-
Notifications
You must be signed in to change notification settings - Fork 0
/
dp1.bib
260 lines (232 loc) · 8.66 KB
/
dp1.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
@misc{flexc++,
author = {F.B. Brokken and J.P. van Oosten and R. Berendsen (until 0.5.3)},
title = {{Flexc++ (Version 2.01.00), User Guide [online]. University of Groningen, The Netherlands}},
year = {[cit. 2014-05-21]},
note = {Available at $<$\url{http://flexcpp.sourceforge.net/flexc++.html}$>$},
}
@misc{bisonc++,
author = {F.B. Brokken},
title = {{Bisonc++ (Version 4.09.01), User Guide [online]. Center for Information Technology, University of Groningen, The Netherlands}},
year = {[cit. 2014-05-21]},
note = {Available at $<$\url{http://bisoncpp.sourceforge.net/bisonc++.html}$>$},
}
@MISC{mpt,
author = {M. Kvasnica and P. Grieder and M. Baoti\'{c}},
title = {{Multi-Parametric Toolbox (MPT) [online]}},
note = {Available at $<$\url{http://control.ee.ethz.ch/~mpt/}$>$},
year = {[cit. 2014-05-17]},
}
@MISC{step,
author = {E.W. Weisstein},
title = {{Heaviside Step Function, From MathWorld--A Wolfram Web Resource [online]}},
note = {Available at $<$\url{http://mathworld.wolfram.com/HeavisideStepFunction.html}$>$},
year = {[cit. 2014-05-17]},
}
@misc{rovergene-site,
author = {G. Batt and C. Belta},
title = {{RoVerGeNe: A tool for the Robust Verification of Gene Networks, Tool Page [online]}},
note = {Available at $<$\url{http://iasi.bu.edu/~batt/rovergene/rovergene.htm}$>$},
year = {[cit. 2014-05-17]},
}
@misc(sybila-biodivine,
author = {J. Barnat and L. Brim and S. Dra\v zan and J. Fabrikov\'a and D. \v{S}afr\'anek},
title = {{BioDiVinE 1.0, Tool Page [online]. Faculty of informatics Masaryk university, Brno, Czech republic}},
key = {SYBILA-BIODIVINE},
year = {[cit. 2014-05-17]},
note = {Available at $<$\url{http://sybila.fi.muni.cz/tools/biodivine/v1/index}$>$}
)
@MastersThesis{Jaros-thesis,
AUTHOR = "M. Jaro\v{s}",
TITLE = "P\v{r}evod formul\'i LTL na automaty [online]",
YEAR = "2004 [cit. 2014-05-19]",
TYPE = "Master thesis",
SCHOOL = "{Faculty of informatics Masaryk university, Brno, Czech republic}",
note = "Available at $<$\url{http://is.muni.cz/th/4017/fi_m/}$>$",
}
@incollection{rovergene,
year= {2007},
ISBN= {978-3-540-71208-4},
booktitle= {Tools and Algorithms for the Construction and Analysis of Systems (TACAS'07)},
volume= {4424},
series= {Lecture Notes in Computer Science},
title= {Model Checking Liveness Properties of Genetic Regulatory Networks},
publisher= {Springer},
author= {G. Batt and C. Belta and R. Weiss},
pages= {323-338},
}
@book{MPI,
author = {M. Snir and S.W. Otto and D.W. Walker and J. Dongarra and S. Huss-Lederman},
title = {MPI: The Complete Reference},
year = {1995},
isbn = {0262691841},
publisher = {MIT Press},
}
@article{Swat:2004,
author = {Swat, M. and Kel, A. and Herzel, H.},
title = {{Bifurcation Analysis of the Regulatory Modules of the Mammalian G1/S Transition}},
journal = {Bioinformatics},
volume = {20},
number = {10},
year = {2004},
pages = {1506--1511},
publisher= {Oxford University Press},
}
@book(Clarke:MC,
author = {E.M. Clarke Jr. and O. Grumberg and D.A. Peled},
title = {Model Checking},
year = {1999},
isbn = {0-262-03270-8},
publisher = {MIT Press},
)
@inbook(Clarke:MC:Process,
author = {E.M. Clarke Jr. and O. Grumberg and D.A. Peled},
title = {Model Checking},
chapter = {1.3. The Process of Model Checking},
pages = {4-4},
year = {1999},
isbn = {0-262-03270-8},
publisher = {MIT Press},
)
@inbook(Clarke:MC:LTL,
author = {E.M. Clarke Jr. and O. Grumberg and D.A. Peled},
title = {Model Checking},
chapter = {3. Temporal Logics},
pages = {27-33},
year = {1999},
isbn = {0-262-03270-8},
publisher = {MIT Press},
)
@inbook(Clarke:MC:BA,
author = {E.M. Clarke Jr. and O. Grumberg and D.A. Peled},
title = {Model Checking},
chapter = {9. Model Checking and Automata Theory},
pages = {121-140},
year = {1999},
isbn = {0-262-03270-8},
publisher = {MIT Press},
)
@inbook(Clarke:MC:LTLtoBA,
author = {E.M. Clarke Jr. and O. Grumberg and D.A. Peled},
title = {Model Checking},
chapter = {9.4. Translating LTL into Automata},
pages = {132-138},
year = {1999},
isbn = {0-262-03270-8},
publisher = {MIT Press},
