diff --git a/Benchmarks/README.md b/Benchmarks/README.md new file mode 100644 index 0000000..a1ba39f --- /dev/null +++ b/Benchmarks/README.md @@ -0,0 +1 @@ +Description here diff --git a/prism/Circuit0x8E/Circuit0x8E_000to011_G1_10_10.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E/Circuit0x8E_000to011_G1_10_10.sm similarity index 100% rename from prism/Circuit0x8E/Circuit0x8E_000to011_G1_10_10.sm rename to GeneticCircuits/Circuit0x8E/Circuit0x8E/Circuit0x8E_000to011_G1_10_10.sm diff --git a/prism/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA.sm similarity index 100% rename from prism/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA.sm rename to GeneticCircuits/Circuit0x8E/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA.sm diff --git a/prism/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA_unb.sm b/GeneticCircuits/Circuit0x8E/Circuit0x8E/Circuit0x8E_000to011_G1_10_10_RBA_unb.sm similarity index 100% rename from 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GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_011to101_G1_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_100to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_100to010_G0_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_100to010_G0_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_100to010_G0_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_100to111_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_100to111_G0_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_100to111_G0_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_100to111_G0_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_101to000_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_101to000_G1_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_101to000_G1_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_101to000_G1_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_101to011_G1_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_101to011_G1_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_101to011_G1_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_101to011_G1_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_111to010_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_111to010_G0_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_111to010_G0_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_111to010_G0_10_10.xml diff --git a/SBML/Circuit_0x8E/Circuit0x8E_TI_111to100_G0_10_10.xml b/GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_111to100_G0_10_10.xml similarity index 100% rename from SBML/Circuit_0x8E/Circuit0x8E_TI_111to100_G0_10_10.xml rename to GeneticCircuits/Circuit0x8E/Circuit_0x8E/Circuit0x8E_TI_111to100_G0_10_10.xml diff --git a/GeneticCircuits/Circuit0x8E/README.md b/GeneticCircuits/Circuit0x8E/README.md new file mode 100644 index 0000000..32491de --- /dev/null +++ b/GeneticCircuits/Circuit0x8E/README.md @@ -0,0 +1,17 @@ +### Circuit0x8E + +This circuit is part of the genetic circuits designed by the software tool Cello [1]. The circuit has three input arguments IPTG, aTc, and Ara and one output argument YFP. + +![Figure1](../../Media/0x8E_Original.png) + +In the laboratory, circuit 0x8E showed an unexpected, glitching behavior. Further analysis resulted in two more designs of the circuit as well as the analysis of its glitching behavior [2]. + +![Figure2](../../Media/0x8E_LogicHazardFree.png) + +![Figure3](../../Media/0x8E_TwoInverter.png) + +There are two types of glitches. In one type, the output should remain in a low state during an input transition (Zero Glitch). In the other type, the output should remain at a high state (One Glitch) during an input transition. More information can be found in [1-2]. + +1. Nielsen, A. A. K.; Der, B. S.; Shin, J.; Vaidyanathan, P.; Paralanov, V.; Strychalski, E. A.; Ross, D.; Densmore, D.; Voigt, C. A. Genetic Circuit Design Automation. Science 2016, 352 (6281), aac7341–aac7341. https://doi.org/10.1126/science.aac7341. + +2. Fontanarrosa, P.; Doosthosseini, H.; Borujeni, A. E.; Dorfan, Y.; Voigt, C. A.; Myers, C. Genetic Circuit Dynamics: Hazard and Glitch Analysis. ACS Synthetic Biology 2020, 15. diff --git a/prism/Dual_Feedback_Oscillator.sm b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.sm similarity index 100% rename from prism/Dual_Feedback_Oscillator.sm rename to GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.sm diff --git a/SBML/Dual_Feedback_Oscillator.xml b/GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml similarity index 100% rename from SBML/Dual_Feedback_Oscillator.xml rename to GeneticCircuits/Dual_Feedback_Osscillator/Default/Dual_Feedback_Oscillator.xml diff --git a/GeneticCircuits/Dual_Feedback_Osscillator/README.md b/GeneticCircuits/Dual_Feedback_Osscillator/README.md new file mode 100644 index 0000000..3cdbc85 --- /dev/null +++ b/GeneticCircuits/Dual_Feedback_Osscillator/README.md @@ -0,0 +1,7 @@ +### Dual Feedback Oscillator + +This design is an improved version of the repressilator [1]. + +![Figure9](../../Media/DualFeedback.png) + +1. Stricker, J., Cookson, S., Bennett, M. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008). https://doi.org/10.1038/nature07389. diff --git a/SBML/Muller_C_Element/Majority.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Majority.xml similarity index 100% rename from SBML/Muller_C_Element/Majority.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Majority.xml diff --git a/SBML/Muller_C_Element/Majority_10_10.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Majority_10_10.xml similarity index 100% rename from SBML/Muller_C_Element/Majority_10_10.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Majority_10_10.xml diff --git a/SBML/Muller_C_Element/Speed_Independent.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Speed_Independent.xml similarity index 100% rename from SBML/Muller_C_Element/Speed_Independent.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Speed_Independent.xml diff --git a/SBML/Muller_C_Element/Speed_Independent_10_10.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Speed_Independent_10_10.xml similarity index 100% rename from SBML/Muller_C_Element/Speed_Independent_10_10.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Speed_Independent_10_10.xml diff --git a/SBML/Muller_C_Element/Toggle.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Toggle.xml similarity index 100% rename from SBML/Muller_C_Element/Toggle.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Toggle.xml diff --git a/SBML/Muller_C_Element/Toggle_10_10.xml b/GeneticCircuits/Muller_C_Element/Muller_C_Element/Toggle_10_10.xml similarity index 100% rename from SBML/Muller_C_Element/Toggle_10_10.xml rename to GeneticCircuits/Muller_C_Element/Muller_C_Element/Toggle_10_10.xml diff --git a/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/allResults.txt b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/allResults.txt new file mode 100644 index 0000000..ad375c0 --- /dev/null +++ b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/allResults.txt @@ -0,0 +1,28 @@ +Results +original | majority | speed-ind | toggle +Genarated | 0.05429919317 | 0.04229449798 | 0.02820598125 +Jetc | 3 | 2 | 1 + +tolerance | majority | speed-ind | toggle +0.00 +0.05 | 3.211804026e-05 | | 0.00178786289 +0.10 | 0.0002705651497 | | 0.00737188158 +0.15 | 0.0009389212581 | 0.02468170587 | 0.05964338214 1 2 3 +0.20 | 0.001305344762 | 0.0291911003 | 0.07038608663 1 2 3 +0.25 | 0.002453363152 | 0.07318766954 | 0.08001999633 1 2 3 +0.30 | 0.002143780977 | 0.188189723 | 0.1039514362 1 3 2 +0.35 | 0.00614008905 | 0.1603816091 | 0.2315218211 1 2 3 +0.40 | 0.006026272635 | 0.1482811183 | 0.2140336699 1 2 3 +0.45 | 0.006138649094 | 0.1470030393 | 0.2459799765 1 2 3 +0.50 | 0.007518941557 | 0.2791356316 | 0.2230133141 1 3 2 +0.55 | 0.01084588519 | 0.308515096 | 0.2463700158 1 3 2 +0.60 | 0.0149490905 | 0.3146735057 | 0.4792942312 1 2 3 +0.65 | 0.0155160164 | 0.3120229424 | 0.4744124959 1 2 3 +0.70 | 0.0142515022 | 0.3083532564 | 0.4701229831 1 2 3 +0.75 | 0.0129137536 | 0.2734091978 | 0.4189413926 1 2 3 +0.80 | 0.01299945386 | 0.2751005182 | 0.4195006419 1 2 3 +0.85 | 0.01696034223 | 0.2580526951 | 0.3360747115 1 2 3 +0.90 | 0.01766635265 | 0.2584110635 | 0.3357933312 1 2 3 +0.95 | 0.01807570789 | 0.2655804684 | 0.344663888 1 2 3 +1.00 | 0.007167327219 | 0.414399965 | 0.3176865782 1 3 2 + diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.05.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.05.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.05.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.05.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.15.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.15.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.15.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.15.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.20.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.20.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.20.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.25.prism 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b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.85.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.85.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.85.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.95.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.95.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority0.95.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority0.95.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority1.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority1.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/majority/majority1.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/majority/majority1.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.05.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.05.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.05.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.05.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.15.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.15.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.15.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.15.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.20.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.20.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.20.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.25.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.25.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.25.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.25.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.30.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.30.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.30.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.30.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.35.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.35.