Handling nodes without incoming edges in bool models

Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference

GNU General Public License v3.0

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Handling nodes without incoming edges in bool models #17

Closed amoghpj closed 5 years ago

amoghpj commented 5 years ago

There are two issues:

[x] The script needs to be modified to accept a list of input states to handle inputs to simulations. This will need some work.
[x] Currently, the script adds a self edge to nodes without any incoming edge. The user should be notified of which nodes are being handled in this manner. (Fixed in https://github.com/Murali-group/BoolODE/commit/2913a8ee8a94f102241ab76ade9f9a4be86abc40)

tmmurali commented 5 years ago

Shouldn't a node without an incoming edge be an input to the model?

amoghpj commented 5 years ago

Yes, I will have to treat them as parameters specifying the input combinations used in the original publication. These will be specified in a separate text file. I will add this functionality tomorrow.

tmmurali commented 5 years ago

Good. Then you do not need to add self loops on these nodes, do you, or are these self loops important for the ODE model?

amoghpj commented 5 years ago

The self loop was a hack to handle inputs. This behavior is retained if no input file is specified.

Commit https://github.com/Murali-group/BoolODE/commit/702ffc3efee1da7ea2920bb5aaff5f6a5cb31160 fixes this. Adds functionality to specify initial conditions as well as model inputs.