Snoopy - A Tool to Design and Animate/Simulate Graph-based - - PowerPoint PPT Presentation
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Snoopy - A Tool to Design and Animate/Simulate Graph-based Formalisms Monika Heiner, Ronny Richter, Martin Schwarick Brandenburg University of Technology
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Brandenburg University of Technology Cottbus Computer Science Department http://www-dssz.informatik.tu-cottbus.de/software/snoopy.html
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ generic design facilitates the addition of new graph classes
◮ simultaneous use of several graph types in a homogeneous
◮ GUI adopts dynamically to graph type in active window
◮ implementation in C++ and wxWidgets framework ◮ supported for Windows, Linux, and Mac
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ graph constraints are considered ◮ hierarchy by subgraphs ◮ logical (fusion) nodes ◮ interaction between graphs
E B A|E A A A|E B E A B E k3 k2 k1 k3 k1, k2 MA1
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ forward and backward animation with different firing rules ◮ dedicated simulation using different algorithms ◮ various shapes and colours for net elements ◮ dynamic colouring of graph elements
◮ automated layout (graphviz)
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ generic XML file format ◮ digital signature for graphs by MD5-checksum ◮ conversion between contained graph classes ◮ export to external analysis tools ◮ import from convenient file formats
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ simple graph class ◮ one node and one edge type ◮ furthermore comment nodes ◮ constructable from
m5 m6 m7 m8 m9 m12 m13 m2 m3 m4 m11 m10 m1 r1 r2 r3 r4 r5 r6 r9 r7 r9 r8 r7 r10 r8 r11 r6 r10 r11 r1 r6 r2 r6 r2 r7 r8 r1 r7 r11 r9 r10 r8
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ contains places and transitions as well as
◮ animation of the token game ◮ interaction manager allows to construct
◮ export to a wide range of external analysis
◮ import of a restricted APNN file format
ready_to_send ready_to_produce buffer ready_to_consume ready_to_receive co_buffer produce send receive consume
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ stochastic Petri nets ◮ generalized stochastic Petri nets ◮ deterministic and stochastic Petri nets ◮ biochemically propensity functions
◮ multiple initial markings, parameter sets,
◮ Gillespie algorithm for simulation ◮ export to PRISM, TimeNet, and Dizzy
Prey Predator reproduction_of_prey consumption_of_prey predator_death 2 2
Prey Predator Prey Predator
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ corresponds to a set of ordinary
◮ visualizes the structure ◮ for a quantitative description of
◮ six stiff and six unstiff solvers
◮ multiple initial markings
◮ export to SBML
MKKK 90 MKKK_P 10 MKK 280 MKK_P 10 MKK_PP 10 MAPK 280 MAPK_P 10 MAPK_PP 10 a_1 a_2 b_1 b_2 b_3 b_4 c_1 c_2 c_3 c_4 Parameters 50 100 150 200 250 300 MAPK_P MAPK_PP MKKK MKKK_P
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ with additional arcs
◮ up to now time intervals or
◮ export to INA
◮ Petri net with modulo arc for
var sc sc sc acc inc reset 5 6 6
count1 count2 t1 t2 m 5
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ for risk management of dependable
◮ describes dependencies of component
◮ qualitative and quantitative analysis ◮ several dependability measures may be
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& & &
>=1
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ for documentation and
◮ describes patterns of
x1 x2 y2 y2 x2 y2 y1 y1 8 2 5 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
fork1 fork3 fork2 fork5 fork4 phil1 phil3 phil2 phil4 phil5
fork1 fork2 p1_eating p1_releasing p1_waiting p1_thinking p1_put_right p1_put_left p1_take_right p1_take_left
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
T54 F54 F64 T64 T63 F63 T65 F65 T74 F74 left64 right64 up64 down64
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
pos1_free pos2_full pos1_full pos2_free pos3_full pos3_free
transportation system with 2 pushers
producer pusher1 consumer pusher2
