-
1
-
-
60349092483
-
An introduction to biomodel engineering, illustrated for signal transduction pathways
-
Springer, Berlin
-
Gilbert D., Breitling R., Heiner M., Donaldson R. An introduction to biomodel engineering, illustrated for signal transduction pathways. WMC 2008; 5391 of LNCS 2009, 13-28. Springer, Berlin.
-
(2009)
WMC 2008; 5391 of LNCS
, pp. 13-28
-
-
Gilbert, D.1
Breitling, R.2
Heiner, M.3
Donaldson, R.4
-
2
-
-
77950325438
-
Biomodel engineering-from structure to behavior (position paper)
-
Springer, Berlin
-
Breitling R., Donaldson R.A., Gilbert D.R., Heiner M. Biomodel engineering-from structure to behavior (position paper). Transactions on computational systems biology XII: special issue on modeling methodologies 2010, vol. 5945:1-12. Springer, Berlin.
-
(2010)
Transactions on computational systems biology XII: special issue on modeling methodologies
, vol.5945
, pp. 1-12
-
-
Breitling, R.1
Donaldson, R.A.2
Gilbert, D.R.3
Heiner, M.4
-
3
-
-
0004068620
-
Kommunikation mit Automaten
-
(in German) [PhD thesis]. Technische Hochschule Darmstadt
-
Petri CA. Kommunikation mit Automaten (in German) [PhD thesis]. Technische Hochschule Darmstadt; 1962.
-
(1962)
-
-
Petri, C.A.1
-
4
-
-
77951956151
-
Snoopy-a unifying Petri net framework to investigate biomolecular networks
-
Rohr C., Marwan W., Heiner M. Snoopy-a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 2010, 26:974-975.
-
(2010)
Bioinformatics
, vol.26
, pp. 974-975
-
-
Rohr, C.1
Marwan, W.2
Heiner, M.3
-
5
-
-
84862502916
-
Snoopy-a unifying Petri net tool. In: Proc. Petri nets 2012; 7347 of LNCS
-
Heiner M., Herajy M., Liu F., Rohr C., Schwarick M. Snoopy-a unifying Petri net tool. In: Proc. Petri nets 2012; 7347 of LNCS. Berlin: Springer 2012, 2012:398-407.
-
(2012)
Berlin: Springer
, vol.2012
, pp. 398-407
-
-
Heiner, M.1
Herajy, M.2
Liu, F.3
Rohr, C.4
Schwarick, M.5
-
7
-
-
78649890897
-
Charlie 2.0-a multithreaded Petri net analyser [Diploma thesis]
-
BTU Cottbus, Dep. of CS
-
Franzke A. Charlie 2.0-a multithreaded Petri net analyser [Diploma thesis]. BTU Cottbus, Dep. of CS; 2009.
-
(2009)
-
-
Franzke, A.1
-
8
-
-
80055034906
-
MARCIE-Model checking And Reachability analysis done effiCIEntly
-
IEEE CS Press, p. 91-100
-
Schwarick M., Heiner M., Rohr C. MARCIE-Model checking And Reachability analysis done effiCIEntly. Proc. QEST, Aachen, Germany 2011, IEEE CS Press, p. 91-100.
-
(2011)
Proc. QEST, Aachen, Germany
-
-
Schwarick, M.1
Heiner, M.2
Rohr, C.3
-
9
-
-
84879619513
-
MARCIE-Model checking And Reachability analysis done effiCIEntly
-
Springer, Berlin, p. 389-99
-
Heiner M., Rohr C., Schwarick M. MARCIE-Model checking And Reachability analysis done effiCIEntly. Proc. PETRI NETS 2013; 7927 of LNCS 2013, Springer, Berlin, p. 389-99.
-
(2013)
Proc. PETRI NETS 2013; 7927 of LNCS
-
-
Heiner, M.1
Rohr, C.2
Schwarick, M.3
-
10
-
-
85053942753
-
MARCIE manual-an analysis tool for extended stochastic Petri nets
-
Tech. Rep. 03-14. BTU Cottbus-Senftenberg, Dep. of CS
-
Schwarick M, Rohr C, Heiner M. MARCIE manual-an analysis tool for extended stochastic Petri nets. Tech. Rep. 03-14. BTU Cottbus-Senftenberg, Dep. of CS; 2014.
