Joseph-Vineland

icon location Bioinformatician at Vineland Research and Innovation Centre. Using NLP and automation to understand the language of life.

Results 3 issues of Joseph-Vineland

sequences with multiple labels

The Basset dataset has DNA sequences each with 164 binary labels. I would like to fine-tune DNABERT with this dataset. However, DNABERT is only built for sequences to have 1...

run_pyrosetta_ver.sh works but run_e2e_ver.sh fails with RuntimeError: CUDA out of memory.

run_pyrosetta_ver.sh works just fine and runs to completion but run_e2e_ver.sh fails with RuntimeError: CUDA out of memory during step 4. end-to-end prediction. It is surprising to me that the full...

Pipeline doesn't work when running RFdiffusion as recommended

When I run RFdiffusion in the following way, all the subsequent steps of the pipeline work just fine. (addFIXEDlabels.py, ProteinMPNN-FastRelax Binder Design, AlphaFold2 Complex Prediction). ``` ../scripts/run_inference.py \ inference.output_prefix=example_outputs/myOutput \...