Hardware simulation of yeast glycolytic oscillations
This paper presents the design of a hardware simulator of biological processes described by chemical-kinetic equations. The simulator is made up of processing elements that use floating point arithmetic and a pipeline architecture. Due to its compact design, several processing elements can be synthe...
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| creator | Duarte, J. E. Velasco-Medina, J. Moreno, P. A. |
| description | This paper presents the design of a hardware simulator of biological processes described by chemical-kinetic equations. The simulator is made up of processing elements that use floating point arithmetic and a pipeline architecture. Due to its compact design, several processing elements can be synthesized into a single FPGA to create a multiprocessing architecture allowing the parallel simulation of several biological processes that are executed simultaneously, and thus, reducing the execution time with respect to software simulations. The design was verified simulating two models: yeast glycolytic oscillations and induced glycolytic oscillations between two cells. The obtained results prove that the architecture designed is suitable to simulate complex biological processes in lower times than in software simulations. |
| doi_str_mv | 10.1109/BIBMW.2011.6112404 |
| format | Conference Proceeding |
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E.</creatorcontrib><creatorcontrib>Velasco-Medina, J.</creatorcontrib><creatorcontrib>Moreno, P. A.</creatorcontrib><title>Hardware simulation of yeast glycolytic oscillations</title><title>2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)</title><addtitle>BIBMW</addtitle><description>This paper presents the design of a hardware simulator of biological processes described by chemical-kinetic equations. The simulator is made up of processing elements that use floating point arithmetic and a pipeline architecture. Due to its compact design, several processing elements can be synthesized into a single FPGA to create a multiprocessing architecture allowing the parallel simulation of several biological processes that are executed simultaneously, and thus, reducing the execution time with respect to software simulations. The design was verified simulating two models: yeast glycolytic oscillations and induced glycolytic oscillations between two cells. The obtained results prove that the architecture designed is suitable to simulate complex biological processes in lower times than in software simulations.</description><subject>Biological processes</subject><subject>Biological system modeling</subject><subject>chemical-kinetic simulations</subject><subject>Computer architecture</subject><subject>Field programmable gate arrays</subject><subject>FPGA</subject><subject>glycolytic oscillations</subject><subject>Hardware</subject><subject>hardware simulation</subject><subject>Mathematical model</subject><subject>Oscillators</subject><isbn>9781457716126</isbn><isbn>1457716127</isbn><isbn>1457716135</isbn><isbn>9781457716133</isbn><fulltext>true</fulltext><rsrctype>conference_proceeding</rsrctype><creationdate>2011</creationdate><recordtype>conference_proceeding</recordtype><sourceid>6IE</sourceid><sourceid>RIE</sourceid><recordid>eNo1j0FLw0AUhFdEUGv-gF7yBxL3bXbf7h5tUVuo9FLxWF6yL7KSGslGJP_eSut3GYaBYUaIW5AlgPT389X85a1UEqBEAKWlPhPXoI21gFCZc5F56_69wkuRpfQhDyA66-FK6CUN4YcGzlPcf3c0xv4z79t8Ykpj_t5NTd9NY2zyPjWxO-bpRly01CXOTjoTr0-P28WyWG-eV4uHdRHBmrEg743C9oBrPLQSHQSu0UvDQZP9W0USmVpQ1tVkbdABgwZGqhkaW83E3bE3MvPua4h7Gqbd6Wj1C5PcR4A</recordid><startdate>201111</startdate><enddate>201111</enddate><creator>Duarte, J. E.</creator><creator>Velasco-Medina, J.</creator><creator>Moreno, P. A.</creator><general>IEEE</general><scope>6IE</scope><scope>6IL</scope><scope>CBEJK</scope><scope>RIE</scope><scope>RIL</scope></search><sort><creationdate>201111</creationdate><title>Hardware simulation of yeast glycolytic oscillations</title><author>Duarte, J. E. ; Velasco-Medina, J. ; Moreno, P. A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-i175t-a99526ffff8c91f0681deb6905ed4a74577a06eaf1278ba77d4d6d41e6abe1c73</frbrgroupid><rsrctype>conference_proceedings</rsrctype><prefilter>conference_proceedings</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Biological processes</topic><topic>Biological system modeling</topic><topic>chemical-kinetic simulations</topic><topic>Computer architecture</topic><topic>Field programmable gate arrays</topic><topic>FPGA</topic><topic>glycolytic oscillations</topic><topic>Hardware</topic><topic>hardware simulation</topic><topic>Mathematical model</topic><topic>Oscillators</topic><toplevel>online_resources</toplevel><creatorcontrib>Duarte, J. E.</creatorcontrib><creatorcontrib>Velasco-Medina, J.</creatorcontrib><creatorcontrib>Moreno, P. A.</creatorcontrib><collection>IEEE Electronic Library (IEL) Conference Proceedings</collection><collection>IEEE Proceedings Order Plan All Online (POP All Online) 1998-present by volume</collection><collection>IEEE Xplore All Conference Proceedings</collection><collection>IEEE Xplore</collection><collection>IEEE Proceedings Order Plans (POP All) 1998-Present</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Duarte, J. E.</au><au>Velasco-Medina, J.</au><au>Moreno, P. A.</au><format>book</format><genre>proceeding</genre><ristype>CONF</ristype><atitle>Hardware simulation of yeast glycolytic oscillations</atitle><btitle>2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)</btitle><stitle>BIBMW</stitle><date>2011-11</date><risdate>2011</risdate><spage>396</spage><epage>399</epage><pages>396-399</pages><isbn>9781457716126</isbn><isbn>1457716127</isbn><eisbn>1457716135</eisbn><eisbn>9781457716133</eisbn><abstract>This paper presents the design of a hardware simulator of biological processes described by chemical-kinetic equations. The simulator is made up of processing elements that use floating point arithmetic and a pipeline architecture. Due to its compact design, several processing elements can be synthesized into a single FPGA to create a multiprocessing architecture allowing the parallel simulation of several biological processes that are executed simultaneously, and thus, reducing the execution time with respect to software simulations. The design was verified simulating two models: yeast glycolytic oscillations and induced glycolytic oscillations between two cells. The obtained results prove that the architecture designed is suitable to simulate complex biological processes in lower times than in software simulations.</abstract><pub>IEEE</pub><doi>10.1109/BIBMW.2011.6112404</doi><tpages>4</tpages></addata></record> |
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| source | IEEE Electronic Library (IEL) Conference Proceedings |
| subjects | Biological processes Biological system modeling chemical-kinetic simulations Computer architecture Field programmable gate arrays FPGA glycolytic oscillations Hardware hardware simulation Mathematical model Oscillators |
| title | Hardware simulation of yeast glycolytic oscillations |
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