-
(2014)
-
-
Schwarick, M.1
Rohr, C.2
Heiner, M.3
-
11
-
-
57049106843
-
A model checking approach to the parameter estimation of biochemical pathways
-
Springer, Berlin, p. 269-87
-
Donaldson R., Gilbert D. A model checking approach to the parameter estimation of biochemical pathways. Proc. CMSB 2008; 5307 of LNCS/LNBI 2008, Springer, Berlin, p. 269-87.
-
(2008)
Proc. CMSB 2008; 5307 of LNCS/LNBI
-
-
Donaldson, R.1
Gilbert, D.2
-
13
-
-
0033593306
-
Molecular bases for circadian clocks
-
Dunlap J.C. Molecular bases for circadian clocks. Cell 1999, 96:271-290.
-
(1999)
Cell
, vol.96
, pp. 271-290
-
-
Dunlap, J.C.1
-
14
-
-
0037197850
-
Mechanisms of noise resistance in genetic oscillators
-
Vilar J.M.G., Kueh H.Y., Barkai N., Leibler S. Mechanisms of noise resistance in genetic oscillators. PNAS 2002, 99:5988-5992.
-
(2002)
PNAS
, vol.99
, pp. 5988-5992
-
-
Vilar, J.M.G.1
Kueh, H.Y.2
Barkai, N.3
Leibler, S.4
-
15
-
-
0024645936
-
Petri nets: properties, analysis and applications
-
Murata T. Petri nets: properties, analysis and applications. Proc IEEE 1989, 77:541-580.
-
(1989)
Proc IEEE
, vol.77
, pp. 541-580
-
-
Murata, T.1
-
16
-
-
84888435568
-
Half a century after Carl Adam Petri's PhD thesis: a perspective on the field
-
Silva M. Half a century after Carl Adam Petri's PhD thesis: a perspective on the field. Ann Rev Control 2013;37:191-219.
-
(2013)
Ann Rev Control
, vol.37
, pp. 191-219
-
-
Silva, M.1
-
19
-
-
0000491652
-
A Petri net application of metabolic processes
-
Hofestädt R. A Petri net application of metabolic processes. J Syst Anal Model Simul 1994, 16:113-122.
-
(1994)
J Syst Anal Model Simul
, vol.16
, pp. 113-122
-
-
Hofestädt, R.1
-
21
-
-
78649903919
-
Petri nets for modelling metabolic pathways: a survey
-
Baldan P., Cocco N., Marin A., Simeoni M. Petri nets for modelling metabolic pathways: a survey. Nat Comput 2010, 9:955-989.
-
(2010)
Nat Comput
, vol.9
, pp. 955-989
-
-
Baldan, P.1
Cocco, N.2
Marin, A.3
Simeoni, M.4
-
22
-
-
78649900844
-
-
Jones and Bartlett Learning Sudbury, Massachusetts, Chapter 3. p. 61-97
-
Heiner M., Donaldson R., Gilbert D. Petri nets for systems biology 2010, Jones and Bartlett Learning Sudbury, Massachusetts, Chapter 3. p. 61-97.
-
(2010)
Petri nets for systems biology
-
-
Heiner, M.1
Donaldson, R.2
Gilbert, D.3
-
25
-
-
16344386047
-
Exact liveness conditions of a Petri net class (in German) [PhD thesis]
-
GMD Report 82, Bonn
-
Lautenbach K. Exact liveness conditions of a Petri net class (in German) [PhD thesis]. GMD Report 82, Bonn; 1973.
-
(1973)
-
-
Lautenbach, K.1
-
26
-
-
85014438978
-
Understanding network behaviour by structured representations of transition invariants-a Petri net perspective on systems and synthetic biology
-
Springer, Berlin, p. 367-89
-
Heiner M. Understanding network behaviour by structured representations of transition invariants-a Petri net perspective on systems and synthetic biology. Natural computing series 2009, Springer, Berlin, p. 367-89.
-
(2009)
Natural computing series
-
-
Heiner, M.1
-
27
-
-
16344380104
-
Determining elementary modes of functioning in biochemical reaction networks at steady state
-
Schuster S., Hilgetag C., Schuster R. Determining elementary modes of functioning in biochemical reaction networks at steady state. Proc. 2nd gauss symposium 1993, 101-114.
