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Hello,
I have a quite wired problem in using this code.
When I use the BioRED.zip file downloaded from:
https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/BioRED.zip
everything works fine. (I only …
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Hi, I'm trying to use DeepRank-Mut. The first problem is that I don't get how to run the tests, because in the documentation it is stated to enter in the test directory and run pytest, but this comman…
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Hi, I'm working on a project to extract features from PAAD patients from the ICGC database for neoantigen immunogenicity prediction in ML. This project follows the steps taken by the model creators. I…
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**Note** that the “memo” for this, final week is motivated by the following prompt:
**Imagine 2051.** Use the materials and medium (or media) of your choice to create one modest object that belongs…
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Hello,
first of all, thank you so much for this amazing work!
Im trying to follow the pipeline.sh script with my own DMS data, but Im getting the following error in the MSA processing
```
C…
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Hi, I have been trying to run antigen garnish for a while with your testdata and now it seems to run fine with parallel and netMHC. The issue is that in the folder as e.g. ag_f236b988a09e438ea2 it doe…
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Awesome work, and thanks for uploading pipelin.sh for convenient evaluation on custom data.
I followed the instruction to set up the three parameters needed (assay_data_location, MSA_location, target…
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When I check the data for this rep., I could not find the additional DMS assays added for the extended benchmark record in the paper. These include: A0A220GHA5, CAS9 STRP1 negative, BAC7 (single and m…
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In proteinMPNN a very powerful feature is the ability to tie arbitrary positions together which allows for the optimization of sequence over repeat proteins and homooligomers. Is this something can be…
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Leave below as comments your memos that grapple with the topic of Pandemics, inspired by the readings, movies, & novels (at least one per quarter), your research, experiences, and imagination! Also ad…