Nathan Mih

Could be integrated with packages such as: https://github.com/Superzchen/iFeature/

A run for a single protein of an external program would be useful to understand how long calculating a property would take.

Sequence to structure pairwise alignment parameter tuning

3

When running QC/QA, the first thing that is done is a pairwise alignment. The quality of this alignment can have a big impact of the result. The setting of gap...

Architectural change todo -- PDBProp objects with the same ID for a GEM-PRO should point to the same object rather than being created under different proteins

1

This also will make the transition to using the hadoop sequence file for structures much easier.

See documentation: https://docs.google.com/document/u/1/d/1566Ub_-WAXMcuOA8gmb2-X9JmYfWuZarrgneNVaBQd8/pub Example: http://aquaria.ws/P51451

https://spark.apache.org/docs/latest/sql-programming-guide.html#parquet-files

Importing ssbio on python2.7 cobra environment

1

Freshly installed cobra environment + ssbio runs into an import error for the package "ruamel_yaml", solved by: pip install ruamel_yaml==0.11.14 See: https://stackoverflow.com/questions/41373834/conda-importerror-no-module-named-ruamel-yaml-comments

\# Temporarily disable logging messages logging.disable(logging.WARNING) \ \# Re-enable logging logging.disable(logging.NOTSET)

Option to run QC/QA for all structures

1

Currently, QC/QA for structures stops when a representative structure is found. However the following case is possible: - Multiple parts of the structure are homology modeled - Another structure has...

Currently, if sequences are provided manually, there is no way to easily map them to KEGG or UniProt other than providing the IDs. It would be nice to be able...