-
(1993)
Proc. 2nd gauss symposium
, pp. 101-114
-
-
Schuster, S.1
Hilgetag, C.2
Schuster, R.3
-
28
-
-
33751361595
-
-
Cambridge University Press, Cambridge
-
Palsson B.O. Systems biology 2006, Cambridge University Press, Cambridge.
-
(2006)
Systems biology
-
-
Palsson, B.O.1
-
30
-
-
84882763283
-
Metabolic pathways analysis: a linear algebraic approach
-
Ch. 8, Academic Press, London, R. Robeva, T.L. Hodge (Eds.)
-
Hodge T.L. Metabolic pathways analysis: a linear algebraic approach. Mathematical concepts and methods in modern biology: using modern discrete models 2013, 239-266. Ch. 8, Academic Press, London. R. Robeva, T.L. Hodge (Eds.).
-
(2013)
Mathematical concepts and methods in modern biology: using modern discrete models
, pp. 239-266
-
-
Hodge, T.L.1
-
31
-
-
27544485048
-
Petri net based model validation in systems biology
-
Springer, Berlin, p. 216-37
-
Heiner M., Koch I. Petri net based model validation in systems biology. Proc. ICATPN 2004; 3099 of LNCS 2004, Springer, Berlin, p. 216-37.
-
(2004)
Proc. ICATPN 2004; 3099 of LNCS
-
-
Heiner, M.1
Koch, I.2
-
32
-
-
77649280061
-
Structural analysis to determine the core of hypoxia response network
-
e8600
-
Heiner M., Sriram K. Structural analysis to determine the core of hypoxia response network. PLoS ONE 2010, 5. e8600.
-
(2010)
PLoS ONE
, vol.5
-
-
Heiner, M.1
Sriram, K.2
-
33
-
-
0003962322
-
-
MIT Press, Cambridge, MA
-
Clarke E.M., Grumberg O., Peled D.A. Model checking 2000, MIT Press, Cambridge, MA.
-
(2000)
Model checking
-
-
Clarke, E.M.1
Grumberg, O.2
Peled, D.A.3
-
34
-
-
49149133038
-
The temporal semantics of concurrent programs
-
Pnueli A. The temporal semantics of concurrent programs. Theor Comput Sci 1981, 13:45-60.
-
(1981)
Theor Comput Sci
, vol.13
, pp. 45-60
-
-
Pnueli, A.1
-
35
-
-
49549083532
-
Temporal logic patterns for querying dynamic models of cellular interaction networks
-
Monteiro P.T., Ropers D., Mateescu R., Freitas A.T., De Jong H. Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics 2008, 24:i227-i233.
-
(2008)
Bioinformatics
, vol.24
, pp. i227-i233
-
-
Monteiro, P.T.1
Ropers, D.2
Mateescu, R.3
Freitas, A.T.4
De Jong, H.5
-
36
-
-
47849126239
-
A case study in model-driven synthetic biology
-
Springer, Berlin, W.C.C. IFIP (Ed.)
-
Gilbert D., Heiner M., Rosser S., Fulton R., Gu X., Trybio M. A case study in model-driven synthetic biology. 2008, 2nd IFIP conference on biologically inspired collaborative computing (BICC 2008); 268 of IFIP (Boston) 2008, 163-175. Springer, Berlin. W.C.C. IFIP (Ed.).
-
(2008)
2008, 2nd IFIP conference on biologically inspired collaborative computing (BICC 2008); 268 of IFIP (Boston)
, pp. 163-175
-
-
Gilbert, D.1
Heiner, M.2
Rosser, S.3
Fulton, R.4
Gu, X.5
Trybio, M.6
-
38
-
-
45749112203
-
-
Springer, Berlin, p. 215-64
-
Heiner M., Gilbert D., Donaldson R. Petri nets for systems and synthetic biology; 5016 of LNCS 2008, Springer, Berlin, p. 215-64.
-
(2008)
Petri nets for systems and synthetic biology; 5016 of LNCS
-
-
Heiner, M.1
Gilbert, D.2
Donaldson, R.3
-
40
-
-
85053950221
-
A Petri net based framework for biomodel engineering
-
Springer, Berlin
-
Blätke M.A., Rohr C., Heiner M., Marwan W. A Petri net based framework for biomodel engineering. Modeling and simulation in science, engineering and technology. Birkhäuser mathematics 2014, Springer, Berlin.
