J Integr Bioinform - An advanced environment for hybrid modeling of biological systems based on modelica.

Tópicos

{ model(3480) simul(1196) paramet(876) }
{ result(1111) use(1088) new(759) }
{ process(1125) use(805) approach(778) }
{ gene(2352) biolog(1181) express(1162) }
{ implement(1333) system(1263) develop(1122) }
{ model(2656) set(1616) predict(1553) }
{ take(945) account(800) differ(722) }
{ concept(1167) ontolog(924) domain(897) }
{ data(3963) clinic(1234) research(1004) }
{ compound(1573) activ(1297) structur(1058) }
{ drug(1928) target(777) effect(648) }
{ decis(3086) make(1611) patient(1517) }
{ method(2212) result(1239) propos(1039) }
{ can(774) often(719) complex(702) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ method(1219) similar(1157) match(930) }
{ network(2748) neural(1063) input(814) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ learn(2355) train(1041) set(1003) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ general(901) number(790) one(736) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ monitor(1329) mobil(1314) devic(1160) }
{ first(2504) two(1366) second(1323) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ estim(2440) model(1874) function(577) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ chang(1828) time(1643) increas(1301) }
{ clinic(1479) use(1117) guidelin(835) }
{ algorithm(1844) comput(1787) effici(935) }
{ extract(1171) text(1153) clinic(932) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ search(2224) databas(1162) retriev(909) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ time(1939) patient(1703) rate(768) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ survey(1388) particip(1329) question(1065) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Resumo Limpo

biolog system often complex appropri formal need model behavior hybrid petri net consist timediscret petri net element well continu one proven ideal task therefor new petri net librari implement base objectori model languag modelica allow model discret stochast continu petri net element differenti algebra discret equat appropri modelicatool perform hybrid simul discret event solut continu differenti equat special sublibrari contain socal wrapper specif reaction simplifi model process modelicamodel can connect simulinkmodel paramet optim sensit analysi stochast simul matlab present paper illustr implement petri net compon model usag within model process coupl modelicatool dymola matlabsimulink applic demonstr model metabol chines hamster ovari cell

Resumos Similares

Comput Math Methods Med - Analytical solutions for the mathematical model describing the formation of liver zones via Adomian's method. ( 0,871938575155005 )
Comput Biol Chem - An efficient nonlinear finite-difference approach in the computational modeling of the dynamics of a nonlinear diffusion-reaction equation in microbial ecology. ( 0,845816375392414 )
Comput Math Methods Med - Modeling innate immune response to early Mycobacterium infection. ( 0,845068563910438 )
Brief. Bioinformatics - Choosing appropriate models for protein-protein interaction networks: a comparison study. ( 0,838058025139931 )
Comput Math Methods Med - Dynamics analysis and simulation of a modified HIV infection model with a saturated infection rate. ( 0,836635746241702 )
Comput. Biol. Med. - Modelling and simulating reaction-diffusion systems using coloured Petri nets. ( 0,813631953750446 )
Comput Math Methods Med - Computational modeling of microabscess formation. ( 0,806999962945694 )
Comput Methods Programs Biomed - Functionality of the baroreceptor nerves in heart rate regulation. ( 0,799214976137742 )
Comput Math Methods Med - Modeling schistosomiasis and HIV/AIDS codynamics. ( 0,785690447666193 )
IEEE Trans Vis Comput Graph - Paraglide: Interactive Parameter Space Partitioning for Computer Simulations. ( 0,783900614025445 )
Comput Math Methods Med - Solutions of a linearized mathematical model for capillary formation in tumor angiogenesis: an initial data perturbation approximation. ( 0,783643291704712 )
