zikunyang / dcvst

DCVST

Positive B: B dataset;

Positive T: T dataset;

Negative B: NB dataset;

Negative T: NT dataset;

Antigens: Protective Antigens and N Protective Antigens dataset;

DeepVacPred: The code for designing and sieving the vaccine datasets, training the DNNs and predicting the vaccine subunits;

quickmodel: The DNN for predicting the vaccine subunits.

dcvst's Issues

Many missing files

There are a few files with incorrect names in the notebook and completely missing:

• V2model.pkl
• Sprotein.txt
• positiveset_12AA
• negativeset_12AA

Could you upload these files please? Thanks

Simple test code

Hi Zikun,

Thanks for the post. I'm interested in applying this to identify chlamydia peptides for vaccine development. I've tried to use your code for a small test with your uploaded files. After running Amodel, I get a larger value for Candidates (see attached). Is there something different with the uploaded files?

Do you expect a long runtime for the Dataset cell after?

Recommendations for less experienced users on using DeepVacPred

Hello,

I'm an undergraduate biotechnology student, currently in a project involving vaccine design. I was having some issues trying to understand how to use the code. I tried to implement it by creating a Jupyter notebook; another attempt was by a GitHub plugin on repl.it, but I'm unsure whether this approach was correct or not, and how to proceed. For example, if I intend to identify the fragments of interest from a protein sequence for designing a vaccine, where should I insert the protein sequence? Also, I'd like to know if there would be a web-based application for less experienced users.

Thank you.