-
(2014)
Modeling and simulation in science, engineering and technology. Birkhäuser mathematics
-
-
Blätke, M.A.1
Rohr, C.2
Heiner, M.3
Marwan, W.4
-
41
-
-
79958020937
-
Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks
-
Marwan W., Wagler A., Weismantel R. Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks. Nat Comput 2011, 10:63954.
-
(2011)
Nat Comput
, vol.10
, pp. 63954
-
-
Marwan, W.1
Wagler, A.2
Weismantel, R.3
-
42
-
-
0037078982
-
Control, exploitation and tolerance of intracellular noise
-
Rao C.V., Wolf D.M., Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 2002, 420:2317.
-
(2002)
Nature
, vol.420
, pp. 2317
-
-
Rao, C.V.1
Wolf, D.M.2
Arkin, A.P.3
-
43
-
-
0020175425
-
Performance analysis using stochastic Petri nets
-
Molloy M.K. Performance analysis using stochastic Petri nets. IEEE Trans Comput 1982, 100:913-917.
-
(1982)
IEEE Trans Comput
, vol.100
, pp. 913-917
-
-
Molloy, M.K.1
-
44
-
-
0003652825
-
-
John Wiley and Sons, London
-
Ajmone Marsan M., Balbo G., Conte G., Donatelli S., Franceschinis G. Modelling with generalized stochastic Petri nets. Wiley series in parallel computing. 2nd ed 1995, John Wiley and Sons, London.
-
(1995)
Modelling with generalized stochastic Petri nets. Wiley series in parallel computing. 2nd ed
-
-
Ajmone Marsan, M.1
Balbo, G.2
Conte, G.3
Donatelli, S.4
Franceschinis, G.5
-
46
-
-
0032499741
-
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
-
Goss P.J.E., Peccoud J. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc Natl Acad Sci 1998, 95:6750-6755.
-
(1998)
Proc Natl Acad Sci
, vol.95
, pp. 6750-6755
-
-
Goss, P.J.E.1
Peccoud, J.2
-
47
-
-
0035812883
-
Stochastic kinetic analysis of the Escherichia coli stress circuit using 32-targeted antisense
-
Srivastava R., Peterson M.S., Bentley W.E. Stochastic kinetic analysis of the Escherichia coli stress circuit using 32-targeted antisense. Biotechnol Bioeng 2001, 75:120-129.
-
(2001)
Biotechnol Bioeng
, vol.75
, pp. 120-129
-
-
Srivastava, R.1
Peterson, M.S.2
Bentley, W.E.3
-
48
-
-
23744463967
-
Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri net modeling and simulation
-
Marwan W., Sujatha A., Starostzik C. Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri net modeling and simulation. J Theor Biol 2005, 236:349-365.
-
(2005)
J Theor Biol
, vol.236
, pp. 349-365
-
-
Marwan, W.1
Sujatha, A.2
Starostzik, C.3
-
50
-
-
70450204413
-
Extended stochastic Petri nets for model-based design of wetlab experiments
-
Springer, Berlin
-
Heiner M., Lehrack S., Gilbert D., Marwan W. Extended stochastic Petri nets for model-based design of wetlab experiments. Transactions on computational systems biology XI; 5750 of LNCS/LNBI 2009, 138-163. Springer, Berlin.
-
(2009)
Transactions on computational systems biology XI; 5750 of LNCS/LNBI
, pp. 138-163
-
-
Heiner, M.1
Lehrack, S.2
Gilbert, D.3
Marwan, W.4
-
51
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977, 81:2340-2361.
-
(1977)
J Phys Chem
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
52
-
-
77958098477
-
Efficient formulations for exact stochastic simulation of chemical systems
-
Mauch S., Stalzer M. Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Trans Comput Biol Bioinform 2011, 8:27-35.
-
(2011)
IEEE/ACM Trans Comput Biol Bioinform
, vol.8
, pp. 27-35
-
-
Mauch, S.1
Stalzer, M.2
-
54
-
-
79955730053
-
IDD-based model validation of biochemical networks
-
Schwarick M., Tovchigrechko A. IDD-based model validation of biochemical networks. Theor Comput Sci 2011, 412:2884-2908.