)
@Book{Keener:1998:MP,
author = "J.P. Keener and J. Sneyd",
title = "Mathematical Physiology",
volume = "8",
publisher = "Springer-Verlag",
year = "1998",
ISBN = "0-387-98381-3",
series = "Interdisciplinary Applied Mathematics"
}
@inBook{Keener:1998:MP:MassAction,
author = "J.P. Keener and J. Sneyd",
title = "Mathematical Physiology",
chapter = "1.1. The Law of Mass Action",
pages = "3-4",
volume = "8",
publisher = "Springer-Verlag",
year = "1998",
ISBN = "0-387-98381-3",
series = "Interdisciplinary Applied Mathematics"
}
@inBook{Keener:1998:MP:Enzymes,
author = "J.P. Keener and J. Sneyd",
title = "Mathematical Physiology",
chapter = "1.2. Enzyme kinetics",
pages = "5-16",
volume = "8",
publisher = "Springer-Verlag",
year = "1998",
ISBN = "0-387-98381-3",
series = "Interdisciplinary Applied Mathematics"
}
@inBook{Keener:1998:MP:MathBackground,
author = "J.P. Keener and J. Sneyd",
title = "Mathematical Physiology",
chapter = "1.4. Appendix: Math Background",
pages = "24-30",
volume = "8",
publisher = "Springer-Verlag",
year = "1998",
ISBN = "0-387-98381-3",
series = "Interdisciplinary Applied Mathematics"
}
@inBook{ODE,
author = "G. Teschl",
title = "Ordinary Differential Equations and Dynamical Systems",
chapter = "1. Introduction",
pages = "3-31",
volume = "140",
publisher = "American Mathematical Society",
year = "2012",
ISBN = "0-8218-8328-3",
series = "Graduate Studies in Mathematics"
}
@article(CURVES,
title = {Optimum polygonal approximation of digitized curves},
author = {J.C. Perez and E. Vidal},
year = {1994},
journal = {Pattern Recognition Letters},
pages = {743-750. Elsevier Science Inc.},
volume = {15},
number = {8},
)
@InProceedings{divine,
author = "J. Barnat and L. Brim and I. \v{C}ern\'{a} and P. \v{S}ime\v{c}ek",
title = "{D}i{V}in{E} -- {T}he {D}istributed {V}erification {E}nvironment",
booktitle = "Proceedings of 4th International Workshop on Parallel and Distributed Methods in verifiCation",
pages = "89--94",
year = "2005",
}
@article(TCBB-2010,
title = {On Parameter Synthesis by Parallel Model Checking},
author = {J. Barnat and L. Brim and A. Krej\v c\'i and D. \v{S}afr\'anek and A. Streck and M. Vejn\'ar and T. Vejpustek},
year = {2012},
journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)},
pages = {693-705. IEEE Computer Society Press},
volume = {9},
number = {3},
)
@article(BIODIVINE,
title = {BioDiVinE: A Framework for Parallel Analysis of Biological Models},
author = {J. Barnat and L. Brim and I. \v{C}ern\'a and S. Dra\v zan and J. Fabrikov\'a and J. L\'an\'ik and H. Ma and D. \v{S}afr\'anek},
year = {2009},
journal = {In Proceedings of 2nd International Workshop on Computational Models for Cell Processes (COMPMOD 2009)},
pages = {31-45. EPTCS 6},
)
@article(HIBI-2010,
title = {Parameter Scanning by Parallel Model Checking with Applications in Systems Biology},
author = {J. Barnat and L. Brim and D. \v{S}afr\'anek and M. Vejn\'ar},
year = {2010},
journal = {In Proceedings of High performance computational systems Biology (HiBi 2010)},
pages = {95-104. IEEE Computer Society Press},
)
@article(HIBI-2009,
title = {Computational Analysis of Large-Scale Multi-Affine ODE Models},
author = {J. Barnat and L. Brim and I. \v{C}ern\'a and S. Dra\v zan and J. Fabrikov\'a and D. \v{S}afr\'anek},
year = {2009},
journal = {In Proceedings of High performance computational systems Biology (HiBi 2009)},
pages = {81-99. IEEE Computer Society Press},
)
@article{RATS,
author = "J. Barnat and L. Brim and I. \v{C}ern\'{a} and S. Dra\v{z}an and J. Fabrikov\'{a} and D. \v{S}afr\'{a}nek",
title = "{On algorithmic analysis of transcriptional regulation by LTL model checking}",
journal = "Theoretical Computer Science",
volume = "410",
number = "33-34",
pages = "3128--3148",
year = "2009",
}
@article(CAV-2011,
title = {From Cardiac Cells to Genetic Regulatory Networks},
author = {R. Grosu and G. Batt and F.H. Fenton and J. Glimm and C. Le Guernic and S.A. Smolka and E. Bartocci},
year = {2011},
journal = {In Proceedings of CAV'11, the 23rd International Conference on Computer Aided Verification, Lecture Notes in Computer Science},
pages = {396-411. Springer},
volume = {6806},
)