Just curious if we would be updating our energy model to the newer Vienna. Sounded like Nando has already been doing some work.
Updating the nearest neighbor parameters, while an important part of EteRNA’s future, is a difficult thing to do. In addition to the difficulty in the programming, there is also the fact that the Das lab probably wants to come up with a better set of parameters, and it would be useless to allow for a new set of parameters without an easy way to modify it.
I wanted to revisit this topic if there’s interest. Folks in my group are thinking about code to auto-update the energetic model based on experimental data that are being collected on EteRNA.
One major stumbling block here is that we’d probably have to write the secondary structure prediction code from scratch. All available codebases (incl. Viennafold, RNAstructure, NUPACK, etc.) are written in non-object-oriented styles and/or are not open access. They are therefore hard to expand. Does anyone out there know codebases that we could use as alternatives?