-
(2011)
Theor Comput Sci
, vol.412
, pp. 2884-2908
-
-
Schwarick, M.1
Tovchigrechko, A.2
-
55
-
-
78649859232
-
A comparative study of stochastic analysis techniques
-
ACM Digital Library, p. 96-106
-
Heiner M., Rohr C., Schwarick M., Streif S. A comparative study of stochastic analysis techniques. Proc. CMSB 2010 2010, ACM Digital Library, p. 96-106.
-
(2010)
Proc. CMSB 2010
-
-
Heiner, M.1
Rohr, C.2
Schwarick, M.3
Streif, S.4
-
56
-
-
84988402010
-
Symbolic on-the-fly analysis of stochastic Petri nets [PhD thesis]
-
BTU Cottbus, Dep. of CS
-
Schwarick M. Symbolic on-the-fly analysis of stochastic Petri nets [PhD thesis]. BTU Cottbus, Dep. of CS; 2014.
-
(2014)
-
-
Schwarick, M.1
-
57
-
-
84883175676
-
Simulative model checking of steady-state and time-unbounded temporal operators
-
Rohr C. Simulative model checking of steady-state and time-unbounded temporal operators. ToPNoC VIII, LNCS 8100 2013, 142-158.
-
(2013)
ToPNoC VIII, LNCS 8100
, pp. 142-158
-
-
Rohr, C.1
-
58
-
-
84855891503
-
-
Ch. 21, Springer, New York, p. 409-37
-
Marwan W., Rohr C., Heiner M. Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks; Volume 804 of methods in molecular biology 2012, Ch. 21, Springer, New York, p. 409-37.
-
(2012)
Petri nets in Snoopy: a unifying framework for the graphical display, computational modelling, and simulation of bacterial regulatory networks; Volume 804 of methods in molecular biology
-
-
Marwan, W.1
Rohr, C.2
Heiner, M.3
-
60
-
-
84891444515
-
-
Springer-Verlag, Berlin
-
David R., Alla H. Discrete, continuous, and hybrid Petri nets 2005, Springer-Verlag, Berlin.
-
(2005)
Discrete, continuous, and hybrid Petri nets
-
-
David, R.1
Alla, H.2
-
61
-
-
33746061326
-
Petri nets to differential equations-an integrative approach for biochemical network analysis
-
Springer, Berlin
-
Gilbert D., From HeinerM. Petri nets to differential equations-an integrative approach for biochemical network analysis. Proc. ICATPN, 4024 of LNCS 2006, 181-200. Springer, Berlin.
-
(2006)
Proc. ICATPN, 4024 of LNCS
, pp. 181-200
-
-
Gilbert, D.1
From, H.2
-
62
-
-
49949085999
-
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
-
Breitling R., Gilbert D., Heiner M., Orton R. A structured approach for the engineering of biochemical network models, illustrated for signalling pathways. Brief Bioinform 2008, 9:404-421.
-
(2008)
Brief Bioinform
, vol.9
, pp. 404-421
-
-
Breitling, R.1
Gilbert, D.2
Heiner, M.3
Orton, R.4
-
63
-
-
84883156507
-
Computational steering of multi-scale biochemical networks [PhD thesis]
-
BTU Cottbus, Dep. of CS
-
Herajy M. Computational steering of multi-scale biochemical networks [PhD thesis]. BTU Cottbus, Dep. of CS; 2013.
-
(2013)
-
-
Herajy, M.1
-
64
-
-
33745217791
-
SUNDIALS: suite of nonlinear and differential/algebraic equation solvers
-
Hindmarsh A.C., Brown P.N., Grant K.E., Lee S.L., Serban R., Shumaker D.E., et al. SUNDIALS: suite of nonlinear and differential/algebraic equation solvers. ACM Trans Math Software 2005, 31:363-396.
-
(2005)
ACM Trans Math Software
, vol.31
, pp. 363-396
-
-
Hindmarsh, A.C.1
Brown, P.N.2
Grant, K.E.3
Lee, S.L.4
Serban, R.5
Shumaker, D.E.6
-
65
-
-
38049142307
-
Machine learning biochemical networks from temporal logic properties
-
Calzone L., Chabrier-Rivier N., Fages F., Soliman S. Machine learning biochemical networks from temporal logic properties. Trans Comput Syst Biol VI 2006, 4220:68-94.
