Artur Meski
56218a3596
some cleanup
2016-12-27 20:57:02 +01:00
Artur Meski
11a2d2ae46
imports
2016-12-27 19:45:07 +01:00
Artur Meski
be3e506cbe
ltl formulae
2016-12-18 18:08:21 +01:00
Artur Meski
7dfc02f613
some log files
2016-09-24 15:50:55 +02:00
Artur Meski
f4528fb287
finalised version used for UCNC2016 experiments
2016-03-22 21:34:37 +01:00
Artur Meski
586e085a80
cleanup: examples
2016-03-22 21:33:04 +01:00
Artur Meski
3780be1fa4
Brought back 'dec' entity
2016-03-10 15:00:35 +01:00
Artur Meski
270c0c86ed
get_max_concentration_level function
2016-03-10 15:00:28 +01:00
Artur Meski
b71e749c53
Meta reactions are enabled only if no ordinary reaction is
2016-03-10 14:59:48 +01:00
Artur Meski
a0e4dc9fe1
Minor changes to the experiments. Changed the .sh cases to be verified (only even values).
2016-03-10 12:37:23 +01:00
Artur Meski
781777ac56
Production of the maximal concentration
...
When multiple reactions are enabled, we produce the maximal concentration by exploiting the fact that reactions are sorted (increasing order). We build the encoding starting from the inner-most reaction (with the lowest concentration level), and then build around that reaction encoding for the reactions with higher concentration levels. This allows us to avoid the disjunctions of possible resulting concentractions. E.g. (x==1 v x==3 v x==7), while we should have only x==7.
2016-03-10 12:33:32 +01:00
Artur Meski
a6aa5e4590
Sorting reactions in the increasing order
...
(per produced entity's concentration level)
2016-03-10 12:30:14 +01:00
Artur Meski
2387e8ad26
Minor modifications
2016-03-07 21:29:02 +01:00
Artur Meski
3a6d771f04
cosmetics... again :)
2016-03-05 00:08:32 +01:00
Artur Meski
7b2f29c9ec
Reachability testing with properties specified with required and blocking entities.
...
Required entitied correspond to reactants, while blocking entities to inhibitors.
This functionality replaces 'exact' state encoding.
2016-03-04 23:51:53 +01:00
Artur Meski
9f3af0b48c
HSR. Translation of properties RSC->RS. Testing with RS and RSC (cmdline args).
2016-03-04 23:50:38 +01:00
Artur Meski
ef1b769654
Translation for permanency (RSC -> RS)
2016-03-04 23:48:28 +01:00
Artur Meski
5d65b4fac2
Added colour.py file
2016-03-04 20:52:30 +01:00
Artur Meski
dc482781e2
Output cosmetics
2016-03-04 20:52:02 +01:00
Artur Meski
45b6db12c4
Pretty printing
2016-03-04 15:10:10 +01:00
Artur Meski
5aec7d8df5
HSR + cosmetics
2016-03-03 16:11:09 +01:00
Artur Meski
ec8e5d1b7d
Fixed permanency encoding: And->Or.
2016-03-03 14:35:47 +01:00
Artur Meski
a2d4912d2e
cleanup
2016-03-03 12:39:28 +01:00
Artur Meski
c686317e16
Use enc_state_with_blocking() for HSR
2016-03-03 12:32:14 +01:00
Artur Meski
7907c0216b
Added the enc_state_with_blocking() function
...
This allows to specify reactants and inhibitors in the provided state.
2016-03-03 12:31:12 +01:00
Artur Meski
a869ed25cb
remove __pycache__
2016-03-03 09:25:34 +01:00
Artur Meski
975c01edea
Heat Shock Response
2016-03-03 09:22:33 +01:00
Artur Meski
063e8063cc
Moved "Next level?" to after we check max_level
2016-03-03 06:54:41 +01:00
Artur Meski
1746bf86c8
still trying with glucose assimilation...
2016-03-02 22:12:50 +01:00
Artur Meski
561413b79f
expire_sugar entity
2016-03-02 18:18:36 +01:00
Artur Meski
e879740162
Removal of the log files.
2016-03-02 18:10:47 +01:00
Artur Meski
02606e32bf
Permanency encoding. Allows preserving concentration levels for a specified entity. Permanency can also be inhibited.
2016-03-02 18:09:07 +01:00
Artur Meski
6ab5304628
Permanent entities implementation. Allows for preserving concentration levels when the inhibitors are not provided.
2016-03-02 18:08:07 +01:00
Artur Meski
3f3690c861
working on Blood-Glucose example
2016-03-01 21:25:34 +01:00
Artur Meski
0137a20867
simplify
2016-02-29 08:35:49 +01:00
Artur Meski
249e8ca594
Just to be sure...
2016-02-28 22:57:37 +01:00
Artur Meski
ef6f2edd33
Incrementation & decrementation by a specified value.
2016-02-28 20:12:43 +01:00
Artur Meski
8a739b0760
Resources reporting. Chain reaction benchmark, etc.
2016-02-24 22:49:40 +01:00
Artur Meski
9c7cbc74f7
Benchmarks. Resources reporting, etc.
2016-02-24 22:49:02 +01:00
Artur Meski
b21a0cee48
Translation RSC->RS for meta-reactions.
2016-02-21 14:55:48 +01:00
Artur Meski
060f5dc1f5
Meta-reactions
2016-02-20 23:35:08 +01:00
Artur Meski
1f5938ba96
Translation RSC -> RS. CA translation - to be done.
2016-02-19 18:19:50 +01:00
Artur Meski
9e025c2c9a
Implementation of reachability testing for RSC using SMT. Intitially tested version. No known issues.
2016-02-17 21:41:43 +01:00
Artur Meski
8853589ff8
Transitioning boolean variables to integer variables in the SMT encoding.
2016-02-16 21:57:55 +01:00
Artur Meski
6018df00d8
SMT for RSC. Initial commit with the stub class.
2016-02-16 20:34:17 +01:00
Artur Meski
9245546d3d
Reaction Systems with Concentrations. Context Automaton class.
2016-02-14 20:25:07 +01:00
Artur Meski
6aaca2ba27
ReactionSystemsWithConcentration. Backup
2016-02-14 16:08:37 +01:00
Artur Meski
7d6a48d2c2
bitctr
2016-02-13 23:41:53 +01:00
Artur Meski
6f86bc0e2a
rs_examples.py
2016-02-13 19:32:40 +01:00
Artur Meski
7cf71c8a22
Messing things up
2016-02-13 19:32:08 +01:00
