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crnverifier-0.3
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مشاهده بیشترتوضیحات
Verify the equivalence of chemical reaction networks (CRNs), or the correctness of an implementation CRN with respect to a formal CRN.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | crnverifier-0.3 |
| نام | crnverifier |
| نسخه کتابخانه | 0.3 |
| نگهدارنده | ['Stefan Badelt'] |
| ایمیل نگهدارنده | ['bad-ants-fleet@posteo.eu'] |
| نویسنده | Stefan Badelt, Seung Woo Shin, Robert Johnson, Qing Dong, Erik Winfree |
| ایمیل نویسنده | - |
| آدرس صفحه اصلی | http://www.github.com/DNA-and-Natural-Algorithms-Group/crnverifier/ |
| آدرس اینترنتی | https://pypi.org/project/crnverifier/ |
| مجوز | MIT |
# CRN verification module
Are two chemical reaction networks (CRNs) the same? This package provides code
to verify the correctness of an implementation CRN with respect to a formal CRN
using the stochastic
trajectory equivalence notions **CRN bisimulation** [[Johnson et al. (2019)]],
**pathway decomposition** [[Shin et al. (2019)]] and preliminary implementations of
**compositional & integrated hybrid** [[Shin et al. (2019)]].
[](https://github.com/DNA-and-Natural-Algorithms-Group/crnverifier/tags)
[](https://github.com/DNA-and-Natural-Algorithms-Group/crnverifier/releases)
[](https://badge.fury.io/py/crnverifier)
[](https://opensource.org/licenses/MIT)
[](https://travis-ci.com/github/DNA-and-Natural-Algorithms-Group/crnverifier)
[](https://codecov.io/gh/DNA-and-Natural-Algorithms-Group/crnverifier)
### Installation
```
$ python setup.py install
```
### Library examples
The following verification functions are currently available:
```py
from crnverifier import (pathway_decomposition_eq,
crn_bisimulation_test,
modular_crn_bisimulation_test,
integrated_hybrid_test,
compositional_hybrid_test)
from crnverifier.utils import parse_crn
# A formal CRN and a corresponding implementation CRN
fcrn = "A -> B"
icrn = "a1 -> b1; x -> a1; x -> b1; y -> b1; y -> a1; x -> a0; a0 -> a1"
# A quick interface to the internal list representation of CRNs,
# the first CRN contains only formal species (fs), the species
# of the second CRN are not important right now.
fcrn, fs = parse_crn(fcrn, is_file = False)
icrn, _ = parse_crn(icrn, is_file = False)
# Verify whether the two CRNs are pathway decomposition equivalent
# given the formal species fs:
v = pathway_decomposition_eq([fcrn, icrn], fs)
print(v)
# For the other notions, we may need a (partial) interpretation:
inter = {'a0': 'A',
'a1': 'A',
'b1': 'B'}
# Test if there exists a correct CRN bisimulation that interprets
# the reactions of icrn as reactions of fcrn.
# The (partial) interpretation is optional here.
v, i = crn_bisimulation_test(fcrn, icrn, fs, interpretation = inter)
print(v, i)
# Verify whether icrn is a correct implementation of fcrn using the
# two supported hybrid notions.
# The (partial) interpretation is required here.
v, i = integrated_hybrid_test(fcrn, icrn, fs, inter)
print(v, i)
v, i = compositional_hybrid_test(fcrn, icrn, fs, inter)
print(v, i)
```
### Commandline examples
For the format *.crn files, see [crnsimulator].
Verify whether two CRNs f.crn and i.crn are pathway decomposition equivalent:
```
$ crnverifier pathway-decomposition --crns f.crn i.crn --formal-species A B C
```
Compute the formal basis of a single CRN:
```
$ crnverifier formal-basis --crn i.crn --formal-species A B C
```
Verify whether a correct CRN bisimulation exists to interpret *i.crn* as *f.crn*:
```
$ crnverifier crn-bisimulation --formal-crn f.crn --implementation-crn i.crn
```
For options, e.g. to provide a partial interpretation, or to choose a more
suitable algorithm for the permissive condition, use
```
$ crnverifier --help
```
Verify whether *i.crn* is a correct implementation of *f.crn* using the two supported hybrid notions.
```
$ crnverifier integrated-hybrid --formal-crn f.crn --implementation-crn i.crn --interpretation itof.crn
$ crnverifier compositional-hybrid --formal-crn f.crn --implementation-crn i.crn --interpretation itof.crn
```
## Version
0.3
## License
MIT
## Cite
The equivalence notions:
- Seung Woo Shin, Chris Thachuk, and Erik Winfree (2019)
"Verifying chemical reaction network implementations: A pathway decomposition approach"
[[Shin et al. (2019)]].
- Robert F. Johnson, Qing Dong, and Erik Winfree (2019)
"Verifying chemical reaction network implementations: A bisimulation approach"
[[Johnson et al. (2019)]].
The implementation (a part of the [Nuskell] compiler project):
- Stefan Badelt, Seung Woo Shin, Robert F. Johnson, Qing Dong, Chris Thachuk, and Erik Winfree (2017)
"A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities"
[[Badelt et al. (2017)]].
[//]: References
[Shin et al. (2019)]: <https://doi.org/10.1016/j.tcs.2017.10.011>
[Johnson et al. (2019)]: <https://doi.org/10.1016/j.tcs.2018.01.002>
[Badelt et al. (2017)]: <https://doi.org/10.1007/978-3-319-66799-7_15>
[Badelt et al. (2020)]: <https://doi.org/10.1098/rsif.2019.0866>
[Nuskell]: <https://www.github.com/DNA-and-Natural-Algorithms-Group/nuskell>
[crnsimulator]: <https://www.github.com/bad-ants-fleet/crnsimulator>
نیازمندی
| مقدار | نام |
|---|---|
| - | pyparsing |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.8 | Python |
نحوه نصب
نصب پکیج whl crnverifier-0.3:
pip install crnverifier-0.3.whl
نصب پکیج tar.gz crnverifier-0.3:
pip install crnverifier-0.3.tar.gz