computational-biology

I was trying to figure out why we get memory leaks in osim-rl. I use a slightly different custom version of osim-rl. However, it seems that everything points towards the integrate function of the Manager. The new version of the Manager does not have a reset mechanism and therefore one must delete the manager and create a new one. I have a minimu

Hi,

It would be nice to have the capability to expand/collapse nodes similar to https://github.com/iVis-at-Bilkent/cytoscape.js-expand-collapse.

Thanks.

Add departments column and values for PIs at Stanford University

Describe the solution you'd like

• inputs for chain selection as a separate .txt file
• Input as list of PDB codes (txt file) rather than PDB directory path

Hello maintainers of the amazing package,

I recently updated cobrapy and am experienced unexpected behavior with cobra.test.create_test_model("salmonella")

Two things are unusual:

1. Now, many warnings are given during loading of the model, whereas none were given in a previous version. Here are a few of the warnings:

`Model does not contain SBML fbc package information.
SBML package

Both mmtf.get_structure() and connect_via_residue_names() assign too many bonds, if two adjacent residues share the same residue ID. An example is LEU/ILE 25 in 1JXT. In this case all terminal hydrogen atoms are connected to the respective carbon atom of both LEU and ILE. The reason is that both function iterate residue-wise over the structure and consider both residues as the same res