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 Cottbus Computer Science Department http://www-dssz.informatik.tu-cottbus.de/software/snoopy.html March 3, 2008 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Contents 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 Basic Properties extensible ◮ generic design facilitates the addition of new graph classes adaptive ◮ simultaneous use of several graph types in a homogeneous environment ◮ GUI adopts dynamically to graph type in active window platform independent ◮ 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 Model Editor Model Creation A A A ◮ graph constraints are considered k1 k1, k2 k2 ◮ hierarchy by subgraphs E E E MA1 ◮ logical (fusion) nodes A|E A|E k3 k3 ◮ interaction between graphs B B B Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Model Editor Model Exploration ◮ 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 (e.g. paths or invariants) ◮ automated layout (graphviz) Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Model Editor File Handling ◮ 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 Reachability Graph m8 r7 r10 r6 r9 m9 m13 r11 r8 r9 r6 ◮ simple graph class r10 r7 m12 m1 m10 r7 r2 ◮ one node and one edge type r8 r9 r1 r10 r6 r11 m11 m4 m2 ◮ furthermore comment nodes r11 r8 r1 r6 r5 r7 r2 ◮ constructable from m5 m3 r1 r8 Petri net animation r2 m6 r3 r4 m7 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Petri Net ◮ contains places and transitions as well as produce hierarchy and logical nodes ready_to_produce ready_to_send ◮ animation of the token game send ◮ interaction manager allows to construct co_buffer buffer the reachability graph ◮ export to a wide range of external analysis receive tools (INA, Lola, Maria, MC-Kit, Pep, ready_to_receive ready_to_consume Prod, Charlie. . . ) ◮ import of a restricted APNN file format consume Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Stochastic Petri Net ◮ stochastic Petri nets reproduction_of_prey predator_death ◮ generalized stochastic Petri nets 2 Predator ◮ deterministic and stochastic Petri nets Prey 2 ◮ biochemically propensity functions consumption_of_prey (mass-action, level) ◮ multiple initial markings, parameter sets, and function sets ◮ Gillespie algorithm for simulation Predator Prey Prey Predator ◮ export to PRISM, TimeNet, and Dizzy is in preparation Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Continuous Petri Net a_1 90 10 MKKK_P ◮ corresponds to a set of ordinary a_2 MKKK Parameters differential equations b_2 b_1 ◮ visualizes the structure 280 10 10 MKK_PP b_3 MKK MKK_P ◮ for a quantitative description of c_2 b_4 c_1 MAPK_P biochemical reaction networks 280 10 10 MAPK MAPK_PP ◮ six stiff and six unstiff solvers c_4 c_3 300 are available 250 ◮ multiple initial markings MAPK_P 200 MAPK_PP and parameter sets MKKK 150 MKKK_P 100 ◮ export to SBML 50 0 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Further Petri Net Classes Extended Petri Net ◮ with additional arcs 5 var sc sc 6 (inhibitor, read, reset, equal) inc reset 6 Time Petri Net acc ◮ up to now time intervals or durations for transitions sc ◮ export to INA t1 t2 Modulo Net count2 count1 ◮ Petri net with modulo arc for 5 counting transitions firing m Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Fault Tree ◮ for risk management of dependable systems >=1 ◮ describes dependencies of component based systems ◮ qualitative and quantitative analysis & & & ◮ several dependability measures may be computed v e1 e2 e2 e3 e1 e3 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Other Graph Classes x1 MTBDD ◮ for documentation and y1 y1 small case studies x2 x2 EDL Signature Nets ◮ describes patterns of y2 y2 y2 computer network attacks 8 2 5 Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Case Studies academic p1_thinking phil1 p1_take_left fork1 p1_waiting phil5 p1_take_right fork2 fork1 p1_eating fork5 phil2 fork2 p1_put_right fork3 fork4 p1_releasing phil4 p1_put_left phil3 dining philosophers Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Case Studies academic T54 F54 left64 T63 T65 up64 T64 down64 F64 F63 F65 right64 T74 F74 solitaire game Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Case Studies technical PUSHER control program RELAY R1 R1_on_P1 aquire_output_area_P1 R1_set_on_P1 R1_set_off_P1 start_moving_P1 init_P1 R1_off_P1 R1_off_P1 tr1_P1 basic_P1 pos1_full aquire_input_area_P1 step1_P1 R1_set_on_P1 RELAY R2 R2_on_P1 waiting_P1 R1_on_P1 transportation system with 2 pushers tr2_P1 pos2_free ext_P1 R2_set_on_P1 R2_set_off_P1 pos2_full pos1_full pos3_full step2_P1 R1_set_off_P1 aquire_output_area_P1 R2_off_P1 R1_off_P1 moving_P1 tr3_P1 ext_P1 release_output_area_P1 consumer producer pusher1 step3_P1 R2_set_on_P1 Pusher without error states pusher2 R2_on_P1 pos2_full R1_on_P1 pos2_free pos3_free pos1_free tr4_P1 basic_P1 releasing_P1 step4_P1 R2_set_off_P1 basic2norm_P1 release_input_area_P1 norm2ext_P1 pos1_free R2_off_P1 tr5_P1 stop_moving_P1 basic_P1 norm_P1 ext_P1 release_output_area_P1 norm2basic_P1 ext2norm_P1 R2_on_P1 concurrent pusher Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Case Studies technical coarse structure of the full refined losed system deposit_belt ch_A2D_full arm2 ch_A2D_free ch_DC_full ch_DC_free ch_PA2_free ch_PA2_full crane press ch_CF_free ch_A1P_full ch_CF_full ch_A1P_free ch_FT_free ch_TA1_free feed_belt ch_FT_full ch_TA1_full arm1 table control program of a production cell Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy
Basic Properties Graph Classes Case Studies Implementation Availability Future Work Case Studies biological - metabolic networks Xu5P 4 E4P S7P Ru5P 4 Ru5P Xu5P 6 7 8 ATP GSSG NADPH GAP F6P 5 S7P E4P 5 2 R5P 6 7 8 1 2 3 2 NADPH ADP 2 GSSG 2 2 2 GAP F6P R5P 2 3 1 GSH NADP+ 4 GSH 2 NADP + Pi Gluc F6P FBP GAP 9 10 11 12 G6P 13 9 10 11 12 Gluc G6P F6P FBP GAP 14 13 NAD+ ATP ADP ATP ADP 14 ATP ATP ADP DHAP NAD + ADP + DHAP Pi Pi 15 15 NADH NAD+ NADH ATP ADP ATP ADP NAD + NADH NADH ATP ADP ATP ADP 20 19 18 17 16 Lac Pyr PEP 2PG 3PG 1,3-BPG 20 19 18 17 16 1,3-BPG Lac Pyr 2PG PEP 3PG glycolysis Monika Heiner, Ronny Richter, Martin Schwarick BTU Cottbus, Chair DSSZ Snoopy ADP NAD NAD
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