Bioinformatics tools running on modal.
pip install modal
python3 -m modal setup
Or alternatively, use uv:
uv run --with modal modal run modal_minimap.py
wget https://files.rcsb.org/download/1YWI.pdb
modal run modal_af2rank.py --input-pdb 1YWI.pdb --run-name 1YWI
Runs minimap2 -ax sr <fasta> <reads>
Just a simple example of running a binary on a powerful box.
wget https://gist.githubusercontent.com/hgbrian/56787d9b3ce2e68f698ac94d537340d8/raw/mito.fasta
wget https://gist.githubusercontent.com/hgbrian/802d8094bb4fed435bbb93a8c9092ee2/raw/mito_reads.fastq
modal run modal_minimap2.py --input-ref-fasta mito.fasta --input-reads-fastq mito_reads.fastq
A very basic implementation.
wget https://www.rcsb.org/fasta/entry/3NIT -O 3NIT.faa
modal run modal_alphafold.py --input-fasta 3NIT.faa
Create a cyclic peptide against a pdb file (using pdb-redo data by default)
modal run modal_afdesign.py --pdb 4MZK --target-chain A
Set the first and last amino acid of the (cyclic) peptide to cysteine.
Here using a small number of iterations for speed reasons...
Use --soft-iters 30 --hard-iters 6 or more for better results.
modal run modal_afdesign.py --pdb 1A00 --target-chain A --soft-iters 2 --hard-iters 2 --binder-len 6 --set-fixed-aas C....C
Create a linear peptide against a local PDB file that has been manually edited. This is unfortunately sometimes necessary when e.g. a chain is too long or there are too many chains.
modal run modal_afdesign.py --pdb in/afdesign/1igy_cropped.fixed.pdb --target-chain B
Dock a .mol2 file against a local pdb file. DiffDock may require an 80GB A100 to run for larger proteins.
wget https://files.rcsb.org/download/1IGY.pdb
wget https://gist.github.com/hgbrian/393ec799893cbf518f3084847c17cb2d/raw/1IGY_example.mol2
modal run modal_diffdock.py --pdb 1IGY.pdb --mol2 in/diffdock/1IGY_example.mol2
Predict the amino acid at a masked position in a sequence.
echo ">1\nMA<mask>GMT" > test_esm2.faa
modal r
8F60
un modal_esm2_predict_masked.py --input-faa test_esm2.faa
A simple pymol-based script to convert PDBs to PNGs for easy output viewing.
wget https://files.rcsb.org/download/1YWI.pdb
modal run modal_pdb2png.py --input-pdb 1YWI.pdb --protein-zoom 0.8 --protein-color 240,200,190
A tool for annotating antibody sequences https://github.com/oxpig/ANARCI
echo ">test_anarci\nDIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLESGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRT" > test_anarci.faa
modal run modal_anarci.py --input-fasta test_anarci.faa
Basic MD
modal run modal_MD_protein_ligand.py --pdb-id in/md_protein_ligand/1A1O_reordered.pdb
Basic MD protein + ligand
modal run modal_md_protein_ligand.py --pdb-id 4O75 --ligand-id 2RC --ligand-chain A
Basic PDL1 binder (example from https://github.com/martinpacesa/BindCraft)
wget https://raw.githubusercontent.com/martinpacesa/BindCraft/refs/heads/main/example/PDL1.pdb
GPU=A100 modal run modal_bindcraft.py --input-pdb PDL1.pdb --number-of-final-designs 1
Minimal hello world app, with conda and nextflow installed (not trivial!)
modal run modal_nextflow_example.py
Boltz, an open source AlphaFold 3-like model.
echo "sequences:\n - protein:\n id: A\n sequence: TDKLIFGKGTRVTVEP" > test_boltz.yaml
modal run modal_boltz.py --input-yaml test_boltz.yaml
Chai-1, another open source AlphaFold 3-like model.
echo ">protein|name=insulin\nMAWTPLLLLLLSHCTGSLSQPVLTQPTSLSASPGASARFTCTLRSGINVGTYRIYWYQQKPGSLPRYLLRYKSDSDKQGSGVPSRFSGSKDASTNAGLLLISGLQSEDEADYYCAIWYSSTS\n>RNA|name=rna\nACUGACUGGAAGUCCCCCGUAGUACCCGACG\n>ligand|name=caffeine\nN[C@@H](Cc1ccc(O)cc1)C(=O)O" > test_chai1.faa
modal run modal_chai1.py --input-faa test_chai1.faa
wget https://files.rcsb.org/download/1IVO.pdb
modal run modal_ligandmpnn.py --input-pdb 1IVO.pdb --extract-chains AC --params-str '--seed 1 --checkpoint_protein_mpnn "/LigandMPNN/model_params/proteinmpnn_v_48_020.pt" --chains_to_design "C" --save_stats 1'
Not working currently due to library incompatibilities!
- RNA Seq Pipeline by @tdsone