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instadeepai / InstaNovo

De novo peptide sequencing with InstaNovo: Accurate, database-free peptide identification for large scale proteomics experiments
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diffusion model is included in instanovo v1.0.0? #66

Open irleader opened 5 days ago

irleader commented 5 days ago

Is diffusion model integrated in instanovo v1.0.0 such that we no longer need to run instanovo+ as we did in v0.1.7?

If not, and we would like to use instanovo+ after instanovo, we need to run instanovo v1.0.0 first, then run instanovo+ with instanovo0.1.7?

Also, can you provide a link of not extended model checkpoint for instanovo v1.0.0? Thanks!

BioGeek commented 2 days ago

Hey @irleader

Is diffusion model integrated in instanovo v1.0.0 such that we no longer need to run instanovo+ as we did in v0.1.7?

No, the diffusion model is not integrated in InstaNovo v1.0.0. The v1.0.0 release does not include the diffusion model, but we're working on updating the diffusion code to make it compatible with the InstaNovo v1.0.0 model.

If not, and we would like to use instanovo+ after instanovo, we need to run instanovo v1.0.0 first, then run instanovo+ with instanovo0.1.7?

That is correct for the time being, until we release the updated InstaNovo+ code in a future release.

Also, can you provide a link of not extended model checkpoint for instanovo v1.0.0? Thanks!

Can you explain a bit more what kind of checkpoint exactly you're looking for or explain your use case?

irleader commented 2 days ago

Hi,

I am looking for a checkpoint with residues matching instanovo/configs/residues/default.yaml, in previous releases, such checkpoint has been provided.

While in v1.0.0, only an extended checkpoint matching instanovo/configs/residues/extended.yaml is provided.

Thanks!