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37 Open 56 Closed
37 Open 56 Closed
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Issues list

Non-mutated fittest networks still disappearing bug
#96 opened Nov 17, 2015 by Treblesteph
@Treblesteph
Make an additional fitness cost to clustering (niching), so population remains diverse. enhancement GA specific
#94 opened May 28, 2015 by Treblesteph
@Treblesteph
Problem encountered when trying to add isequal method for Network bug
#93 opened May 28, 2015 by Treblesteph Maternity leave
@Treblesteph
Fitness keeps jumping up in new, faster version of code. bug
#92 opened May 28, 2015 by Treblesteph Maternity leave
@Treblesteph
2
Slow running in parallel. help wanted Runtime optimisation
#91 opened Apr 28, 2015 by Treblesteph
@Treblesteph
Fitness not going down when running in parallel. bug help wanted
#90 opened Apr 28, 2015 by Treblesteph Maternity leave
@Treblesteph
1
Concentration time series plots for genes 3 and 4 might come out wrongly... bug
#89 opened Apr 13, 2015 by Treblesteph
@Treblesteph
Perhaps I should be calculating the harmonic mean over days for overall fitness.
#88 opened Apr 13, 2015 by Treblesteph
@Treblesteph
Don't run simulation following crossover between identical parents Runtime optimisation
#87 opened Apr 13, 2015 by Treblesteph
@Treblesteph
Possible bug - when mutations were switched off, crossovers did not seem to function. bug GA specific
#86 opened Apr 12, 2015 by Treblesteph
@Treblesteph
Mutations only happen to one thing at a time - this is not the desired behaviour enhancement GA specific
#84 opened Apr 12, 2015 by Treblesteph
@Treblesteph
Running evolved networks in continuous time after they have been evolved in boolean system. enhancement
#83 opened Apr 2, 2015 by Treblesteph
@Treblesteph
1
Check that semi-continuous method is valid alternative.
#82 opened Apr 2, 2015 by Treblesteph
@Treblesteph
Give networks with environmental noise more time to converge to clocks. bug
#81 opened Apr 2, 2015 by Treblesteph Maternity leave
@Treblesteph
1
Save fittest network to a file every 100 generations (and overwrite) in case evo takes ages. enhancement Runtime optimisation
#79 opened Mar 26, 2015 by Treblesteph Maternity leave
@Treblesteph
Parallel code is using ~30GB RAM - need to delete timeseries when finished with. Runtime optimisation
#77 opened Mar 26, 2015 by Treblesteph
@Treblesteph
Get rid of non-clocks (fitness >=0.1) in data collection function from make_troein_fig2
#76 opened Mar 26, 2015 by Treblesteph
@Treblesteph
Read about differences in limitations of behaviours modelled with boolean vs ode models.
#75 opened Mar 25, 2015 by Treblesteph
@Treblesteph
Make function to count circadian oscillators.
#62 opened Feb 19, 2015 by Treblesteph
@Treblesteph
3
Add number of circadian oscillations count to network cartoon.
#60 opened Feb 19, 2015 by Treblesteph
@Treblesteph
Finish off repression/activation counting function.
#58 opened Feb 19, 2015 by Treblesteph
3 tasks
@Treblesteph
Write tests for repression/activation counting function.
#57 opened Feb 19, 2015 by Treblesteph
@Treblesteph
Explore the effect of &&/|| gates in Troein figure 1 networks.
#56 opened Feb 11, 2015 by Treblesteph
@Treblesteph
Sort out labelling of genes in concentration plot in plotOutput.jl help wanted
#48 opened Feb 6, 2015 by Treblesteph
@Treblesteph
1
Ideas for experiments that can only be done in the faster boolean framework.
#46 opened Feb 5, 2015 by Treblesteph
@Treblesteph
2
ProTip! no:milestone will show everything without a milestone.