Comput Math Methods Med - Global hopf bifurcation on two-delays leslie-gower predator-prey system with a prey refuge. ( 0,779694708639512 )
Comput. Biol. Med. - Network and Nakamura tridiagonal computational simulation of electrically-conducting biopolymer micro-morphic transport phenomena. ( 0,77765680300703 )
Med Biol Eng Comput - CSF dynamic analysis of a predictive pulsatility-based infusion test for normal pressure hydrocephalus. ( 0,777031113189491 )
Comput. Biol. Med. - Modeling multiple experiments using regularized optimization: A case study on bacterial glucose utilization dynamics. ( 0,777023268017009 )
Neural Comput - Cross-talk induces bifurcations in nonlinear models of synaptic plasticity. ( 0,775774354750871 )
Comput Math Methods Med - ModeLang: a new approach for experts-friendly viral infections modeling. ( 0,775289755256577 )
Comput. Biol. Med. - On a reusable and multilevel methodology for modeling and simulation of pharmacokinetic-physiological systems: a preliminary study. ( 0,774316309152618 )
Comput Biol Chem - A stochastic evolution model for residue Insertion-Deletion Independent from Substitution. ( 0,770776829975798 )
Neural Comput - Effect of phase response curve skewness on synchronization of electrically coupled neuronal oscillators. ( 0,767576703547716 )
Comput Math Methods Med - Uncertainty quantification in simulations of epidemics using polynomial chaos. ( 0,767204397647016 )
Comput. Biol. Med. - ODE/PDE analysis of corneal curvature. ( 0,766999798865674 )
Comput. Biol. Med. - Semi-computational simulation of magneto-hemodynamic flow in a semi-porous channel using optimal homotopy and differential transform methods. ( 0,766999798865674 )
Neural Comput - Analytical integrate-and-fire neuron models with conductance-based dynamics and realistic postsynaptic potential time course for event-driven simulation strategies. ( 0,766230077752018 )
Comput Methods Programs Biomed - Development of a computer algorithm for feedback controlled electrical nerve fiber stimulation. ( 0,762138451062116 )
Comput. Biol. Med. - Examples of testing global identifiability of biological and biomedical models with the DAISY software. ( 0,759696681492496 )
Neural Comput - Computing confidence intervals for point process models. ( 0,757629232463073 )
Comput Math Methods Med - Numerical solutions for a model of tissue invasion and migration of tumour cells. ( 0,75653184039531 )
Wiley Interdiscip Rev Syst Biol Med - Influenza A virus infection kinetics: quantitative data and models. ( 0,748035427796811 )
Comput Methods Programs Biomed - Reprint of Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin. ( 0,745273261386949 )
Wiley Interdiscip Rev Syst Biol Med - A conceptual framework for computational models of Achilles tendon homeostasis. ( 0,743807523328339 )
Comput Methods Programs Biomed - Design of a framework for modeling, integration and simulation of physiological models. ( 0,739604853900842 )
Brief. Bioinformatics - Investigating biocomplexity through the agent-based paradigm. ( 0,732585763132524 )
J Clin Monit Comput - The standard strong ion difference, standard total titratable base, and their relationship to the Boston compensation rules and the Van Slyke equation for extracellular fluid. ( 0,731240987091227 )
Comput. Biol. Med. - Numerical investigation into blood clotting at the bone-dental implant interface in the presence of an electrical stimulus. ( 0,726760693699295 )
Comput Math Methods Med - Complexity analysis and parameter estimation of dynamic metabolic systems. ( 0,726299508325855 )
J. Comput. Biol. - Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible? ( 0,721671674532503 )
Comput. Biol. Med. - Mathematical modeling of brain glioma growth using modified reaction-diffusion equation on brain MR images. ( 0,720615707018279 )
Comput Math Methods Med - Numerical stability of partitioned approach in fluid-structure interaction for a deformable thin-walled vessel. ( 0,717750654404425 )
J Integr Bioinform - From binary to multivalued to continuous models: the lac operon as a case study. ( 0,717423851566063 )
