Running CAMP on own data

[fteufel]

Hi,

I want to try CAMP to predict my own dataset. I understand that the raw sequences are not enough, and some third-party tools are required that I need to run online manually.

Could you provide a step-by-step instruction how I need to format the peptide-protein pairs, what input files I need to submit to the online services and what output to download, and what scripts I then need to run?

I understand that technically I am supposed to run step3_generate_features.py, but as all paths are hardcoded it is a bit hard to figure out how to get there starting completely from the beginning.

Thanks for your help!

[dlemas]

I am having the same issues processing my dataset. I would be happy to work with the @twopin team to develop tutorial-style documentation for CAMP implementation.

[twopin]

Hi, can you describe the detailed difficulties you meet during feature generation? You need to run all third-party tools first before running the script of step3.

[twopin]

Since many researchers raise similar requests, I re-implemented CAMP using Python3+pytorch recently and the model file with corresponding training/predicting scripts will be uploaded this month. ( You can still use the original version trained by Python2+Keras).

[suxww]

Since many researchers raise similar requests, I re-implemented CAMP using Python3+pytorch recently and the model file with corresponding training/predicting scripts will be uploaded this month. ( You can still use the original version trained by Python2+Keras).

Could you please tell me where is the 「CAMP using Python3+pytorch recently and the model file with corresponding training/predicting scripts」?

[twopin]

The python3 and pytorch script and ckpts are in CAMP_pytorch. Sorry for the delay.

[twopin]

I am having the same issues processing my dataset. I would be happy to work with the @twopin team to develop tutorial-style documentation for CAMP implementation.

I'm also happy to do so if you are interested. You can email me via twopinlei@hotmail.com for further discussion. I also realized that there raised many questions due to code and feature generation procedures. Maybe we can collaborate to make a good tool.

[leofossilis]

hello @twopin , I was wondering if I can use predict.py for predictions of PyTorch models or I have to use my own PyTorch scripts for the purpose.

also I was wondering if you could provide a sample dataset for training pytorch models