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bad-ants-fleet committed Sep 25, 2017
1 parent 117b137 commit 1d968d796686e3bcd83d5330356c15b4c02cf46e
Showing with 92 additions and 82 deletions.
  1. +17 −3 README.md
  2. +1 −1 docs/compiler.rst
  3. +4 −4 docs/index.rst
  4. +1 −1 docs/objects.rst
  5. +2 −1 docs/tlstutorial.rst
  6. +67 −72 nuskell/objects.py
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@@ -19,7 +19,11 @@ of an ODE system to simulate the dynamics of the compiled DSD network.
Implement a formal CRN using a particular translation-scheme:
```
$ echo "A + B <=> X + Y; X -> A" | nuskell --ts scheme.ts [options]
$ echo "A + B <=> X + Y; X -> A" | nuskell --ts scheme.ts --verify modular-bisimulation
```
for options see:
```
$ nuskell --help
```
## Translation Schemes
Detailed information about translation schemes can be found in the ``/schemes`` directory.
@@ -28,10 +32,13 @@ Detailed information about translation schemes can be found in the ``/schemes``
```
$ python setup.py install
```
or
```
$ python setup.py install --user
```
## Documentation
A preview of the documentation for the first official release v1.0 can be found
at: [documentation].
A preview of the documentation for release v1.0 can be found at: [documentation].
## Version
0.5
@@ -46,7 +53,14 @@ at: [documentation].
### License
MIT
## Cite
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
[Badelt et al. (2017)]: <https://doi.org/10.1007/978-3-319-66799-7_15>
[Grun et al. (2014)]: <https://arxiv.org/abs/1505.03738>
[Shin et al. (2014)]: <http://dna.caltech.edu/DNAresearch_publications.html#PathwayDecomposition>
[Johnson et al. (2016)]: <http://dna.caltech.edu/DNAresearch_publications.html#CRN-Bisimulation>
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@@ -2,5 +2,5 @@ nuskell.compiler
==========================
.. automodule:: nuskell.compiler
:members: translate, printCRN, InvalidSchemeError
:members: translate, genCRN, InvalidSchemeError
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@@ -39,7 +39,7 @@ underlying the Nuskell library. More details can be found in the publications
cited below.
**Cite:**
* Nuskell: Badelt et al. (accepted manuscript)
* Nuskell: `Badelt et al. (2017)`_
* CRN bisimulation: `Johnson et al. (2016)`_
* Peppercornenumerator: `Grun et al. (2014)`_
* Pathway decomposition equivalence: `Shin et al. (2014)`_
@@ -350,7 +350,7 @@ Developer Guidelines
In order to ensure sustainability of the Nuskell compiler package, there
are a few rules for developers before submitting a pull request.
* **Use Google docstring format** `[Google Dochstring Guidelines] <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_
* **Use Google docstring format** `[Google Docstring Guidelines] <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_
The Nuskell `repository`_ can be found on ``GitHub``:
@@ -361,8 +361,8 @@ https://github.com/DNA-and-Natural-Algorithms-Group/nuskell
.. _peppercornenumerator: https://github.com/DNA-and-Natural-Algorithms-Group/peppercornenumerator
.. _crnsimulator: https://github.com/bad-ants-fleet/crnsimulator
.. .. _Badelt et al. (2017):
.. _Grun et al. (2014): https://arxiv.org/abs/1505.03738
.. _Badelt et al. (2017): http://dna.caltech.edu/DNAresearch_publications.html#NuskellCompiler
.. _Grun et al. (2014): http://dna.caltech.edu/DNAresearch_publications.html#Peppercorn
.. _Shin et al. (2014): http://dna.caltech.edu/DNAresearch_publications.html#PathwayDecomposition
.. _Johnson et al. (2016): http://dna.caltech.edu/DNAresearch_publications.html#CRN-Bisimulation
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@@ -4,6 +4,6 @@ nuskell.objects
API documentation of the nuskell.objects library
.. automodule:: nuskell.objects
:members: TestTube, TestTubeIO, Complex, Domain, Reaction
:members: TestTube, TestTubeIO, NuskellComplex, NuskellDomain, NuskellReaction
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@@ -238,6 +238,8 @@ to design fuel complexes specific for a reaction of formal species.
# Translate formal reactions with two reactants and two products.
# Lakin et. al (2012) "Abstractions for DNA circuit design." [Figure 5]
# -----------------------------------------------------------------------------
#
# Coded by Stefan Badelt (badelt@caltech.edu)
# Define a global short toehold domain
global toehold = short();
@@ -268,7 +270,6 @@ to design fuel complexes specific for a reaction of formal species.
else
bimol_fuels(r.reactants, r.products);
# Coded by Stefan Badelt (badelt@caltech.edu)
# Write the module *main* that applies *rxn* to the crn.
module main(crn) = sum(map(rxn, crn))
where crn = irrev_reactions(crn);
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