DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results
Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped wi...
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| Veröffentlicht in: | BMC systems biology 2010-08, Vol.4 (1), p.109-109, Article 109 |
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| container_title | BMC systems biology |
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| creator | Gizzatkulov, Nail M Goryanin, Igor I Metelkin, Eugeny A Mogilevskaya, Ekaterina A Peskov, Kirill V Demin, Oleg V |
| description | Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting.
We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle.
DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru. |
| doi_str_mv | 10.1186/1752-0509-4-109 |
| format | Article |
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We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle.
DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.</description><identifier>ISSN: 1752-0509</identifier><identifier>EISSN: 1752-0509</identifier><identifier>DOI: 10.1186/1752-0509-4-109</identifier><identifier>PMID: 20698988</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Computer Graphics ; Computer programs ; Computer simulation ; Computer-generated environments ; Kinetics ; Models, Biological ; Molecular dynamics ; Science ; Software</subject><ispartof>BMC systems biology, 2010-08, Vol.4 (1), p.109-109, Article 109</ispartof><rights>COPYRIGHT 2010 BioMed Central Ltd.</rights><rights>Copyright ©2010 Gizzatkulov et al; licensee BioMed Central Ltd. 2010 Gizzatkulov et al; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c493t-f6af3acc96d2569b4a63d69e6c92dee6b6b5115f7bdcb66c0b2c07e4fcdc75d3</citedby><cites>FETCH-LOGICAL-c493t-f6af3acc96d2569b4a63d69e6c92dee6b6b5115f7bdcb66c0b2c07e4fcdc75d3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925829/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2925829/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20698988$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gizzatkulov, Nail M</creatorcontrib><creatorcontrib>Goryanin, Igor I</creatorcontrib><creatorcontrib>Metelkin, Eugeny A</creatorcontrib><creatorcontrib>Mogilevskaya, Ekaterina A</creatorcontrib><creatorcontrib>Peskov, Kirill V</creatorcontrib><creatorcontrib>Demin, Oleg V</creatorcontrib><title>DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results</title><title>BMC systems biology</title><addtitle>BMC Syst Biol</addtitle><description>Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting.
We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle.
DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.</description><subject>Computer Graphics</subject><subject>Computer programs</subject><subject>Computer simulation</subject><subject>Computer-generated environments</subject><subject>Kinetics</subject><subject>Models, Biological</subject><subject>Molecular dynamics</subject><subject>Science</subject><subject>Software</subject><issn>1752-0509</issn><issn>1752-0509</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNptks1r3DAQxU1pab567q0Ieig9OJFlS7Z6CKRp0gYCgSZ3IUsjrxrZ2ljybpO_vjKbLlkIOkh685sHM7ws-1jg46Jo2ElRU5Jjinle5QXmb7L9rfL2xXsvOwjhD8a0JKR-n-0RzHjDm2Y_e_jx_da7FaCbZbT91H9DEgVv4lqOgJZS3csOkPEjurcDRKtQ7zU4O3RovbBqgaRzfh2Qfhxkn6orGybp7JOM1g_IGxSSqdv8RgiTi-Eoe2ekC_Dh-T7M7i4v7s5_5dc3P6_Oz65zVfEy5oZJU0qlONOEMt5WkpWacWCKEw3AWtbSoqCmbrVqGVO4JQrXUBmlVU11eZidbmyXU9uDVjDEUTqxHG0vx0fhpRW7lcEuROdXgnBCG8KTwZdng9E_TBCi6G1Q4JwcwE9B1FXDa4pxk8jPG7KTDoQdjE-GaqbFGSkpIQ0rWaKOX6HS0ZA25wcwNuk7DV93GhIT4W_s5BSCuLr9vcuebFg1-hBGMNtBCyzmpIg5C2LOgqiSNo_36eV-tvz_aJT_AH9xu0k</recordid><startdate>20100810</startdate><enddate>20100810</enddate><creator>Gizzatkulov, Nail M</creator><creator>Goryanin, Igor I</creator><creator>Metelkin, Eugeny A</creator><creator>Mogilevskaya, Ekaterina A</creator><creator>Peskov, Kirill V</creator><creator>Demin, Oleg V</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20100810</creationdate><title>DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results</title><author>Gizzatkulov, Nail M ; Goryanin, Igor I ; Metelkin, Eugeny A ; Mogilevskaya, Ekaterina A ; Peskov, Kirill V ; Demin, Oleg V</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c493t-f6af3acc96d2569b4a63d69e6c92dee6b6b5115f7bdcb66c0b2c07e4fcdc75d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Computer Graphics</topic><topic>Computer programs</topic><topic>Computer simulation</topic><topic>Computer-generated environments</topic><topic>Kinetics</topic><topic>Models, Biological</topic><topic>Molecular dynamics</topic><topic>Science</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gizzatkulov, Nail M</creatorcontrib><creatorcontrib>Goryanin, Igor I</creatorcontrib><creatorcontrib>Metelkin, Eugeny A</creatorcontrib><creatorcontrib>Mogilevskaya, Ekaterina A</creatorcontrib><creatorcontrib>Peskov, Kirill V</creatorcontrib><creatorcontrib>Demin, Oleg V</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC systems biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gizzatkulov, Nail M</au><au>Goryanin, Igor I</au><au>Metelkin, Eugeny A</au><au>Mogilevskaya, Ekaterina A</au><au>Peskov, Kirill V</au><au>Demin, Oleg V</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results</atitle><jtitle>BMC systems biology</jtitle><addtitle>BMC Syst Biol</addtitle><date>2010-08-10</date><risdate>2010</risdate><volume>4</volume><issue>1</issue><spage>109</spage><epage>109</epage><pages>109-109</pages><artnum>109</artnum><issn>1752-0509</issn><eissn>1752-0509</eissn><abstract>Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting.
We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle.
DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>20698988</pmid><doi>10.1186/1752-0509-4-109</doi><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; BioMedCentral; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; PubMed Central Open Access; Springer Nature OA Free Journals |
| subjects | Computer Graphics Computer programs Computer simulation Computer-generated environments Kinetics Models, Biological Molecular dynamics Science Software |
| title | DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results |
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