Comput. Biol. Med. - epiModel: a system to build automatically systems of differential equations of compartmental type-epidemiological models. ( 0,716424885402837 )
Med Biol Eng Comput - A fluid-structure interaction model of the aortic valve with coaptation and compliant aortic root. ( 0,713894308097854 )
Neural Comput - Active data collection for efficient estimation and comparison of nonlinear neural models. ( 0,71154940722351 )
Comput Methods Programs Biomed - A Java simulator of Rescorla and Wagner's prediction error model and configural cue extensions. ( 0,708209663531615 )
Comput Methods Programs Biomed - An efficient passive planar micromixer with ellipse-like micropillars for continuous mixing of human blood. ( 0,707415636247279 )
IEEE Trans Image Process - Efficiency of semi-implicit schemes for anisotropic diffusion in the hypercube. ( 0,707290864989113 )
Comput Methods Programs Biomed - Solving delay differential equations in S-ADAPT by method of steps. ( 0,707282759595428 )
Comput Math Methods Med - A theoretical model for the transmission dynamics of the Buruli ulcer with saturated treatment. ( 0,706521465860967 )
Comput. Biol. Med. - A compartment model of alveolar-capillary oxygen diffusion with ventilation-perfusion gradient and dynamics of air transport through the respiratory tract. ( 0,704002599323331 )
Comput Methods Programs Biomed - A therapy parameter-based model for predicting blood glucose concentrations in patients with type 1 diabetes. ( 0,701752019385253 )
J Chem Inf Model - Full and partial agonism of ionotropic glutamate receptors indicated by molecular dynamics simulations. ( 0,698810481252132 )
Comput Biol Chem - Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. ( 0,69675053246823 )
Comput. Biol. Med. - Phase lagging model of brain response to external stimuli-modeling of single action potential. ( 0,695182328513265 )
Comput Math Methods Med - Towards patient-specific modeling of coronary hemodynamics in healthy and diseased state. ( 0,694957222337469 )
Lifetime Data Anal - Bayesian dynamic regression models for interval censored survival data with application to children dental health. ( 0,694212084040337 )
Comput Math Methods Med - Noninvasive monitoring of hepatic damage from hepatitis C virus infection. ( 0,689141225585139 )
Comput Methods Programs Biomed - The most precise computations using Euler's method in standard floating-point arithmetic applied to modelling of biological systems. ( 0,688474895385829 )
Comput Math Methods Med - Dynamics of Mycobacterium and bovine tuberculosis in a human-buffalo population. ( 0,687539873202346 )
Comput. Biol. Med. - Computing the stability of steady-state solutions of mathematical models of the electrical activity in the heart. ( 0,683320603062982 )
IEEE Trans Image Process - Additive log-logistic model for networked video quality assessment. ( 0,683224481653927 )
J. Comput. Biol. - An overview of population genetic data simulation. ( 0,678050874052239 )
Lifetime Data Anal - An extended cure model and model selection. ( 0,674880642545597 )
Comput Methods Programs Biomed - Modelling the Double Peak Phenomenon in pharmacokinetics. ( 0,674555248402575 )
Neural Comput - MOSAIC for multiple-reward environments. ( 0,672048258354635 )
Int J Neural Syst - A generalized Leaky Integrate-and-Fire neuron model with fast implementation method. ( 0,671269454903135 )
IEEE Trans Pattern Anal Mach Intell - Bi-polynomial Modeling of Low-frequency Reflectances. ( 0,671210524081773 )
Comput Math Methods Med - A mathematical model of cancer treatment by radiotherapy. ( 0,667013840130181 )
Med Biol Eng Comput - Power type strain energy function model and prediction of the anisotropic mechanical properties of skin using uniaxial extension data. ( 0,666234262236594 )
Comput. Biol. Med. - An implicit evolution scheme for active contours and surfaces based on IIR filtering. ( 0,665893666064583 )
Neural Comput - How sample paths of leaky integrate-and-fire models are influenced by the presence of a firing threshold. ( 0,665657286063381 )
