Merck/BioPhi

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BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluation (OASis) and an interface for computer-assisted antibody sequence design.

Stars: 265
Forks: 65
Open beginner issues: 0
Indexed issues: 44

Dominant language: Python
License: MIT
Last GitHub push: May 13, 2025
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

44 open issues indexed

Tasks are waiting in queue... Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Merck/BioPhi#89 · Opened Jun 24, 2026
OASis local set prevalence threshold Open

Difficulty 2/5 1-3 hours Newbie friendliness 57/100

Merck/BioPhi#87 · Opened Apr 29, 2026
OASis prevalence threshold for custom Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

Merck/BioPhi#86 · Opened Apr 17, 2026
bootstrap加载优化 Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

Merck/BioPhi#85 · Opened Mar 5, 2026
The server is waiting indefinitely Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

Merck/BioPhi#84 · Opened Jan 27, 2026
The BioPhi server is not working Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#83 · Opened Nov 3, 2025
Error: [Errno 24] Too many open files: '/tmp/tmps9os6anr.fasta' Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#82 · 2 comments · Opened Oct 26, 2025
BioPhi failed with TypeError: predict_scores() got an unexpected keyword argument 'model_version' Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#81 · 1 comment · Opened Oct 23, 2025
The biophi server is not working! Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#80 · Opened Oct 21, 2025
Cannot get image from quay.io Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#79 · 3 comments · Opened Oct 16, 2025
Error: [Errno 12] Cannot allocate memory Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#78 · 1 comment · Opened Oct 15, 2025
Tasks waiting in queue indefinitely Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#77 · 5 comments · Opened Sep 23, 2025
Tasks are still waiting in queue... indefintiely Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#76 · Opened Sep 19, 2025
Tasks are waiting in queue...indefinitely...not a repeat ticket Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

Merck/BioPhi#75 · Opened Sep 15, 2025
No processing occurs Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Merck/BioPhi#73 · Opened Nov 2, 2024
Tasks are waiting in queue...indefinitely Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#72 · Opened Oct 25, 2024
Task waiting in queue Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

Merck/BioPhi#71 · Opened Oct 25, 2024
Error when exporting Full Table from Humanization results Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

Merck/BioPhi#68 · Opened May 8, 2024
how to set the OASis prevalence threshold when using biophi on command line? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#66 · Opened Feb 28, 2024
Simplified server installation issue Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Merck/BioPhi#65 · Opened Feb 22, 2024
Control number of mutations when humanizing Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#64 · Opened Feb 22, 2024
Cannot build docker Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#54 · Opened Oct 27, 2023
Integration of additional language models? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Merck/BioPhi#53 · Opened Sep 5, 2023
how to get raw peptide data(sequence datasets)? Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

Merck/BioPhi#52 · Opened Sep 5, 2023
Smaller docker images Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#50 · Opened Aug 8, 2023
Allowing humanization to make multiple outputs Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Merck/BioPhi#47 · Opened Aug 1, 2023
Enable cli for humanization cdr grafting Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

Merck/BioPhi#46 · Opened Aug 1, 2023
Add mypy type checks Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Merck/BioPhi#45 · Opened Aug 1, 2023
BioPhi failed with HMMscanError: b'Parse failed (sequence file /var/folders/j7/j8sdcdk16nn_ngnyt1nc9vlw0000gn/T/tmpuhcuvvsc.fasta):\nLine 3: illegal character }\n\n' 0it [00:00, ?it/s] Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#43 · Opened Jul 18, 2023
Error: module 'numpy' has no attribute 'int' Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#42 · 5 comments · Opened Jul 13, 2023
Specify pandas version Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#40 · 1 comment · Opened Jun 26, 2023
Specify flask version Open

Difficulty 1/5 Under an hour Newbie friendliness 35/100

Merck/BioPhi#35 · Opened Apr 7, 2023
Error: Invalid sequence for "antibody" Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#34 · Opened Feb 17, 2023
Observation and Fix: Sqlalchemy 2.0 Compatibility - Downgrade to Sqlalchemy 1.x Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Merck/BioPhi#33 · 1 reaction · Opened Feb 1, 2023
Navigation arrows between individual results Open

enhancement good first issue

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#15 · Opened Sep 2, 2021
Enable generating multiple humanized sequence variants at once Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

Merck/BioPhi#13 · Opened Aug 21, 2021
Simplify export of suggested mutations from Designer Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

Merck/BioPhi#12 · Opened Aug 21, 2021
Problems about human germline sequence Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Merck/BioPhi#9 · 4 comments · Opened Aug 18, 2021
Provide instructions on mounting OASis database through Docker Open

documentation good first issue help wanted

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

Merck/BioPhi#8 · Opened Aug 14, 2021
Implement shopping cart functionality in Designer Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

Merck/BioPhi#5 · Opened Aug 12, 2021
Humanization Benchmark Data Availability Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

Merck/BioPhi#4 · 2 comments · Opened Aug 11, 2021
Highlight mutations in humanization screen same as in the Designer Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

Merck/BioPhi#3 · Opened Aug 4, 2021
Implement sorting on the backend Open

enhancement good first issue help wanted

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Merck/BioPhi#2 · Opened Aug 4, 2021
Add number of mutations to humanization & designer panel Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

Merck/BioPhi#1 · Opened Aug 4, 2021

Merck/BioPhi

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