When incorporating new libraries into opensim-core, the library is assumed to have some specific layout (platform dependent). That typically includes "cmake" folder and have specific contents in this folder that defines include and lib paths etc.
If this is documented somewhere that would be great (appreciate a link here for future reference), if not we need to document these requirements so tha

I just started using biopandas and it seems nice. Toward promoting discussion related to its design, I have a general question regarding the column names, particularly for df['ATOM']. Note that I work with simulations of molecular structures so I care most about the df['ATOM'] field.

Coming from using VMD for several years, I noticed many differences to access the PDB fields. I have not

Problem description

When going through an I/O cycle with a model that has subsystems stored as groups, the members of each group in the sbml file get scrambled on each cycle, as those members are stored in set() structures, which are unordered. This significantly hinders cobrapy to be used for updating a model that has groups and is stored in a Github repository, as hundreds of lines in

It would be helpful to have a complete list of all standard Python modules and a guide as to which ones are supported, in progress, going to be supported, or not going to be supported ever. For example, is the threading module ever going to be supported? Will threading be handled with Seq's pipelines only? Will the multiprocessing module be supported?

Having this list will encourage people t

Have you checked the list of proposed tips to see if the tip has already been proposed?

• [ x] Yes

**Did you add yourself as a contributor by making a pull request if t

Currently, learning about the features of bioSyntax and what they translate to involves looking through the manual on our site. If we could package this together with the installation, I think users would be a lot more willing to learn it, especially if we could create custom help text within the editor. e.g. with vim we could possibly [incorporate the manual into the

His website is probably the best comp neuro resource outside of NIF. Should communicate with him and add everything he's found over the years to the list.

Add departments column and values for PIs at Stanford University

With the latest version of tensorflow (2.0), the function tf.to_float() is no longer implemented.
This results in an error when compiling the model in the 1D_double_well.ipynb tutorial:

AttributeError: module 'tensorflow' has no attribute 'to_float'

In the previous version 1.15

The indra/tools/expand_families.py file should be moved to indra/preassembler. We will need to track down where it's used in other repos and fix imports. It should also be properly documented.

Since extensions modules do not provide its source code, the doctest module cannot extract the docstring via the getsourcefile() function.
Consequently, the doctests in these docstrings are not executed by tests/test_doptest.py.

One thing that is very useful when working with simulation software is to have some way to compare the results with other similar simulation frameworks. Benchmarks are very useful to both compare solutions of specific problems as well as a nice toy example to work with to get a good understanding of how to use the software.

I would encourage you to add a section in your documentation where you

The current tutorial is vastly outdated in some areas:

• Screenshots
• Buildsystem
• URLs
• List of developers
• List of publications

We should update this as soon as we have the new infrastructure in place.

There is a demo for how to use the library on the README.md, as well as the wiki. The demo is manually maintained, at the moment, which is error prone during refactoring. Update the documentation generator to test the source in the example, before adding it to the documentation.

Singularity offers ro or rw mounts, with the syntax:

singularity shell --mount /host:/guest:ro ...

Would be nice to use for cache and inputs.