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.35.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.35.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.40.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.40.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.40.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.40.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.45.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.45.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.45.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.45.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.50.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.50.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.50.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.50.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.55.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.55.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.55.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.55.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.60.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.60.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.60.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.60.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.65.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.65.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.65.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.65.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.70.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.70.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.70.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.70.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.75.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.75.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.75.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.75.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.80.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.80.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.80.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.80.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.85.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.85.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.85.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.85.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.95.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.95.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.95.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed0.95.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed1.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed1.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/speed-ind/speed1.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/speed-ind/speed1.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.05.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.05.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.05.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.05.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.15.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.15.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.15.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.15.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.20.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.20.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.20.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.25.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.25.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.25.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.25.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.30.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.30.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.30.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.30.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.35.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.35.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.35.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.35.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.40.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.40.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.40.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.40.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.45.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.45.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.45.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.45.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.50.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.50.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.50.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.50.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.55.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.55.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.55.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.55.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.60.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.60.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.60.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.60.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.65.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.65.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.65.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.65.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.70.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.70.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.70.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.70.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.75.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.75.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.75.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.75.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.80.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.80.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.80.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.80.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.85.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.85.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.85.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.85.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.95.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.95.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle0.95.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle0.95.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle1.00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle1.00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/OldStyle/toggle/toggle1.00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/OldStyle/toggle/toggle1.00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p20.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p20.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p20.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p30.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p30.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p30.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p30.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p40.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p40.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p40.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p40.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p50.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p50.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p50.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p50.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p60.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p60.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p60.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p60.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p70.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p70.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p70.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p70.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p80.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p80.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p80.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p80.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_0p90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_1p00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_1p00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_1p00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Majority/Majority_1p00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p20.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p20.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p20.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p30.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p30.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p30.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p30.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p40.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p40.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p40.prism rename to 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rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p60.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p70.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p70.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p70.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p70.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p80.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p80.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p80.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p80.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_0p90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_1p00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_1p00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_1p00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Speed-ind/Speed-Ind_1p00.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p10.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p10.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p10.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p10.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p20.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p20.prism similarity index 100% rename from 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prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p80.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p80.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p90.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p90.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p90.