Zeng, Wen-Feng

Possible solution is to start the server and GUI separately.

Tutorial: basic settings in alphabase

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The tutorial notebook of basic settings in alphabase: 1. base DF structures 2. spec libs 3. HDF5 storage

1. mass calculation 2. digestion 3. TBD psm readers 4. TBD hdf 5. isotopes

just a note, there's a cool "registry" pattern, that we could use here, if we wanted ;-) https://charlesreid1.github.io/python-patterns-the-registry.html _Originally posted by @mschwoer in https://github.com/MannLabs/alphabase/pull/172#discussion_r1607821869_

The pretrained RT model does not perform well in many datasets

The epoch parameter in `scheduler.step()` was not necessary and is being deprecated where possible

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``` [.../site-packages/torch/optim/lr_scheduler.py:232]: UserWarning: The epoch parameter in `scheduler.step()` was not necessary and is being deprecated where possible. Please use `scheduler.step()` to step the scheduler. During the deprecation, if epoch is...

``` [peptdeep/model/model_interface.py:731] FutureWarning: You are using `torch.load` with `weights_only=False` (the current default value), which uses the default pickle module implicitly. It is possible to construct malicious pickle data which will...

x 1. speclib from search engines, for example load speclib.tsv file 2. speclib from fasta (peptdeep) 3. merge multiple speclibs

### Discussed in https://github.com/MannLabs/alphapeptdeep/discussions/184 Originally posted by **liuwenrui917** July 16, 2024 Hello Dr. Zeng Thank you for your reply. And I want to ask you that I will use High-pH...