-
(2006)
Trans Comput Syst Biol VI
, vol.4220
, pp. 68-94
-
-
Calzone, L.1
Chabrier-Rivier, N.2
Fages, F.3
Soliman, S.4
-
66
-
-
78650971919
-
A unique transformation from ordinary differential equations to reaction networks
-
e14284
-
Soliman S., Heiner M. A unique transformation from ordinary differential equations to reaction networks. PLoS ONE 2010, 5. e14284.
-
(2010)
PLoS ONE
, vol.5
-
-
Soliman, S.1
Heiner, M.2
-
68
-
-
0036881072
-
Petri nets and integrality relaxations: a view of continuous Petri net models
-
Silva M., Recalde L. Petri nets and integrality relaxations: a view of continuous Petri net models. IEEE Trans Syst Man Cybern Part C Appl Rev 2002, 32:314-327.
-
(2002)
IEEE Trans Syst Man Cybern Part C Appl Rev
, vol.32
, pp. 314-327
-
-
Silva, M.1
Recalde, L.2
-
70
-
-
79958037323
-
Boundedness analysis for open chemical reaction networks with mass-action kinetics
-
Angeli D. Boundedness analysis for open chemical reaction networks with mass-action kinetics. Nat Comput 2011, 10:751-774.
-
(2011)
Nat Comput
, vol.10
, pp. 751-774
-
-
Angeli, D.1
-
71
-
-
77949398351
-
Structural sources of robustness in biochemical reaction networks
-
Shinar G., Feinberg M. Structural sources of robustness in biochemical reaction networks. Science 2010, 327:1389-1391.
-
(2010)
Science
, vol.327
, pp. 1389-1391
-
-
Shinar, G.1
Feinberg, M.2
-
72
-
-
77649279538
-
-
Springer, London
-
Nagasaki M., Saito A., Doi A., Matsuno H., Miyano S. Foundations of systems biology using cell illustrator and pathway databases, vol. 13. Series: computational biology 2009, Springer, London.
-
(2009)
Foundations of systems biology using cell illustrator and pathway databases, vol. 13. Series: computational biology
-
-
Nagasaki, M.1
Saito, A.2
Doi, A.3
Matsuno, H.4
Miyano, S.5
-
73
-
-
84865545231
-
Hybrid representation and simulation of stiff biochemical networks
-
Herajy M., Heiner M. Hybrid representation and simulation of stiff biochemical networks. Nonlinear Anal Hybrid Syst 2012, 6:942-959.
-
(2012)
Nonlinear Anal Hybrid Syst
, vol.6
, pp. 942-959
-
-
Herajy, M.1
Heiner, M.2
-
74
-
-
84904115349
-
A steering server for collaborative simulation of quantitative Petri nets
-
Springer, Berlin
-
Herajy M., Heiner M. A steering server for collaborative simulation of quantitative Petri nets. PETRI NETS 2014; 8489 of LNCS 2014, 374-384. Springer, Berlin.
-
(2014)
PETRI NETS 2014; 8489 of LNCS
, pp. 374-384
-
-
Herajy, M.1
Heiner, M.2
-
75
-
-
84893684114
-
Petri net-based collaborative simulation and steering of biochemical reaction networks
-
Herajy M., Heiner M. Petri net-based collaborative simulation and steering of biochemical reaction networks. Fund Inform 2014, 129:49-67.
-
(2014)
Fund Inform
, vol.129
, pp. 49-67
-
-
Herajy, M.1
Heiner, M.2
-
76
-
-
84893695566
-
Snoopy computational steering framework User manual version 1.0
-
Tech. Rep. 02-13 BTU Cottbus, Dep. of CS
-
Herajy M, Heiner M. Snoopy computational steering framework User manual version 1.0. Tech. Rep. 02-13 BTU Cottbus, Dep. of CS; 2013.
-
(2013)
-
-
Herajy, M.1
Heiner, M.2
-
79
-
-
0000678601
-
System modelling with high-level Petri nets
-
Genrich H.J., Lautenbach K. System modelling with high-level Petri nets. Theor Comput Sci 1981, 13:109-135.