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_0p90.prism diff --git a/prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_1p00.prism b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_1p00.prism similarity index 100% rename from prism/Muller_C_Element/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_1p00.prism rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/C-Element_w_Tolerances/SynchronizedStyle/Toggle/Toggle_1p00.prism diff --git a/prism/Muller_C_Element/Majority.props b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Majority.props similarity index 100% rename from prism/Muller_C_Element/Majority.props rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Majority.props diff --git a/prism/Muller_C_Element/Majority.sm b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Majority.sm similarity index 100% rename from prism/Muller_C_Element/Majority.sm rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Majority.sm diff --git a/prism/Muller_C_Element/Majority_10_10.props b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Majority_10_10.props similarity index 100% rename from prism/Muller_C_Element/Majority_10_10.props rename to 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a/prism/Muller_C_Element/Speed_Independent_10_10.props b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Speed_Independent_10_10.props similarity index 100% rename from prism/Muller_C_Element/Speed_Independent_10_10.props rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Speed_Independent_10_10.props diff --git a/prism/Muller_C_Element/Speed_Independent_10_10.sm b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Speed_Independent_10_10.sm similarity index 100% rename from prism/Muller_C_Element/Speed_Independent_10_10.sm rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Speed_Independent_10_10.sm diff --git a/prism/Muller_C_Element/Toggle.props b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle.props similarity index 100% rename from prism/Muller_C_Element/Toggle.props rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle.props diff --git a/prism/Muller_C_Element/Toggle.sm b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle.sm similarity index 100% rename from prism/Muller_C_Element/Toggle.sm rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle.sm diff --git a/prism/Muller_C_Element/Toggle_10_10.props b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle_10_10.props similarity index 100% rename from prism/Muller_C_Element/Toggle_10_10.props rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle_10_10.props diff --git a/prism/Muller_C_Element/Toggle_10_10.sm b/GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle_10_10.sm similarity index 100% rename from prism/Muller_C_Element/Toggle_10_10.sm rename to GeneticCircuits/Muller_C_Element/Muller_C_Element_Prism/Toggle_10_10.sm diff --git a/GeneticCircuits/Muller_C_Element/README.md b/GeneticCircuits/Muller_C_Element/README.md new file mode 100644 index 0000000..50a0156 --- /dev/null +++ b/GeneticCircuits/Muller_C_Element/README.md @@ -0,0 +1,11 @@ +### Muller C-element + +This genetic circuit implements a state-holding gate called Muller C-element. If both inputs are high, its output goes high. If both inputs are low, the output is low. If the inputs are mixed, it retains its previous state. The three designs are the Majority, Speed_Independent, and Toggle Switch design [1]. + +![Figure4](../../Media/Majority.png) + +![Figure5](../../Media/Speed_Independent.png) + +![Figure6](../../Media/Toggle.png) + +1. Madsen, C.; Zhang, Z.; Roehner, N.; Winstead, C.; Myers, C. Stochastic Model Checking of Genetic Circuits. J. Emerg. Technol. Comput. Syst. 2014, 11 (3), 1–21. https://doi.org/10.1145/2644817. diff --git a/GeneticCircuits/README.md b/GeneticCircuits/README.md new file mode 100644 index 0000000..a685882 --- /dev/null +++ b/GeneticCircuits/README.md @@ -0,0 +1,13 @@ +## Genetic Circuits + +## Naming Convention + +* 10_10: Production and degradation of molecules in steps of 10 + +* RBA: Reaction-based abstraction (remove irrelevant or rapid reactions) + +* G0: Static zero glitch + +* G1: Static one glitch + +* unb: unbound prsim models diff --git a/prism/Repressilator.sm b/GeneticCircuits/Repressilator/Default/Repressilator.sm similarity index 100% rename from prism/Repressilator.sm rename to GeneticCircuits/Repressilator/Default/Repressilator.sm diff --git a/SBML/Repressilator.xml b/GeneticCircuits/Repressilator/Default/Repressilator.xml similarity index 100% rename from SBML/Repressilator.xml rename to GeneticCircuits/Repressilator/Default/Repressilator.xml diff --git a/GeneticCircuits/Repressilator/README.md b/GeneticCircuits/Repressilator/README.md new file mode 100644 index 0000000..4f0747f --- /dev/null +++ b/GeneticCircuits/Repressilator/README.md @@ -0,0 +1,7 @@ +### Repressilator + +The repressilator consists of three promoters each with a repressor gene. It is a cyclic negative-feedback loop, periodically inducing the synthesis of green fluorescent proteins [1]. + +![Figure8](../../Media/Repressilator.PNG) + +1. Elowitz, M. B.; Leibler, S. A Synthetic Oscillatory Network of Transcriptional Regulators. Nature 2000, 403 (6767), 335–338. https://doi.org/10.1038/35002125. diff --git a/SBML/Toggle_Switch.xml b/GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml similarity index 100% rename from SBML/Toggle_Switch.xml rename to GeneticCircuits/Toggle_Switch/Default/Toggle_Switch.xml diff --git a/prism/Toggle_Switch_RBA.sm b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm similarity index 100% rename from prism/Toggle_Switch_RBA.sm rename to GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.sm diff --git a/SBML/Toggle_Switch_RBA.xml b/GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml similarity index 100% rename from SBML/Toggle_Switch_RBA.xml rename to GeneticCircuits/Toggle_Switch/RBA/Toggle_Switch_RBA.xml diff --git a/GeneticCircuits/Toggle_Switch/README.md b/GeneticCircuits/Toggle_Switch/README.md new file mode 100644 index 0000000..294a1e4 --- /dev/null +++ b/GeneticCircuits/Toggle_Switch/README.md @@ -0,0 +1,7 @@ +### Toggle Switch + +The toggle switch is a state holding gate and consists of two promoters each followed by a coding sequence. Each promoter is repressed by the protein transcribed by the other promoter [1]. + +![Figure7](../../Media/ToggleSwitch.png) + +1. Gardner, T. S.; Cantor, C. R.; Collins, J. J. Construction of a Genetic Toggle Switch in Escherichia Coli. Nature 2000, 403 (6767), 339–342. https://doi.org/10.1038/35002131. diff --git a/Figures/0x8E_LogicHazardFree.png b/Media/0x8E_LogicHazardFree.png similarity index 100% rename from Figures/0x8E_LogicHazardFree.png rename to Media/0x8E_LogicHazardFree.png diff --git a/Figures/0x8E_Original.png b/Media/0x8E_Original.png similarity index 100% rename from Figures/0x8E_Original.png rename to Media/0x8E_Original.png diff --git a/Figures/0x8E_TwoInverter.png b/Media/0x8E_TwoInverter.png similarity index 100% rename from Figures/0x8E_TwoInverter.png rename to Media/0x8E_TwoInverter.png diff --git a/Figures/DualFeedback.png b/Media/DualFeedback.png similarity index 100% rename from Figures/DualFeedback.png rename to Media/DualFeedback.png diff --git a/Figures/Majority.png b/Media/Majority.png similarity index 100% rename from Figures/Majority.png rename to Media/Majority.png diff --git a/Figures/Repressilator.PNG b/Media/Repressilator.PNG similarity index 100% rename from Figures/Repressilator.PNG rename to Media/Repressilator.PNG diff --git a/Figures/Speed_Independent.png b/Media/Speed_Independent.png similarity index 100% rename from Figures/Speed_Independent.png rename to Media/Speed_Independent.png diff --git a/Figures/Toggle.png b/Media/Toggle.png similarity index 100% rename from Figures/Toggle.png rename to Media/Toggle.png diff --git a/Figures/ToggleSwitch.png b/Media/ToggleSwitch.png similarity index 100% rename from Figures/ToggleSwitch.png rename to Media/ToggleSwitch.png diff --git a/Nanotechnology/README.md b/Nanotechnology/README.md new file mode 100644 index 0000000..a1ba39f --- /dev/null +++ b/Nanotechnology/README.md @@ -0,0 +1 @@ +Description here diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.xml b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.xml rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to011.xml diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to101.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to101.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to101.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch One/Circuit0x8E_LHF_000to101.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch 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Zero/Circuit0x8E_LHF_100to010.xml b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to010.xml rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to010.xml diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.xml b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.xml rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_100to111.xml diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.xml b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.xml rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to010.xml diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.xml b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.xml rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Circuit0x8E_LHF_111to100.xml diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to100_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to100_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to100_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to100_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to111_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to111_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to111_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_010to111_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to010_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to010_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to010_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to010_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to111_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to111_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to111_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_100to111_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to010_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to010_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to010_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to010_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to100_unb.sm b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to100_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to100_unb.sm rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/Circuit0x8E_LHF_111to100_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to100_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to100_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to100_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to100_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to111_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to111_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to111_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_010to111_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to010_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to010_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to010_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to010_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to111_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to111_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to111_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_100to111_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to010_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to010_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to010_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to010_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to100_unb.