pos1_free pos2_full pos1_full pos2_free waiting_P1 releasing_P1 init_P1 aquire_output_area_P1 release_output_area_P1 aquire_input_area_P1 release_input_area_P1 moving_P1
ext_P1 ext_P1 ext_P1 norm_P1 basic_P1 basic_P1 basic_P1 R2_off_P1 R2_off_P1 R1_off_P1 R1_off_P1 R1_off_P1 R1_on_P1 R1_on_P1 R1_on_P1 R2_on_P1 R2_on_P1 R2_on_P1 stop_moving_P1 step3_P1 step4_P1 step2_P1 step1_P1 start_moving_P1 aquire_output_area_P1 release_output_area_P1 ext2norm_P1 norm2ext_P1 norm2basic_P1 basic2norm_P1 R2_set_on_P1 R2_set_on_P1 R2_set_off_P1 R2_set_off_P1 R1_set_off_P1 R1_set_off_P1 R1_set_on_P1 R1_set_on_P1 tr3_P1 tr4_P1 tr2_P1 tr1_P1 tr5_P1
Pusher without error states RELAY R2 RELAY R1 PUSHER control program
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
ch_DC_full ch_DC_free ch_CF_free ch_CF_full ch_A1P_full ch_A1P_free ch_TA1_full ch_TA1_free ch_A2D_full ch_A2D_free ch_FT_free ch_FT_full ch_PA2_free ch_PA2_full
coarse structure of the full refined losed system
press table deposit_belt feed_belt arm2 arm1 crane
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Ru5P 4 5 Xu5P R5P 6 S7P GAP 7 E4P F6P 8 GAP 15 NAD+ + Pi G6P F6P 10 ATP ADP FBP 11 12 DHAP 13 14 ATP ADP 9 Gluc 1,3-BPG ATP ADP 16 ATP ADP 19 NAD+ NADH 20 3PG 17 2PG PEP 18 Pyr Lac 2 NADP+ 2 NADPH 4 GSH 2 3 1 2 GSSG NADH
ADP NAD NAD
Pi Pi NADP+ NADPH GSSG GSH Ru5P Xu5P R5P S7P GAP GAP E4P F6P F6P Gluc G6P FBP DHAP 1,3-BPG 3PG 2PG PEP Pyr Lac ATP ATP ATP ATP ATP ADP ADP ADP ADP ADP NAD+ NAD+ NADH NADH 15 16 17 18 19 20 13 14 12 11 10 9 2 1 3 4 5 6 7 8 2 2 2 2
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Suc eSuc Glc Frc UDPglc G6P F6P G1P UDP UDP UTP ATP ATP ATP ATP ATP ATP ADP 29 ADP 29 ADP 29 ADP 29 ADP 29 ADP 29 S6P Pi 28 Pi 28 Pi 28 Pi 28 PP PP starch AMP SucTrans Inv HK FK SPP StaSy(b) Glyc(b) ATPcons(b) PPase rstarch geSuc SuSy SPS PGI PGM NDPkin UGPase AdK
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Ca++ PL Thrombos_PL Nahrung_Ca++ Abdeckung_PL Akt_XII_Plasmin Gewebe_ngOF Gewebe_TF Bldg_TTMK Abdeckung_ngOF Haemostase Fibrinolyse_System Inhibitoren Akt_Fibrinolyse Fibrinolyse Inh_Haemostase Inh_Fibrinolyse Ca++ PL F_XIIa F_XII Pre_KK HMWK KK ngOF F_XI F_XIa F_IX F_IXa TK F_VIIIa F_VIII Akt_XII_Plasmin Gewebe_ngOF Abdeckung_ngOF Akt_VIII_IIa Akt_IX_TF:VIIa Akt_X_TK Akt_XI_IIa Akt_VII_XIIa Leber_FXII Leber_PreKK Leber_HMWK Akt_PreKK_XIIa Akt_XII_ngOF Akt_XII_KK Leber_FXI Akt_XI_XIIa Leber_FIX Leber_FVIII Akt_IX_XIa Bldg_TK Abbau_TK Abbau_HMWK Akt_Plsmg_XIIa Akt_scuPA_XIIa Akt_Plsmg_KK Akt_scuPA_KK Inh_IXa_AT Inh_XIa_AT Inh_XIIa_AT Inh_KK_AT Inh_VIIIa_APC Inh_XIa_C1 Inh_XIIa_C1 Inh_KK_C1
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Raf-1Star m1 RKIP m2 Raf-1Star_RKIP m3 ERK-PP m9 MEK-PP_ERK m8 Raf-1Star_RKIP_ERK-PP m4 RKIP-P_RP m11 MEK-PP m7 ERK m5 RKIP-P m6 RP m10 k1 k2 k3 k4 k6 k7 k9 k10 k5 k8 k11
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Raf RasGTP Raf_RasGTP RafP RafP_Phase1 MEK_RafP MEKP_RafP MEKP_Phase2 MEKPP_Phase2 ERK ERK_MEKPP ERKP_MEKPP ERKP MEKPP ERKPP_Phase3 ERKP_Phase3 MEKP ERKPP Phase2 Phase3 MEK Phase1 k3 k6 k21 k18 k9 k12 k15 k24 k27 k30 k7/k8 k1/k2 k4/k5 k10/k11 k16/k17 k22/k23 k19/k20 k13/k14 k28/k29 k25/k26
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
signal response reporter TF TFS precursor pfb 1' TFS degradation 5 reporter degradation 7 response degradation 9 response production 8 reporter expression 6 TF degradation 2 TF expression 1 TFS disassociation 4 TFS association 3
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ based on the experience of the predecessor PED ◮ Snoopy was started 1997 as student project ◮ now 120.000 lines of code ◮ Acknowledgement: Matthias Dube, Markus Fieber, Anja
◮ maintenance and improvements ensured in future by students’
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ free of charge for non-commercial use ◮ source code is available on request ◮ further informations: http://www-dssz.informatik.tu-cottbus.de/software/snoopy.html
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
◮ import from bio databases ◮ import and animation of counter examples or
◮ automatic conversion between stochastic and
◮ hybrid models ◮ PNML support
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work
Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy