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  • 2cd8c52d9f adding batch size patch to catch low N edge cases main fix/sequence-based-mmseqs-batching Ben Perry 2026-05-04 12:18:27 -04:00
  • ebacb8e45c removing legacy download code from setup_databases.sh Ben Perry 2026-05-04 11:39:39 -04:00
  • a0cf8b472c adding alternative HF endpoint as documentation Ben Perry 2026-05-04 11:18:25 -04:00
  • 9be5f46a83 applying patch to preserve mmseqs tstart and tend 1-indexing in mmseqs template search Ben Perry 2026-04-19 23:32:02 -04:00
  • e38651c4a6 removing rogue git merge conflict text Ben Perry 2026-04-19 23:29:00 -04:00
  • 74ee907dcf updating temp_dir flag to passthrough to MMSeqs for HPC Benjamin Perry 2026-04-11 11:25:21 -04:00
  • 902c2f065d adding --jax_compilation_cache_dir flag to avoid model recompilation across runs Benjamin Perry 2026-04-10 22:29:00 -04:00
  • 9b1e5653d4 updating readme Benjamin Perry 2026-04-10 16:45:33 -04:00
  • e79c6db693 Merge branch 'feature/rna-nhmmer' Benjamin Perry 2026-04-10 16:41:51 -04:00
  • e7b7783364 adding modal HF_TOKEN secret feature/rna-nhmmer Benjamin Perry 2026-04-10 16:26:27 -04:00
  • 257c4796c3 updating README instructions Benjamin Perry 2026-04-10 15:50:38 -04:00
  • 5abb19b7b8 deleting unneeded scripts for benchmarking for clean repo Benjamin Perry 2026-04-10 15:50:27 -04:00
  • 288bc9dbe8 updating modal data prep to handle DNA/RNA Benjamin Perry 2026-04-10 15:50:07 -04:00
  • 77ac2217e4 updating help docs for setup databases Benjamin Perry 2026-04-10 15:49:45 -04:00
  • 50fd34d6e6 removing jackhmmer seq limit patch from alphafast dockerfile Benjamin Perry 2026-04-10 15:49:12 -04:00
  • acf04188b5 removing benchmarks for clean repo Benjamin Perry 2026-04-10 15:31:45 -04:00
  • d4e3910dcb adding setup_databases with simpler flags Benjamin Perry 2026-04-10 15:31:07 -04:00
  • fca97294d4 final setup db script Benjamin Perry 2026-04-10 15:21:50 -04:00
  • f61a919772 modifying setup to only grab .zst files Benjamin Perry 2026-04-10 10:01:42 -04:00
  • 7679d1321e reverting rna background to semi-parallel to prevent massive RAM usage in multi-GPU Benjamin Perry 2026-04-08 00:57:24 -04:00
  • 71560437c1 updating device passing arg Benjamin Perry 2026-04-07 23:41:44 -04:00
  • 9a6174ea70 fixing gpu cli arg for run model Benjamin Perry 2026-04-07 23:37:47 -04:00
  • 72d699deb5 adding fully parallel rna search Benjamin Perry 2026-04-07 20:13:44 -04:00
  • a7fd4a5b08 adding absolute path Benjamin Perry 2026-04-07 19:57:42 -04:00
  • 3e69663016 updating hmmer paths Benjamin Perry 2026-04-07 19:46:01 -04:00
  • 92e53c77cf adding new dockerfile with hmmer compatability Benjamin Perry 2026-04-07 19:34:41 -04:00
  • f1752ed393 adding fixed alphafold3.mmcif parser Benjamin Perry 2026-04-07 18:30:43 -04:00
  • 5086a904c6 adding edge case handling on mixed benchmarks Benjamin Perry 2026-04-07 18:15:35 -04:00
  • 5d1e3d001c updating benchmark query script to ignore common solvents Benjamin Perry 2026-04-07 18:05:54 -04:00
  • 7720b28833 updating setup databases with rna option Benjamin Perry 2026-04-07 17:16:44 -04:00
  • fcce4fcf5a fixing modal database script to include config from python Benjamin Perry 2026-04-07 17:15:25 -04:00
  • 57be42894a adding final testing scripts for RNA mode Benjamin Perry 2026-04-06 22:47:45 -04:00
  • f0e51e4603 adding RNA search functionality Benjamin Perry 2026-04-06 12:59:38 -04:00
  • 89a3f47d4e Merge pull request #15 from RomeroLab/fix/modal-config-mount Jeonghyeon Kim 2026-03-19 14:09:20 -04:00