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to100_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to100_unb.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_LHF_111to100_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/pro.csl b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/pro.csl rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/Unbounded/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/err.txt b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/err.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/err.txt rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/err.txt diff --git a/prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/pro.csl b/Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/pro.csl rename to Other/HazardCct/Circuit0x8E_LogicHazardFree/Glitch Zero/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to011.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_000to101.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to000.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_011to101.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to000.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Circuit0x8E_TI_101to011.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to011_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to011_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to011_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to011_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to101_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to101_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to101_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_000to101_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to000_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to000_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to000_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to000_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to101_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to101_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to101_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_011to101_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to000_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to000_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to000_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to000_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to011_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to011_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to011_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/Circuit0x8E_TI_101to011_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to011_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to011_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to011_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to011_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to101_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to101_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to101_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_000to101_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to000_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to000_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to000_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to000_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to101_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to101_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to101_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_011to101_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to000_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to000_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to000_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to000_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to011_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to011_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to011_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/FinalResults/Circuit0x8E_TI_101to011_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/pro1.csl b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/pro1.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/pro1.csl rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/Unbounded/pro1.csl diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/pro1.csl b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/pro1.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/pro1.csl rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/pro1.csl diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/results.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/results.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/results.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch One/results.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to100.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_010to111.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to010.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_100to111.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to010.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.xml b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.xml rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Circuit0x8E_TI_111to100.xml diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to100_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to100_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to100_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to100_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to111_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to111_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to111_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_010to111_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to010_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to010_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to010_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to010_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to111_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to111_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to111_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_100to111_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to010_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to010_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to010_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to010_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to100_unbounded.sm b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to100_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to100_unbounded.sm rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/Circuit0x8E_TI_111to100_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to100_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to100_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to100_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to100_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to111_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to111_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to111_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_010to111_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to010_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to010_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to010_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to010_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to111_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to111_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to111_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_100to111_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to010_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to010_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to010_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to010_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to100_unbounded.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to100_unbounded.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to100_unbounded.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/FinalResults/Circuit0x8E_TI_111to100_unbounded.txt diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/pro.csl b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/pro.csl rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/Unbounded/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/pro.csl b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/pro.csl rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/results.txt b/Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/results.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/results.txt rename to Other/HazardCct/Circuit0x8E_Two_Inverter/Glitch Zero/results.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011_test.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011_test.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011_test.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to011_test.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_000to101.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to000.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_011to101.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to000.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Circuit0x8E_101to011.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_combined b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_combined similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_combined rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_combined diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_merged.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_merged.