Installation - Google Colab Version Release Action Items

[jhmlam]

A few action items before release. A good reference is ColabFold where they put AF2 rosettafold all on Colab.

• [x] Less busy texts. Hide the text e.g. the verbose imports. See https://github.com/sokrypton/ColabFold/blob/main/beta/Alphafold_single.ipynb and compare when you click "Open in Colab"
• [x] Create Upload button of a pdb file
• [x] Put Notebook07 from main to the colab notebook https://github.com/jhmlam/NucleicNet/blob/master/Notebooks/07_DownstreamApplication.ipynb
• [x] Create Download button for the pymol session (.pse) generated.
• [x] Create Download button for sequence logo (.png/.svg) generated if any.

Statistics

• [ ] Uncertainty. We have a stacks of models stored in https://github.com/jhmlam/NucleicNetLite/tree/main/Models. I would suggest to calculate reliability at each position for the sequence logo generated; this can be calculated from the different results in models in the ensemble (e.g. when we have 3 models from 3 different 3-cross-validation). For simplicity, maybe we can use the brier 3-component score. See here and here and here. Take observed probability as the expectation collected from all models i.e. MLE. Frequentest alert.

[JoshuaChou2018]

• [x] add a button to allow users to select models (w or w/o mmseq)

[JoshuaChou2018]

• [x] add a button to allow users to select models (w or w/o mmseq)

Added in ColabNucleicNet_v1.0_ARCHIVED.ipynb

[jhmlam]

@JoshuaChou2018 Thank you Joshua, too busy these days I will try to work on it this weekend or so. Sorry for all the delays lol I am also downsizing this repo to make the git clone faster. For the google drive please keep an archive of a working version. I realize when I open the notebook on colab it actually auto-save, so I copied the original untampered version as ARCHIVE. Any solid deadlines from Prof Gao?

[JoshuaChou2018]

@JoshuaChou2018 Thank you Joshua, too busy these days I will try to work on it this weekend or so. Sorry for all the delays lol I am also downsizing this repo to make the git clone faster. For the google drive please keep an archive of a working version. I realize when I open the notebook on colab it actually auto-save, so I copied the original untampered version as ARCHIVE. Any solid deadlines from Prof Gao?

Hi Jordy, I am thinking about what other possible modules we can add to the colab version to make it fancier, lol, eg. an embedded pdb visualizer. Btw, I do not see any ddl from Prof. Gao, I guess it should be up to you?