-
(1981)
Theor Comput Sci
, vol.13
, pp. 109-135
-
-
Genrich, H.J.1
Lautenbach, K.2
-
81
-
-
84896689115
-
Executable Petri net models for the analysis of metabolic pathways
-
Genrich H., Küffner R., Voss K. Executable Petri net models for the analysis of metabolic pathways. Int J Software Tools Technol Tran 2001, 3(4):394-404.
-
(2001)
Int J Software Tools Technol Tran
, vol.3
, Issue.4
, pp. 394-404
-
-
Genrich, H.1
Küffner, R.2
Voss, K.3
-
82
-
-
0042828946
-
Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets
-
Bahi-Jaber N., Pontier D. Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets. Math Biosci 2003, 185:1-13.
-
(2003)
Math Biosci
, vol.185
, pp. 1-13
-
-
Bahi-Jaber, N.1
Pontier, D.2
-
83
-
-
84862491494
-
The manual for colored Petri nets in snoopy-QPNC/SPNC/CPNC/GHPNC
-
Tech. Rep. 02-12 BTU Cottbus, Dep. of CS
-
Liu F, Heiner M, Rohr C. The manual for colored Petri nets in snoopy-QPNC/SPNC/CPNC/GHPNC. Tech. Rep. 02-12 BTU Cottbus, Dep. of CS; 2012.
-
(2012)
-
-
Liu, F.1
Heiner, M.2
Rohr, C.3
-
84
-
-
84862493851
-
Colored Petri nets for systems biology [PhD thesis]
-
BTU Cottbus, Dep. of CS
-
Liu F. Colored Petri nets for systems biology [PhD thesis]. BTU Cottbus, Dep. of CS; 2012.
-
(2012)
-
-
Liu, F.1
-
85
-
-
84879642133
-
Colouring space-a coloured framework for spatial modelling in systems biology
-
Springer, Berlin
-
Gilbert D., Heiner M., Liu F., Saunders N. Colouring space-a coloured framework for spatial modelling in systems biology. PETRI NETS 2013; 7927 of LNCS 2013, 230-249. Springer, Berlin.
-
(2013)
PETRI NETS 2013; 7927 of LNCS
, pp. 230-249
-
-
Gilbert, D.1
Heiner, M.2
Liu, F.3
Saunders, N.4
-
86
-
-
84885999784
-
Modelling and analysis of phase variation in bacterial colony growth
-
Springer, Berlin
-
Parvu O., Gilbert D., Heiner M., Liu F., Saunders N. Modelling and analysis of phase variation in bacterial colony growth. Proc. CMSB 2013; 8130 of LNCS/LNBI 2013, 78-91. Springer, Berlin.
-
(2013)
Proc. CMSB 2013; 8130 of LNCS/LNBI
, pp. 78-91
-
-
Parvu, O.1
Gilbert, D.2
Heiner, M.3
Liu, F.4
Saunders, N.5
-
87
-
-
84907090291
-
Modelling and simulating reaction-diffusion systems using colored Petri nets
-
Liu F., Blätke M.A., Heiner M., Yang M. Modelling and simulating reaction-diffusion systems using colored Petri nets. Computers in Biology and Medicine October 2014, 53:297308.
-
(2014)
Computers in Biology and Medicine
, vol.53
, pp. 297308
-
-
Liu, F.1
Blätke, M.A.2
Heiner, M.3
Yang, M.4
-
88
-
-
84883056967
-
Multiscale modelling and analysis of planar cell polarity in the Drosophila wing
-
Gao Q., Gilbert D., Heiner M., Liu F., Maccagnola D., Tree D. Multiscale modelling and analysis of planar cell polarity in the Drosophila wing. IEEE ACM Trans Comput Biol Bioinform 2013, 10:337-351.
-
(2013)
IEEE ACM Trans Comput Biol Bioinform
, vol.10
, pp. 337-351
-
-
Gao, Q.1
Gilbert, D.2
Heiner, M.3
Liu, F.4
Maccagnola, D.5
Tree, D.6
-
89
-
-
85032552909
-
Gecode: an open constraint solving library
-
Gecode. Gecode: an open constraint solving library; 2013. Available from: . http://www.gecode.org.
-
(2013)
-
-
-
90
-
-
85053976600
-
-
Proc. CPN workshop. University of Aarhus, In, p. 15-34
-
Heiner M., Koch I., Voss K. Analysis and simulation of steady states in metabolic pathways with Petri nets 2001, Proc. CPN workshop. University of Aarhus, In, p. 15-34.
