Merge pull request #1 from ADDALemos/gh-pages

All in one

_config.yml

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+title: Repairing Boolean Networks using ASP
+description: 
+google_analytics: 
+show_downloads: true
+theme: jekyll-theme-cayman
+
+gems:
+  - jekyll-mentions

index.md

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+# Abstract 
+***
+Bla
+
+***
+# How to run the project
+
+`./Converter type [asynchronous|synchronous|steady_state] repair[e|i|g|combinations] examples/Model.net [examples/Obs1.obs examples/Obsn.obs]`
+This will generate the repair models in the examples folder.
+
+## Arguments of the program
+### Type:
+
+If the model is asynchronous, synchronous or is in steady state.
+
+### Available repair operations:
+
+* Repair e - removes regulator
+* Repair i - negates a regulator
+* Repair g - changes AND function to OR function
+
+Note: All the combinations of repairs are allowed, and they need to be written in alphabetical order.
+
+Some examples with small networks are available in the folder: `examples/steady/repairs`, showing the effects of the repair operations.
+
+### Model
+
+The model has to be encoded in Boolsim ([format](http://www.colomoto.org/formats/boolsim.html)). 
+
+### Experimental values
+
+The program can deal with 0 or more observations. The observations correspond to a time-series and the time-series is organized in a matrix. As this argument is optional when not present the program will infer the data to minimize the number of repair operations needed.
+
+
+***
+# Dependencies
+An ASP solver (contained in the source folder) and available at:
+
+[clingo](https://github.com/potassco/clingo)
+
+Uses the Quince McCluskey algorithm available at:
+
+[Quine-McCluskey](https://github.com/pfpacket/Quine-McCluskey) (to compile requires the Boost C++ Libraries) [boost.org](http://www.boost.org/)
+
+***
+## Data Sets
+### Steady State
+In the folder `examples/steady/ecoli` two data sets originally obtained from  are available.
+As the model did not have functions associated with them, all nodes are explained by the same function, where a biological component is present if it has at least one activator and has no inhibitors.
+### Time-series
+The data sets in the folder `examples/time` were randomly generated using the program available on the folder scripts. The model was generated using the script available at [BoolNetR2GINsim](https://github.com/ptgm/BoolNetR2GINsim).
+***
+# Authors
+Alexandre Lemos, [Pedro T. Monteiro](http://pedromonteiro.org/) and [Inês Lynce](http://sat.inesc-id.pt/~ines/).
+# Contacts:
+If you have any comments or questions, please [contact us](mailto:[email protected];[email protected];[email protected];?subject=[Repairing%20Boolean%20regulatory%20networks]).
+
+# Previous Work
+[Repairing Steady State Boolean Regulatory Network](http://web.ist.utl.pt/~alexandre.lemos/rbn/)