Bryce Cronkite-Ratcliff

This is essentially the same as issue #16

Wanted to emphasize @drennalls point. That quote from the bats-support readme is especially confusing, because it makes it sound like bats-core is a support library for bats instead of the...

Hi momalik11, Thanks for the message! A few things that might help understand this issue: * What are you doing when you encounter this error? Are you applying the Constraint...

There is a static linking option available on constraintTemplates via the `libs` field: https://github.com/open-policy-agent/frameworks/tree/master/constraint#what-is-a-constraint-template That's all that is supported for now. Dynamic linking can result in dependency version conflicts so...

is there a workaround for this currently? I'm interested in supporting dynamic backing data, where dimensions enter and leave. So far in my attempts, parcoords has put the new data...

It has been some time since I reviewed TPT, but I believe the implementation of TPT in MSMExplorer is based on this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832055/ The statement of the reactive flux...

On the issue of divergence with msmbuilder results, my recollection was that while the reactive flux matrix is precisely defined, the process for extracting top paths was in fact unspecified...

Given equation #9 from the paper references, the equilibrium probabilities are used to calculate the reactive flux matrix. Thus, on line 300 (or so, depending exactly which commit you have)...

@tjlane Yes, I'm cutting the bottleneck and subtracting the bottleneck flux out of all edges along the path. There's a note in the code that claims this should be optimal,...

@tjlane , when you say the sum of all paths, does that preclude a constant matrix that contains no paths? I see your point, I think, on the example you...