-
(2001)
Analysis and simulation of steady states in metabolic pathways with Petri nets
-
-
Heiner, M.1
Koch, I.2
Voss, K.3
-
91
-
-
0345096675
-
Steady state analysis of metabolic pathways using Petri nets
-
Voss K., Heiner M., Koch I. Steady state analysis of metabolic pathways using Petri nets. In Silico Biol 2003, 3:367-387.
-
(2003)
In Silico Biol
, vol.3
, pp. 367-387
-
-
Voss, K.1
Heiner, M.2
Koch, I.3
-
93
-
-
84890562030
-
Modeling membrane systems using colored stochastic Petri nets
-
Liu F., Heiner M. Modeling membrane systems using colored stochastic Petri nets. Nat Computing 2013, 12:617-629.
-
(2013)
Nat Computing
, vol.12
, pp. 617-629
-
-
Liu, F.1
Heiner, M.2
-
94
-
-
84879629991
-
Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets
-
Liu F., Heiner M. Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets. IET Syst Biol 2013, 7:106-113.
-
(2013)
IET Syst Biol
, vol.7
, pp. 106-113
-
-
Liu, F.1
Heiner, M.2
-
95
-
-
84940263170
-
Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development
-
Liu F., Heiner M., Yang M. Modeling and analyzing biological systems using colored hierarchical Petri nets, illustrated by C. elegans vulval development. WSPC J Biol Syst 2014, 22:463-493.
-
(2014)
WSPC J Biol Syst
, vol.22
, pp. 463-493
-
-
Liu, F.1
Heiner, M.2
Yang, M.3
-
96
-
-
84907937847
-
Coloured hybrid Petri nets for systems biology
-
In: Proc. BioPPN 2014; 1159 of CEUR workshop proceedings. CEUR-WS.org
-
Herajy M, Liu F, Rohr C. Coloured hybrid Petri nets for systems biology. In: Proc. BioPPN 2014; 1159 of CEUR workshop proceedings. CEUR-WS.org; 2014. p. 60-76.
-
(2014)
, pp. 60-76
-
-
Herajy, M.1
Liu, F.2
Rohr, C.3
-
97
-
-
84867863368
-
Predicting phenotype from genotype through automatically composed Petri nets
-
Springer, Berlin
-
Blätke M.A., Heiner M., Marwan W. Predicting phenotype from genotype through automatically composed Petri nets. Proc. CMSB 2012; 7605 of LNCS/LNBI 2012, 87-106. Springer, Berlin.
-
(2012)
Proc. CMSB 2012; 7605 of LNCS/LNBI
, pp. 87-106
-
-
Blätke, M.A.1
Heiner, M.2
Marwan, W.3
-
98
-
-
84877748605
-
JAK/STAT signalling-an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology
-
Blätke M.A., Dittrich A., Rohr C., Heiner M., Schaper F., Marwan W. JAK/STAT signalling-an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology. Mol Biosyst 2013, 9:1290-1307.
-
(2013)
Mol Biosyst
, vol.9
, pp. 1290-1307
-
-
Blätke, M.A.1
Dittrich, A.2
Rohr, C.3
Heiner, M.4
Schaper, F.5
Marwan, W.6
-
99
-
-
84878161581
-
Biomodel engineering for multiscale systems biology progress
-
Heiner M., Gilbert D. Biomodel engineering for multiscale systems biology progress. Biophys Mol Biol 2013, 111:119-128.
-
(2013)
Biophys Mol Biol
, vol.111
, pp. 119-128
-
-
Heiner, M.1
Gilbert, D.2
-
100
-
-
77958488960
-
Engineering a novel self-powering electrochemical biosensor
-
Gu X., Trybilo M., Ramsay S., Jensen M., Fulton R., Rosser S., et al. Engineering a novel self-powering electrochemical biosensor. Syst Synth Biol 2010, 4(3):203-214.
-
(2010)
Syst Synth Biol
, vol.4
, Issue.3
, pp. 203-214
-
-
Gu, X.1
Trybilo, M.2
Ramsay, S.3
Jensen, M.4
Fulton, R.5
Rosser, S.6
|