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_merged.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/000to011_merged.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb_test.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb_test.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb_test.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to011_unb_test.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to101_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to101_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to101_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_000to101_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to000_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to000_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to000_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to000_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to101_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to101_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to101_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_011to101_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to000_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to000_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to000_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to000_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to011_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to011_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to011_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/Circuit0x8E_101to011_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to011_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to011_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to011_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to011_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to101_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to101_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to101_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_000to101_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to000_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to000_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to000_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to000_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to101_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to101_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to101_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_011to101_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to000_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to000_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to000_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to000_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to011_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to011_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to011_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/FinalResults/Circuit0x8E_101to011_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/pro1.csl b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/pro1.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/pro1.csl rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/pro1.csl diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/results.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/results.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/results.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/Unbound/results.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/pro1.csl b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/pro1.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/pro1.csl rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/pro1.csl diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/results.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/results.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/results.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_One/results.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to100.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_010to111.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to010.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_100to111.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to010.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.xml b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.xml similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.xml rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_111to100.xml diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_Zero_Glitches b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_Zero_Glitches similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_Zero_Glitches rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Circuit0x8E_Zero_Glitches diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to100_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to100_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to100_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to100_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to111_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to111_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to111_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_010to111_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to010_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to010_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to010_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to010_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to111_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to111_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to111_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_100to111_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to010_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to010_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to010_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to010_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to100_unb.sm b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to100_unb.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to100_unb.sm rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/Circuit0x8E_111to100_unb.sm diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/010to111.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/010to111.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/010to111.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/010to111.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_010to100_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_010to100_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_010to100_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_010to100_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to010_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to010_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to010_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to010_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to111_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to111_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to111_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_100to111_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to010_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to010_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to010_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to010_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to100_unb.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to100_unb.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to100_unb.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/FinalResults/Circuit0x8E_111to100_unb.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/pro.csl b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/pro.csl rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/results.txt b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/results.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/results.txt rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/Unbounded/results.txt diff --git a/prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/pro.csl b/Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/pro.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/pro.csl rename to Other/HazardCct/Circuit0x8E_original/No_abstraction/Glitch_Zero/pro.csl diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Circuit0x8E_flat_10.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Circuit0x8E_flat_10.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Circuit0x8E_flat_10.sm rename to 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b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_000to101_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_000to101_unbounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_000to101_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_bounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_bounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_bounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_bounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_unbounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_unbounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to000_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_bounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_bounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_bounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_bounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_unbounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_unbounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_011to101_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_bounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_bounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_bounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_bounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_unbounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_unbounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to000_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_bounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_bounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_bounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_bounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_unbounded.sm b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_unbounded.sm similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_unbounded.sm rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/Circuit0x8E_flat_10_101to011_unbounded.sm diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/hazard_glitch_one.csl b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/hazard_glitch_one.csl similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/hazard_glitch_one.csl rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/hazard_glitch_one.csl diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011.txt b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011.txt rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011.txt diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_greater_eq_30.txt b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_greater_eq_30.txt similarity index 100% rename from prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_greater_eq_30.txt rename to Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_greater_eq_30.txt diff --git a/prism/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_less_eq_30.txt b/Other/HazardCct/Circuit0x8E_original/Reaction_based_abstraction/Glitch-One/stamina_results/stamina_results_000to011_less_eq_30.txt similarity index 100% rename from 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b/Other/Polling/polling_T_10_N_20.prism similarity index 100% rename from prism/Polling/polling_T_10_N_20.prism rename to Other/Polling/polling_T_10_N_20.prism diff --git a/prism/README.md b/Other/README.md similarity index 96% rename from prism/README.md rename to Other/README.md index d03bb5a..28a2ca6 100644 --- a/prism/README.md +++ b/Other/README.md @@ -1,14 +1,15 @@ + ### Genetic Toggle Switch -This genetic circuit model for the toggle switch has two inputs aTc and IPTG. It can be set to the OFF state by supplying it with aTc and set to ON state by supplying IPTG. Two important properties for a toggle switch circuit are the response time and failure rate. The CSL property is given by "P=? [true U<=2100 (TetR>40 & LacI<20)]". +This genetic circuit model for the toggle switch has two inputs aTc and IPTG. It can be set to the OFF state by supplying it with aTc and set to ON state by supplying IPTG. Two important properties for a toggle switch circuit are the response time and failure rate. The CSL property is given by "P=? [true U<=2100 (TetR>40 & LacI<20)]". ### Robot World -This case study considers a robot moving in an n×n grid world taken from and a janitor moving in a larger grid KnxKn, where $K$ is constant scaling factor which makes the system practically infinite state. The robot starts from the bottom left corner to reach the top right corner. The Janitor moves around the larger grid randomly. Only robot or janitor can occupy one position at any given time. The robot also randomly communicates with the base station. We calculate the probability that the robot reaches the top right corner within $100$ time units while periodically communicating with the base station. The CSL formula describing the property is "P_{=?} [(P>=0.5 [ true U<=7 (c=1)]) U<=100 ((x1=n)&(y1=n))]"$''". +This case study considers a robot moving in an n×n grid world taken from and a janitor moving in a larger grid KnxKn, where $K$ is constant scaling factor which makes the system practically infinite state. The robot starts from the bottom left corner to reach the top right corner. The Janitor moves around the larger grid randomly. Only robot or janitor can occupy one position at any given time. The robot also randomly communicates with the base station. We calculate the probability that the robot reaches the top right corner within $100$ time units while periodically communicating with the base station. The CSL formula describing the property is "P_{=?} [(P>=0.5 [ true U<=7 (c=1)]) U<=100 ((x1=n)&(y1=n))]"$''". ### Jackson Queuing Network -A Jackson Queuing Network (JQN) consists of $N$ interconnected nodes (queues) with infinite queue capacity. Initially, all queues are considered empty. Each station is connected to a single server which distributes the arrived jobs to different stations. Customers arrive as a Poisson stream with intensity $\lambda$ for $N$ queues. A customer, upon completing service at a node $i$, either leaves the network or enters another node $j$. We consider the case with $N=4,5$ with constant $\lambda=5$. We compute the probability that, within 10 time units, the first queue has more that $3$ jobs and the second queue has more than $5$ jobs, given by the CSL property "P_{=?} [true U[0.0,10.0] (s\_1>=4) & (s_2>=6)]". +A Jackson Queuing Network (JQN) consists of $N$ interconnected nodes (queues) with infinite queue capacity. Initially, all queues are considered empty. Each station is connected to a single server which distributes the arrived jobs to different stations. Customers arrive as a Poisson stream with intensity $\lambda$ for $N$ queues. A customer, upon completing service at a node $i$, either leaves the network or enters another node $j$. We consider the case with $N=4,5$ with constant $\lambda=5$. We compute the probability that, within 10 time units, the first queue has more that $3$ jobs and the second queue has more than $5$ jobs, given by the CSL property "P_{=?} [true U[0.0,10.0] (s\_1>=4) & (s_2>=6)]". ### Cyclic Server Polling System -This case study taken from the PRISM's benchmark suite. It is based on a cyclic server attending N stations. For model checking, we consider the probability that station one is polled within 10 time units, described by the CSL formula "P=? [true U<=10 (s=1 & a=0)]". +This case study taken from the PRISM's benchmark suite. It is based on a cyclic server attending N stations. For model checking, we consider the probability that station one is polled within 10 time units, described by the CSL formula "P=? [true U<=10 (s=1 & a=0)]". -### Tandem Queuing Network -Tandem queuing network is the simplest interconnected queuing network with two queues with one server each. Customers join the first queue and enters the second queue immediately after completing the service. We consider both queues with capacity c. In this paper we consider the probability that, first queue becomes full in 0.25 time units given by CSL property "P_{=?} [true U<=T sc=c]". +### Tandem Queuing Network +Tandem queuing network is the simplest interconnected queuing network with two queues with one server each. Customers join the first queue and enters the second queue immediately after completing the service. We consider both queues with capacity c. In this paper we consider the probability that, first queue becomes full in 0.25 time units given by CSL property "P_{=?} [true U<=T sc=c]". diff --git a/prism/RobotWorld/robot_n_32.csl b/Other/RobotWorld/robot_n_32.csl similarity index 100% rename from prism/RobotWorld/robot_n_32.csl rename to Other/RobotWorld/robot_n_32.csl diff --git a/prism/RobotWorld/robot_n_32.prism b/Other/RobotWorld/robot_n_32.prism similarity index 100% rename from prism/RobotWorld/robot_n_32.prism rename to Other/RobotWorld/robot_n_32.prism diff --git a/prism/RobotWorld/robot_n_64.csl b/Other/RobotWorld/robot_n_64.csl similarity index 100% rename from prism/RobotWorld/robot_n_64.csl rename to Other/RobotWorld/robot_n_64.csl diff --git a/prism/RobotWorld/robot_n_64.prism b/Other/RobotWorld/robot_n_64.prism similarity index 100% rename from prism/RobotWorld/robot_n_64.prism rename to Other/RobotWorld/robot_n_64.prism diff --git a/prism/Tandem/tandem_c_2047_T_0.25.csl b/Other/Tandem/tandem_c_2047_T_0.25.csl similarity index 100% rename from prism/Tandem/tandem_c_2047_T_0.25.csl rename to Other/Tandem/tandem_c_2047_T_0.25.csl diff --git a/prism/Tandem/tandem_c_2047_T_0.25.prism b/Other/Tandem/tandem_c_2047_T_0.25.prism similarity index 100% rename from prism/Tandem/tandem_c_2047_T_0.25.prism rename to Other/Tandem/tandem_c_2047_T_0.25.prism diff --git a/prism/Tandem/tandem_c_4095_T_0.25.csl b/Other/Tandem/tandem_c_4095_T_0.25.csl similarity index 100% rename from prism/Tandem/tandem_c_4095_T_0.25.csl rename to Other/Tandem/tandem_c_4095_T_0.25.csl diff --git a/prism/Tandem/tandem_c_4095_T_0.25.prism b/Other/Tandem/tandem_c_4095_T_0.25.prism similarity index 100% rename from prism/Tandem/tandem_c_4095_T_0.25.prism rename to Other/Tandem/tandem_c_4095_T_0.25.prism diff --git a/prism/Toggle/results.txt b/Other/Toggle/results.txt similarity index 100% rename from prism/Toggle/results.txt rename to Other/Toggle/results.txt diff --git a/prism/Toggle/toggle_IPTG_0.csl b/Other/Toggle/toggle_IPTG_0.csl similarity index 100% rename from prism/Toggle/toggle_IPTG_0.csl rename to Other/Toggle/toggle_IPTG_0.csl diff --git a/prism/Toggle/toggle_IPTG_0.prism b/Other/Toggle/toggle_IPTG_0.prism similarity index 89% rename from prism/Toggle/toggle_IPTG_0.prism rename to Other/Toggle/toggle_IPTG_0.prism index 9bad692..f26961f 100644 --- a/prism/Toggle/toggle_IPTG_0.prism +++ b/Other/Toggle/toggle_IPTG_0.prism @@ -1,5 +1,7 @@ ctmc +// Tags: Toggle Switch, Unbounded, Infinite, TetR, LacI + const int aTc = 0; const int IPTG = 0; @@ -25,4 +27,4 @@ module LacI_def [] LacI>0 -> p_l : (LacI'=LacI+10) + 0.0075*LacI:(LacI'=LacI-1); -endmodule \ No newline at end of file +endmodule diff --git a/prism/Toggle/toggle_IPTG_100.csl b/Other/Toggle/toggle_IPTG_100.csl similarity index 100% rename from prism/Toggle/toggle_IPTG_100.csl rename to Other/Toggle/toggle_IPTG_100.csl diff --git a/prism/Toggle/toggle_IPTG_100.prism b/Other/Toggle/toggle_IPTG_100.prism similarity index 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a/crn/DonovanYeastPolarization/pythonScripts/data_stat.py b/Other/crn/DonovanYeastPolarization/pythonScripts/data_stat.py similarity index 100% rename from crn/DonovanYeastPolarization/pythonScripts/data_stat.py rename to Other/crn/DonovanYeastPolarization/pythonScripts/data_stat.py diff --git a/crn/DonovanYeastPolarization/pythonScripts/temp.py b/Other/crn/DonovanYeastPolarization/pythonScripts/temp.py similarity index 100% rename from crn/DonovanYeastPolarization/pythonScripts/temp.py rename to Other/crn/DonovanYeastPolarization/pythonScripts/temp.py diff --git a/crn/DonovanYeastPolarization/pythonScripts/tempone.py b/Other/crn/DonovanYeastPolarization/pythonScripts/tempone.py similarity index 100% rename from crn/DonovanYeastPolarization/pythonScripts/tempone.py rename to Other/crn/DonovanYeastPolarization/pythonScripts/tempone.py diff --git a/crn/KuwaharaEnzyme/simple_enzyme.csl b/Other/crn/KuwaharaEnzyme/simple_enzyme.csl similarity index 100% rename from crn/KuwaharaEnzyme/simple_enzyme.csl rename to Other/crn/KuwaharaEnzyme/simple_enzyme.csl diff --git a/crn/KuwaharaEnzyme/simple_enzyme.jani b/Other/crn/KuwaharaEnzyme/simple_enzyme.jani similarity index 100% rename from crn/KuwaharaEnzyme/simple_enzyme.jani rename to Other/crn/KuwaharaEnzyme/simple_enzyme.jani diff --git a/crn/KuwaharaEnzyme/simple_enzyme.modest b/Other/crn/KuwaharaEnzyme/simple_enzyme.modest similarity index 100% rename from crn/KuwaharaEnzyme/simple_enzyme.modest rename to Other/crn/KuwaharaEnzyme/simple_enzyme.modest diff --git a/crn/KuwaharaEnzyme/simple_enzyme.sm b/Other/crn/KuwaharaEnzyme/simple_enzyme.sm similarity index 100% rename from crn/KuwaharaEnzyme/simple_enzyme.sm rename to Other/crn/KuwaharaEnzyme/simple_enzyme.sm diff --git a/crn/KuwaharaEnzyme/simple_enzyme_11.ivy b/Other/crn/KuwaharaEnzyme/simple_enzyme_11.ivy