mdhelgen/evodevo

version 2.0

evodevo's Issues

Consider moving memory objects from heap to stack

No memory leaks exist, but many objects are allocated to the heap in a non dynamic manner, and could be moved to the stack.

Clean up CustomInteractions logic

The CustomInteraction classes have confusing logic in their getEffect virtual methods.

Prevent scoring/graphing of DNA

DNA data currently does not display any interesting info, so the time spent calculating a score or displaying a graph of the data is wasted.

Either overload DNA::getScore and short circuit DerivGraph::outputDataPlot, or modify the DNA data to show effective transcription rates

Add option to toggle DNA binding site steady state assumption

The DNA binding model uses the steady state assumption (Goodwin term) G = 1/ 1+kf/kr [R]^n, which is derived from differential equations describing the binding state of the DNA.

An idea would be to allow choosing between the steady state assumption and direct modeling of the binding state by the differential equations.

Promoter Rate Changes

Allow the forward and reverse rates of binding to be changed by forward or reverse rates.

These exist already:
int PromoterBind::kf int PromoterBind::kr

Create:

PromoterBind::setRevRate(float)```
(Forward rate > reverse rate)

Complexation Interaction Pairs

Eliminate the nodeID's from the Complexation Interaction constructors, and make use of the PairArcID and a simple utility function to get the pair's source(or target)

Verify Goodwin Oscillation

Goodwin ocsillations were observed in a Single-PTM feedback loop (DNA -> mRNA -> P1 -> PTM(P1) -> (DNA repression)) with a hill coefficient of 1, which was unexpected.

The interaction code for transcription, translation, forward/reverse ptm, and protein-promoters should be checked for any errors.

Dampening Scoring

Add a scoring function to assess whether an oscillation is dampened / stable.

Clean and Simplify Mutation Code

The selection of random molecules or interactions for action in most mutations should be cleaned up.

The molecules/interactions available for each selection should also be checked for completeness.
For example, DerivGraph::ForwardRateChange() only selects from the Translation and ForwardComplexation interaction lists, but does not select from ForwardPTM interactions, as they were implemented after the ForwardRateChange method

Complexation Rate Changes

If a forward rate or reverse rate for a particular complexation interaction is modified, the corresponding rate for the other molecule in the complexation interaction should also be changed.