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computational-biology

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StevenCHowell
StevenCHowell commented May 5, 2017

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

BenjaSanchez
BenjaSanchez commented Dec 3, 2019

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

hashbackup
hashbackup commented Jan 22, 2020

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

alyeffy
alyeffy commented Apr 6, 2018

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

finsberg
finsberg commented Nov 8, 2019

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

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