similarity index 100% rename from crn/KuwaharaEnzyme/simple_enzyme_11.ivy rename to Other/crn/KuwaharaEnzyme/simple_enzyme_11.ivy diff --git a/prism/toy/toy.csl b/Other/toy/toy.csl similarity index 100% rename from prism/toy/toy.csl rename to Other/toy/toy.csl diff --git a/prism/toy/toy1_combined.prism b/Other/toy/toy1_combined.prism similarity index 100% rename from prism/toy/toy1_combined.prism rename to Other/toy/toy1_combined.prism diff --git a/prism/toy/toy1_separate.prism b/Other/toy/toy1_separate.prism similarity index 100% rename from prism/toy/toy1_separate.prism rename to Other/toy/toy1_separate.prism diff --git a/prism/toy/toy2_combined.prism b/Other/toy/toy2_combined.prism similarity index 100% rename from prism/toy/toy2_combined.prism rename to Other/toy/toy2_combined.prism diff --git a/prism/toy/toy2_combined2.prism b/Other/toy/toy2_combined2.prism similarity index 100% rename from prism/toy/toy2_combined2.prism rename to Other/toy/toy2_combined2.prism diff --git a/prism/toy/toy2_combined3.prism b/Other/toy/toy2_combined3.prism similarity index 100% rename from prism/toy/toy2_combined3.prism rename to Other/toy/toy2_combined3.prism diff --git a/prism/toy/toy2_combined4.prism b/Other/toy/toy2_combined4.prism similarity index 100% rename from prism/toy/toy2_combined4.prism rename to Other/toy/toy2_combined4.prism diff --git a/prism/toy/toy2_separate.prism b/Other/toy/toy2_separate.prism similarity index 100% rename from prism/toy/toy2_separate.prism rename to Other/toy/toy2_separate.prism diff --git a/README.md b/README.md index be3c14e..5e1ecdb 100644 --- a/README.md +++ b/README.md @@ -24,72 +24,7 @@ Contains PRISM and IVy files for the reaction of the Kuwahara Enzyme. Various relevant PRISM models (mostly conversions of the SBML files in `./SBML`) that can be used to model certain properties of systems. Can be run in STORM, PRISM, or STAMINA. -## Naming Convention -* 10_10: Production and degradation of molecules in steps of 10 -* RBA: Reaction-based abstraction (remove irrelevant or rapid reactions) - -* G0: Static zero glitch - -* G1: Static one glitch - -* unb: unbound prsim models - -## Genetic Circuits - -### Circuit0x8E - -This circuit is part of the genetic circuits designed by the software tool Cello [1]. The circuit has three input arguments IPTG, aTc, and Ara and one output argument YFP. - -![Figure1](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/0x8E_Original.png "Figure 1") - -In the laboratory, circuit 0x8E showed an unexpected, glitching behavior. Further analysis resulted in two more designs of the circuit as well as the analysis of its glitching behavior [2]. - -![Figure2](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/0x8E_LogicHazardFree.png "Figure 2") - -![Figure3](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/0x8E_TwoInverter.png "Figure 3") - -There are two types of glitches. In one type, the output should remain in a low state during an input transition (Zero Glitch). In the other type, the output should remain at a high state (One Glitch) during an input transition. More information can be found in [1-2]. - -### Muller C-element - -This genetic circuit implements a state-holding gate called Muller C-element. If both inputs are high, its output goes high. If both inputs are low, the output is low. If the inputs are mixed, it retains its previous state. The three designs are the Majority, Speed_Independent, and Toggle Switch design [3]. - -![Figure4](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/Majority.png "Majority Design") - -![Figure5](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/Speed_Independent.png "Speed-Speed_Independent") - -![Figure6](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/Toggle.png "Toggle-Switch") - -### Toggle Switch - -The toggle switch is a state holding gate and consists of two promoters each followed by a coding sequence. Each promoter is repressed by the protein transcribed by the other promoter [4]. - -![Figure7](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/ToggleSwitch.png "Toggle-Switch") - -### Repressilator - -The repressilator consists of three promoters each with a repressor gene. It is a cyclic negative-feedback loop, periodically inducing the synthesis of green fluorescent proteins [5]. - -![Figure8](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/Repressilator.PNG "Repressilator") - -### Dual Feedback Oscillator - -This design is an improved version of the repressilator [6]. - -![Figure9](https://github.com/fluentverification/CaseStudies_StochasticModelChecking/blob/refactor/Figures/DualFeedback.png "Dual Feedback Oscillator") ### References - -1. Nielsen, A. A. K.; Der, B. S.; Shin, J.; Vaidyanathan, P.; Paralanov, V.; Strychalski, E. A.; Ross, D.; Densmore, D.; Voigt, C. A. Genetic Circuit Design Automation. Science 2016, 352 (6281), aac7341–aac7341. https://doi.org/10.1126/science.aac7341. - -2. Fontanarrosa, P.; Doosthosseini, H.; Borujeni, A. E.; Dorfan, Y.; Voigt, C. A.; Myers, C. Genetic Circuit Dynamics: Hazard and Glitch Analysis. ACS Synthetic Biology 2020, 15. - -3. Madsen, C.; Zhang, Z.; Roehner, N.; Winstead, C.; Myers, C. Stochastic Model Checking of Genetic Circuits. J. Emerg. Technol. Comput. Syst. 2014, 11 (3), 1–21. https://doi.org/10.1145/2644817. - -4. Gardner, T. S.; Cantor, C. R.; Collins, J. J. Construction of a Genetic Toggle Switch in Escherichia Coli. Nature 2000, 403 (6767), 339–342. https://doi.org/10.1038/35002131. - -5. Elowitz, M. B.; Leibler, S. A Synthetic Oscillatory Network of Transcriptional Regulators. Nature 2000, 403 (6767), 335–338. https://doi.org/10.1038/35002125. - -6. Stricker, J., Cookson, S., Bennett, M. et al. A fast, robust and tunable synthetic gene oscillator. Nature 456, 516–519 (2008). https://doi.org/10.1038/nature07389. diff --git a/Tools/README.md b/Tools/README.md new file mode 100644 index 0000000..592f1ea --- /dev/null +++ b/Tools/README.md @@ -0,0 +1,7 @@ +### iBioSim + +(https://github.com/MyersResearchGroup/iBioSim) + +### STAMINA + +(https://github.com/fluentverification/stamina) diff --git a/indexing/index.json b/indexing/index.json new file mode 100644 index 0000000..2489196 --- /dev/null +++ b/indexing/index.json @@ -0,0 +1,3788 @@ +[ +{ + "name":"crn" + , "type":"folder" + , "contents":[ + { + "name":"KuwaharaEnzyme" + , "type":"folder" + , "contents":[ + , { + "name":"simple_enzyme.csl" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"simple_enzyme.modest" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"simple_enzyme.jani" + , "type":"file" + , "tags":[] + , "format":"JANI" + } + , { + "name":"simple_enzyme.sm" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { 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"tags":[] + , "format":"Prism" + } + , { + "name":"Toggle_0p40.prism" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"Toggle_0p60.prism" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + ] + } + ] + } + ] + } + , { + "name":"Toggle.props" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"Toggle_10_10.sm" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"Majority_10_10.sm" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"Speed_Independent_10_10.props" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"Toggle.sm" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"Speed_Independent.props" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + ] + } + { + "name":"Toggle" + , "type":"folder" + , "contents":[ + , { + "name":"toggle_IPTG_100.prism" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"toggle_IPTG_0.csl" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"toggle_IPTG_0.prism" + , "type":"file" + , "tags":[] + , "format":"Prism" + } + , { + "name":"toggle_IPTG_100.csl" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + , { + "name":"results.txt" + , "type":"file" + , "tags":[] + , "format":"Unknown" + } + ] + } + ] +} +] diff --git a/indexing/indexer.py b/indexing/indexer.py new file mode 100755 index 0000000..da8d571 --- /dev/null +++ b/indexing/indexer.py @@ -0,0 +1,50 @@ +#!/usr/bin/env python3 + +import os + +class Formats: + PRISM = 0 + IVY = 1 + SBML = 2 + JANI = 3 + UNKNOWN = 4 + formatNames = ["Prism", "IVy", "SBML", "JANI", "Unknown"] + +o = '{' +c = '}' + +def getTags(fullPath): + return [] # TODO + +def getFormat(fileName): + if fileName.endswith(".prism") or fileName.endswith(".sm"): + return Formats.PRISM + elif fileName.endswith(".ivy"): + return Formats.IVY + elif fileName.endswith(".sbml") or fileName.endswith(".xml"): + return Formats.SBML + elif fileName.endswith(".jani"): + return Formats.JANI + return Formats.UNKNOWN + +def createJSONFromFolder(folder, indentationLevel = 0): + json = "[" + tabs = "\t" * indentationLevel + tabsExtra = f"{tabs}\t" + for f in os.listdir(folder): + if os.path.isdir(folder + '/' + f) and not f.startswith('.'): + json += f"\n{tabs}{o}\n{tabsExtra}\"name\":\"{f}\"\n{tabsExtra}, \"type\":\"folder\"\n{tabsExtra}, \"contents\":{createJSONFromFolder(folder + '/' + f, indentationLevel + 1)} \n{tabs}{c}" + elif os.path.isfile(folder + '/' + f): + tags = "" + for tag in getTags(folder + '/' + f): + tags += f"\"tag\"," + tags = f"[{tags[:len(tags) - 1]}]" + fileFormatName = Formats.formatNames[getFormat(f)] + json += f"\n{tabs}, {o}\n{tabsExtra}\"name\":\"{f}\"\n{tabsExtra}, \"type\":\"file\"\n{tabsExtra}, \"tags\":{tags}" + json += f"\n{tabsExtra}, \"format\":\"{fileFormatName}\"\n{tabs}{c}" + json += f"\n{tabs}]" + return json + +if __name__=='__main__': + print(createJSONFromFolder(os.getcwd())) + diff --git a/indexing/webpage/index.html b/indexing/webpage/index.html new file mode 100644 index 0000000..bf93d09 --- /dev/null +++ b/indexing/webpage/index.html @@ -0,0 +1,127 @@ + + + + FLUENT Verification Case Studies + + + + + + + + + +
+
 
+ +
+
+ Circuit0x8E/hazardFree.prism + Prism + Infinite + Benchmark +
+ Some information about the model here +
+
+
+
+ + + diff --git a/indexing/webpage/scripts/indexReader.js b/indexing/webpage/scripts/indexReader.js new file mode 100644 index 0000000..cf8e635 --- /dev/null +++ b/indexing/webpage/scripts/indexReader.js @@ -0,0 +1,161 @@ +const indexLocation = "../../index.json" + +// Get the index +// let index = require(indexLocation); +let index = []; + +function loadSuggestions() { + let mySuggestions = []; + // Suggestions are all of the names + index.forEach(el => { + mySuggestions[mySuggestions.length] = el["name"]; + }) + return mySuggestions; +} + +function loadTags() { + let tags = []; + index.forEach(el => { + el["tags"].forEach(tag => { + tags[tags.length] = tag; + }); + }); + return tags; +} + +// TODO: this suggestions array needs to be populated with actual suggestions + +let suggestions = [ + "foo" + , "bar" + , "baz" + , "foobar" + , "foobaz" + , "fun" + , "zedd" + , "case" + , "never" + , "gonna" + , "give" + , "you" + , "up" +]; + +let tagSuggestionsArray = [ + "foo" + , "bar" + , "baz" + , "foobar" + , "foobaz" + , "fun" + , "zedd" + , "case" + , "never" + , "gonna" + , "give" + , "you" + , "up" +]; + +const usedTags = new Set(); + +function hideAllSuggestions() { + // console.log("hiding all suggestions"); + let querySuggestions = document.getElementById('query-suggestions'); + let tagSuggestions = document.getElementById('tag-suggestions'); + querySuggestions.innerHTML = ""; + tagSuggestions.innerHTML = ""; + querySuggestions.style.display = "None"; + tagSuggestions.style.display = "None"; +} + +/* Query Suggestions */ + +function showSuggestions() { + let queryText = document.getElementById('query'); + let querySuggestions = document.getElementById('query-suggestions'); + let currentQuery = queryText.value.toLowerCase(); + querySuggestions.innerHTML = ""; + querySuggestions.style.display = "None"; + if (currentQuery.length == 0) { return; } + if (suggestions.length > 0) { querySuggestions.style.display = "Block"; } + suggestions.forEach(s => { + let locationIndex = s.indexOf(currentQuery) + if (locationIndex >= 0 && s != currentQuery) { + querySuggestions.innerHTML += "