Comput Methods Programs Biomed - Computation of restoration of ligand response in the random kinetics of a prostate cancer cell signaling pathway. ( 0,663636354733518 )
IEEE J Biomed Health Inform - Prediction of Hemodynamic Response to Epinephrine via Model-Based System Identification. ( 0,6633517607039 )
IEEE Trans Image Process - Fast cartoon + texture image filters. ( 0,66069998714567 )
Comput Methods Programs Biomed - Innovative model to simulate exhalation phase in human respiratory system. ( 0,660555264367762 )
Comput. Biol. Med. - Model-based assessment of baroreflex and cardiopulmonary couplings during graded head-up tilt. ( 0,659703162738109 )
J. Comput. Biol. - Compound Poisson approximation and testing for gene clusters with multigene families. ( 0,659353797722241 )
J Chem Inf Model - Fitting of dihedral terms in classical force fields as an analytic linear least-squares problem. ( 0,658539072092534 )
IEEE Trans Image Process - Reinitialization-free level set evolution via reaction diffusion. ( 0,656431127741791 )
Med Biol Eng Comput - An improved curvilinear gradient method for parameter optimization in complex biological models. ( 0,656059863884506 )
Wiley Interdiscip Rev Syst Biol Med - Modeling the control of planar cell polarity. ( 0,651109521864827 )
Comput Methods Programs Biomed - Simulating and analysing infectious disease data in a heterogeneous population with migration. ( 0,64929767962453 )
Neural Comput - Diffusive information accumulation by minimal recurrent neural models of decision making. ( 0,648868778116506 )
Comput Biol Chem - Stochastic synchronization of interacting pathways in testosterone model. ( 0,645199153580784 )
Comput Math Methods Med - Spongiosa primary development: a biochemical hypothesis by Turing patterns formations. ( 0,64468895961702 )
Comput Math Methods Med - Theorems and application of local activity of CNN with five state variables and one port. ( 0,644117522244411 )
J. Comput. Biol. - An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes. ( 0,642638597609027 )
Neural Comput - A calcium-based simple model of multiple spike interactions in spike-timing-dependent plasticity. ( 0,641965265153818 )
J Clin Monit Comput - Simulating physiological interactions in a hybrid system of mathematical models. ( 0,641864203496157 )
Comput Math Methods Med - Optimal control of HIV/AIDS in the workplace in the presence of careless individuals. ( 0,640478897757746 )
Comput Methods Programs Biomed - Comparison of interval and Monte Carlo simulation for the prediction of postprandial glucose under uncertainty in type 1 diabetes mellitus. ( 0,639284688578627 )
Comput Math Methods Med - A numerical method of reduced complexity for simulating vascular hemodynamics using coupled 0D lumped and 1D wave propagation models. ( 0,638609515492356 )
Comput Math Methods Med - Global stability analysis of SEIR model with holling type II incidence function. ( 0,638220022340161 )
Neural Comput - Synchronization of stochastic competitive neural networks with different timescales and reaction-diffusion terms. ( 0,636610794004327 )
Comput Methods Programs Biomed - System approach to modeling of liver glucose metabolism with physiologically interpreted model parameters outgoing from [18F]FDG concentrations measured by PET. ( 0,635909429906847 )
Comput Methods Programs Biomed - Graphical simulation environments for modelling and simulation of integrative physiology. ( 0,63555323555509 )
Neural Comput - Integration of reinforcement learning and optimal decision-making theories of the basal ganglia. ( 0,634563016771083 )
AMIA Annu Symp Proc - Simulation Analysis Platform (SnAP): a tool for evaluation of public health surveillance and disease control strategies. ( 0,634455801527861 )
Artif Intell Med - Multi-agent model of hepatitis C virus infection. ( 0,632263689758271 )
Comput. Biol. Med. - Density-based Monte Carlo filter and its applications in nonlinear stochastic differential equation models. ( 0,630033229736961 )
Med Biol Eng Comput - Experimental validation of quasi-one-dimensional and two-dimensional steady glottal flow models. ( 0,629832241926292 )