling and simulation of living organisms,primarily cells. It has been designed to be a tool for a wide range of scientists,from experimental cell biologists to theoretical biophysicists.
LibSBML is an open-source software library that provides an application programming interface (API) for the SBML format. The libSBML library can be embedded in a software application or used in a web servlet as part of the application or servlet's implementation of support for reading,writing,and manipulating SBML documents and data streams. The core of libSBML is written in ISO standard C++;the library provides API for many programming languages via interfaces generated with the help of SWIG.
Nicolas Le Novère is a British and French biologist. His research focuses on modeling signaling pathways and developing tools to share mathematical models.
The Centre for Genomic Regulation is a biomedical and genomics research centre based on Barcelona. Most of its facilities and laboratories are located in the Barcelona Biomedical Research Park,in front of Somorrostro beach.
Genome Informatics is a scientific study of information processing in genomes.
Herbert M. Sauro works in the field of metabolic control analysis and systems biology.
References
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- ↑ Sisu, Diana. "Inaugural Lecture by Professor Igor Goryanin". www.inf.ed.ac.uk. Retrieved 26 April 2021.
- ↑ "Igor Goryanin". OIST Groups. 31 May 2012. Retrieved 26 April 2021.
- ↑ Goryanin, I.; Hodgman, T. C.; Selkov, E. (1 September 1999). "Mathematical simulation and analysis of cellular metabolism and regulation". Bioinformatics. 15 (9): 749–758. doi: 10.1093/bioinformatics/15.9.749 . PMID 10498775.
- ↑ Holden, Constance (30 August 2002). "Alliance Launched to Model E. coli". Science. 297 (5586): 1459–1460. doi:10.1126/science.297.5586.1459a. PMID 12202792. S2CID 82478432.
- ↑ Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B. J.; Bray, D.; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles, E. D.; Ginkel, M.; Gor, V.; Goryanin, I. I.; Hedley, W. J.; Hodgman, T. C.; Hofmeyr, J.-H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novère, N.; Loew, L. M.; Lucio, D.; Mendes, P.; Minch, E.; Mjolsness, E. D.; Nakayama, Y.; Nelson, M. R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B. E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J. (1 March 2003). "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–531. doi: 10.1093/bioinformatics/btg015 . PMID 12611808.
- ↑ "About". Systems Biology Graphical Notation. Retrieved 26 April 2021.