" + s + "
"; + // console.log(s); + } + // else { + // console.log("Omitting " + s + " since query is " + currentQuery); + // } + }); +} + +function acceptSuggestion(suggestion) { + let queryText = document.getElementById('query'); + queryText.value = suggestion; + showSuggestions(); +} + +/* Tag suggestions */ + +function showTagSuggestions() { + let tagText = document.getElementById('tags'); + let tagSuggestions = document.getElementById('tag-suggestions'); + let currentTag = tagText.value.toLowerCase(); + tagSuggestions.innerHTML = ""; + tagSuggestions.style.display = "None"; + if (currentTag.length == 0) { return; } + if (suggestions.length > 0) { tagSuggestions.style.display = "Block"; } + tagSuggestionsArray.forEach(s => { + if (usedTags.has(s)) { + return; + } + let locationIndex = s.indexOf(currentTag) + if (locationIndex >= 0 && s != currentTag) { + tagSuggestions.innerHTML += "
" + s + "
"; + } + }); +} + +function tagKeyPressHandler(event) { + if (event.keyCode == 13) { + createTag(document.getElementById('tags').value); + } +} + +function createTag(suggestion) { + let tagText = document.getElementById('tags'); + tagText.value = ""; + if (usedTags.has(suggestion)) { + // alert("Tag '" + suggestion + "' exists!"); + hideAllSuggestions(); + return; + } + usedTags.add(suggestion); + let tagList = document.getElementById('tags-box'); + tagList.innerHTML += "" + suggestion + ""; + showTagSuggestions(); +} + +function deleteTag(tag) { + document.getElementById('tag-' + tag).remove(); + usedTags.delete(tag); +} + +function queryKeyPressHandler(event) { + if (event.keyCode == 13) { + search(); + } +} + +function search() { + alert("Search not implemented yet!"); + // TODO +} + +function clearAllTags() { + let tagList = document.getElementById('tags-box'); + tagList.innerHTML = ""; + usedTags.clear(); +} diff --git a/indexing/webpage/scripts/scripts.js b/indexing/webpage/scripts/scripts.js new file mode 100644 index 0000000..f2c1211 --- /dev/null +++ b/indexing/webpage/scripts/scripts.js @@ -0,0 +1,51 @@ +let advancedVisible = false; +let navExpanded = false; + +function toggleAdvanced() { + if (advancedVisible) { + document.getElementById("advanced").classList.remove("visible"); + document.getElementById("toggle-advanced").classList.remove("toggled"); + } + else { + document.getElementById("advanced").classList.add("visible"); + document.getElementById("toggle-advanced").classList.add("toggled"); + } + advancedVisible = !advancedVisible; +} + +function toggleNavbar() { + if (!navExpanded) { + console.log("Expanding navbar"); + document.querySelectorAll(".navlink").forEach(a => a.classList.add('navlink-expanded')); + document.getElementById("toggle-nav").innerHTML = "×"; + } + else { + console.log("Retracting navbar"); + document.querySelectorAll(".navlink").forEach(a => a.classList.remove('navlink-expanded')); + document.getElementById("toggle-nav").innerHTML = "☰"; + } + navExpanded = !navExpanded; +} + +function setDarkMode() { + var rt = document.querySelector(":root"); + rt.style.setProperty("--color", "#eeeeee"); + rt.style.setProperty("--background", "#212121"); + +} + +function setLightMode() { + var rt = document.querySelector(":root"); + rt.style.setProperty("--color", "#444444"); + rt.style.setProperty("--background", "#ffffff"); +} + +function setDarkOrLightMode() { + var darkMode = document.getElementById("dark-light").checked; + if (darkMode) { + setDarkMode(); + } + else { + setLightMode(); + } +} diff --git a/indexing/webpage/styles/styles.css b/indexing/webpage/styles/styles.css new file mode 100644 index 0000000..a8ab312 --- /dev/null +++ b/indexing/webpage/styles/styles.css @@ -0,0 +1,346 @@ +@import url('https://fonts.googleapis.com/css2?family=Quicksand:wght@400;700&display=swap'); + +:root { + --accent: #1370c1; + --accent-light: #40aef3; +} + +@media (prefers-color-scheme: light) { + :root { + --background: #ffffff; + --color: #444444; + } +} + +@media (prefers-color-scheme: dark) { + :root { + --background: #212121; + --color: #eeeeee; + } +} + + +body { + font-family: 'Quicksand', sans-serif; + color: var(--color); + background-color: var(--background); + transition: all 200ms ease; +} + +a { + text-decoration: none; + color: var(--accent); +} + +a:hover { + color: var(--accent-light); +} + +#navbar { + position: fixed; + width: 100%; + display: block; + top: 0px; + left: 0px; + background-color: var(--accent); + color: var(--background);; + z-index: 500; +} + +#navbar a { + color: white; + text-decoration: none; + padding: 15px; + display: inline-block; + border-bottom: 4px solid var(--accent); + border-top: 4px solid var(--accent); + transition: all 200ms ease; +} + +#navbar a:hover { + border-bottom: 4px solid #abe6ff; + color: #abe6ff; +} + +#logo { + font-weight: bold; +} + +#top-buffer { + height: 70px; +} + +#search input[type="text"], #search select { + border: none; + border-bottom: 1px solid #cccccc; + padding: 10px; +/* border-radius: 20px; */ + padding-left: 30px; + padding-right: 30px; + margin-bottom: 20px; + background-color: var(--background);; + color: var(--color); +} + +#search input[type="text"] { + width: calc(100% - 65px); +} + +#contents { + padding-left: 10%; + padding-right: 10%; +} + +#results, .results { +/* border: 1px solid #7d7d7d; */ + display: block; + padding: 10px 0px 10px 0px; + border-radius: 25px; + height: 80%; + position: relative; +} + +.result { + background-color: var(--background); + display: inline-block; + width: calc(100% - 40px); +/* border: 1px solid #7d7d7d; */ +/* border-radius: 25px; */ + padding: 20px; + margin-bottom: 20px; +} + +.result .result-title { + display: inline-block; + width: 100%; + font-weight: bold; + padding-bottom: 10px; + padding-top: 10px; +} + +.result-info { + padding-top: 10px; +} + +.tag { + display: inline-block; +/* border-radius: 20px; */ + background-color: var(--accent); + color: white; + padding: 3px; +/* padding-left: 20px; + padding-right: 20px;*/ + padding-left: 10px; + padding-right: 10px; + transition: all 200ms ease; + cursor: pointer; + font-size: 14px; + margin-right: 5px; +} + +.tag:hover { + color: var(--accent); + border: 1px solid var(--accent); + background-color: var(--background);; +} + +#footer { + background-color: #cccccc22; + position: absolute; + display: block; + left: 0px; + margin: 0px; + margin-top: 30px; + padding: 50px; + padding-left: 20%; + padding-right: 20%; + width: 60%; /*calc(100% - 100px);*/ + font-size: 9pt; +} + +label.hidden { + display: none; +} + +#toggle-advanced { + display: block; +/* width: 100%; */ +/* border-bottom: 2px solid var(--accent); */ + margin-bottom: 10px; +/* margin-left: 20px; */ + padding: 0px 10px 0px 10px; + cursor: pointer; + position: relative; + right: 0px; +} + +#toggle-advanced:before { + content: '\2B9F'; + padding-right: 10px; + color: var(--accent); +} + +#toggle-advanced:hover { + color: var(--accent); +} + +#toggle-advanced.toggled:before { + content: '\2B9D'; +} + +#advanced { + overflow-y: hidden; + height: 0px; + transition: all 400ms ease; +} + +#advanced.visible { + height: auto; +} + +/* Checkbox stuff */ +input[type=checkbox] { + visibility: hidden; +} +.checkbox-styled { + width: 45px; + height: 15px; + border: 1px solid #888888; + margin: 20px 10px; + position: relative; + border-radius: 12px; + display: inline-block; +} +.checkbox-styled label { + display: block; + width: 24px; + height: 24px; + border-radius: 50%; + transition: all .5s ease; + cursor: pointer; + position: absolute; + top: -5px; + left: -3px; + background: #888888; +} +.checkbox-styled input[type=checkbox]:checked + label { + left: 27px; + background: var(--accent); +} + +.check-label { + display: inline-block; + width: calc(100% - 100px); +} + +.column-half { + display: inline-block; + width: 49%; + position: relative; + top: 0px; +} + +/* Search suggestions */ + +.suggestions { + display: none; + border: 1px solid #cccccc; + border-top: 1px solid var(--background); +/* box-shadow: 0px 8px 7px var(--background); ALT: #ebebeb55; */ + padding-left: 30px; + padding-right: 30px; + position: absolute; + background-color: var(--background); + z-index: 5; + width: 70%; +/* border-radius: 0px 0px 20px 20px; */ +} + +.suggestion { + padding: 10px; + cursor: pointer; + color: var(--color); + border-bottom: 1px solid var(--background); +} + +.suggestion:hover { + border-bottom: 1px solid var(--accent); + color: var(--accent); +} + +#query-suggestions { + top: 199px; +} + +#tag-suggestions { + top: 314px; +} + +/*.search-button { + position: absolute; + top: 170px; + left: 200px; +}*/ +.search-button:hover, .icon-overlay:hover { + color: var(--accent); +} + +.icon-overlay, .search-button { + cursor: pointer; + display: block !important; + position: relative; + z-index: 2; + top: -50px; + width: 20px; + margin-left: 5px; +} + +.deletable:before { + content: '\1F5D9'; + padding-right: 10px; +} + +#clear-tags:hover { +/* width: 100px; */ + font-family: 'Quicksand', sans-serif; +/* color: var(--background);; */ +/* color: #c10541; */ +/* padding: 10px; */ +} + +#clear-tags:hover:before { + content: '\1F5D9'; +} + +/* Navbar adaptivity */ + +.navlink, .full-width { + cursor: pointer; + transition: all 300ms ease; + color: var(--color); + text-align: center; +} + +#navbar .full-width { +/* float: right; */ + width: 100%; + display: none; +} + + +@media screen and (max-width: 900px) { + #navbar .navlink { + display: none; + height: 0px; + width: 100%; + } + + #navbar .navlink-expanded { + display: block !important; + height: auto; + } + + #navbar .full-width { + display: inline-block; + } +} diff --git a/spec.ver b/spec.ver new file mode 100644 index 0000000..5cfc9ee --- /dev/null +++ b/spec.ver @@ -0,0 +1 @@ +current specification version diff --git a/tags.txt b/tags.txt new file mode 100644 index 0000000..69bf5ea --- /dev/null +++ b/tags.txt @@ -0,0 +1,5 @@ +Contrived +Unbounded Models/Massive Models +Bounded Models +Challenging Models +Low probability events