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## Deadline - 27th of October, by that time both changes and tests should be merged into "master" branch
As opposed to built-in ode45 function gras.ode.ode45reg cannot handle reverse time just yet. T…
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In Sympy 0.7.6.1, if you substitute a MatrixSymbol in a polynomial expression, the computations are not performed, even if you call the `doit` method:
```
>>> x = MatrixSymbol('x', 2, 2)
>>> A = Matr…
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It would be useful to generalize the [template-target alignment code](https://github.com/choderalab/ensembler/blob/master/ensembler/modeling.py#L400-L410) to allow the user to specify alternative subs…
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```
The task in tightly related to issue 58. The goal here is to identify the
implementation problems within the class and have them fixed. Rewriting parts
of the class code might be necessary. As t…
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Here's what we need to do:
- given a tree (i.e. Primates, Gentianales), replicate its general properties - birth/death rate, tree size, depth, genus size distribution - on a simulated tree (done: http…
rvosa updated
8 years ago
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Like almost all others we could start with Trilinos. It has Python bindings so I guess it's usable in Julia too with some effort. Unfortunately nothing compiles for me but maybe some other has better …
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As mentioned on [this sage-devel thread](https://groups.google.com/forum/#!topic/sage-devel/n2Sc8moP7Jk) the `.subs()` method of matrices behaves badly with polynomials.
```python
sage: x = polygen…
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Very low priority:
We could create `GP.solution_check(self, sol)`. It would validate that a particular primal/dual solution pair solves the GP. Could be useful for sanity checks and trying out 'suspe…
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Hi all — I was wondering if there was an example or template batch file for running [Spidermonkey/BGM](http://www.datamonkey.org/help/spidermonkey.php) on _protein alignments_ locally.
I found the th…
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For small complex eigenvalues of the Hessenberg matrix, `beast.evolution.substitutionmodel.DefaultEigenSystem.hqr2` tries to access index `-1` of `double[][] h`.
When `en==1`, the loop starting in li…