  • 01e86bad65 fix: replace deprecated modal.Mount with Image.add_local_python_source fix/modal-config-mount jasonkim8652 2026-03-19 14:06:43 -04:00
  • 92c571db71 Merge pull request #13 from RomeroLab/fix/modal-config-mount Jeonghyeon Kim 2026-03-19 11:59:56 -04:00
  • 631c9f8842 fix: mount config.py into Modal remote containers jasonkim8652 2026-03-19 11:58:24 -04:00
  • fca90950d3 adding MMseqs vs. NHMMER options to alphafast run script and database download Benjamin Perry 2026-03-18 13:16:57 -04:00
  • 7aa6cdc423 adding temporary test of mmseqs RNA/DNA search + NHmmer fallback Benjamin Perry 2026-03-17 20:04:24 -04:00
  • 83815ff767 iniital testing scripts for dna/rna support Ben Perry 2026-03-16 14:08:16 -04:00
  • 840b2cc46c updating README and CLI install instructions Ben Perry 2026-03-16 11:06:01 -04:00
  • 4336d7678c switching over to hf cli Ben Perry 2026-03-16 10:55:35 -04:00
  • b1c2290546 removing inline python scripting Ben Perry 2026-03-16 10:50:25 -04:00
  • 6b57ce6181 testing hf download flag Ben Perry 2026-03-16 10:43:25 -04:00
  • 4f3905e679 adding custom a3m conversion to include headers needed for paired msa Ben Perry 2026-03-07 16:16:14 -05:00
  • 2323d0c25d changing find to work with symlinks Ben Perry 2026-03-05 09:27:19 -05:00
  • 7ee3d40223 setting sequential MSA mode to be the default Ben Perry 2026-03-04 12:40:52 -05:00
  • 86b9cc2ff2 adding guard to only have N GPUs if less than N + 1 inputs requested. Additionally, fixing logdir and model weights path pointers Ben Perry 2026-03-03 10:01:14 -05:00
  • e832926dbe remove MSA server, add HuggingFace pre-built DB download and upload scripts jasonkim8652 2026-03-02 09:15:42 -05:00
  • 08e651505a fixing glob pattern to only grab MSA data outputs with _data suffix Benjamin Perry 2026-02-28 19:49:20 -05:00
  • 2f7bac62ed removing benchmark timing from production code Benjamin Perry 2026-02-28 19:49:01 -05:00
  • ddbc628838 updating dockerignore for lightweight docker image Benjamin Perry 2026-02-28 16:57:32 -05:00
  • 262ed23c44 fixing production version of run_alphafast.sh to also use one-time af3 model setup for folding Benjamin Perry 2026-02-28 16:56:34 -05:00
  • 109dda415a updating model dir path to match /data/ directory path Benjamin Perry 2026-02-28 12:30:35 -05:00
  • 91e068887a updating paths in docker to data/ instead of root/ to avoid root perms issue Benjamin Perry 2026-02-27 21:34:44 -05:00
  • e40eb852a7 adding user ID flag to fix root owned output files on some setups Ben Perry 2026-02-27 14:55:40 -05:00
  • 83cac316ea updating documentation for correct run modal command Benjamin Perry 2026-02-26 22:26:22 -05:00
  • d03bb91924 adding weights streaming to prevent OOM error on local machine when running modal Benjamin Perry 2026-02-26 22:21:42 -05:00
  • e1c001837d adding alphfadol3 wheel to scikit-build to fix naming clashes Benjamin Perry 2026-02-26 22:21:14 -05:00
  • 846284d7d0 rebuilding lock file for new python version and name change Benjamin Perry 2026-02-25 21:56:21 -05:00
  • 9d35cb7716 Change Python version requirement to exact match of 3.12 Ben Perry 2026-02-25 12:08:56 -05:00
  • 576201671d Update README.md Ben Perry 2026-02-19 19:10:01 -05:00
  • e91a05e93d Update README.md Ben Perry 2026-02-19 01:36:24 -05:00
  • a59ef81777 Update README.md Ben Perry 2026-02-19 01:35:54 -05:00
  • 5dd6579685 Update building.md Ben Perry 2026-02-19 01:32:45 -05:00
  • 17cc3a61b0 Update README.md Ben Perry 2026-02-19 01:29:04 -05:00
  • 0b68229f4b Update README.md Ben Perry 2026-02-18 23:45:31 -05:00
  • 625a3839ef initial commit Ben Perry 2026-02-17 14:10:40 -05:00