biotender

Workflow for regulatory network inference, regulon scoring, perturbation-aware comparison, and network visualization.

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Binder design campaign planning, monitoring, and troubleshooting. Use this skill when: (1) Planning a complete binder design campaign, (2) Converting high-level goals into runnable pipelines, (3) Assessing campaign health and pass rates, (4) Diagnosing why designs are failing QC, (5) Estimating time, cost, and expected yields, (6) Selecting between design tools for a specific target. This skill orchestrates the other protein design tools. For individual tool parameters, use the specific tool skills.

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Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.

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Workflow for Hi-C and related 3D genomics analyses including compartments, loops, TADs, differential contacts, and visualization.

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Workflow for retrieving public omics datasets, sequences, annotations, and literature-linked biological resources.

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Workflow for multiplexed imaging or IMC segmentation, phenotyping, and spatial summarization.

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Workflow for fine-mapping, colocalization, mediation, pleiotropy analysis, and Mendelian randomization.

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Workflow for nanopore or PacBio long-read QC, alignment, polishing, methylation-aware analysis, and structural variant discovery.

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Workflow for orthology, synteny, ancestral reconstruction, and evolutionary comparison across genomes.

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Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.

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Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design. For backbone generation, use rfdiffusion or bindcraft. For ligand-aware design, use ligandmpnn. For solubility optimization, use solublempnn.

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Boltz-1 / Boltz-2 structure prediction for proteins, complexes, and ligand-aware validation. Use this skill when: (1) Predicting protein complex structures, (2) Validating designed binders, (3) Need open-source alternative to AF2, (4) Predicting protein-ligand complexes, (5) Using local GPU resources. For QC thresholds, use protein-design-qc. For AlphaFold2 prediction, use alphafold2-multimer. For Chai prediction, use chai1-structure-prediction.

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Workflow for copy-number estimation, segmentation, annotation, and visualization in sequencing-based assays.

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End-to-end EHR predictive modeling pipeline with PyHealth, covering dataset loading, task definition, model training, evaluation, calibration, and clinical interpretation.

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Workflow for methylation alignment or calling, DMR analysis, methylation QC, and locus-level interpretation.

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Workflow for amplicon microbiome analysis including denoising, taxonomy assignment, diversity analysis, and differential abundance.

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AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm2-sequence-scoring. For QC thresholds, use protein-design-qc.

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Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.

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Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.

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First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.

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Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.

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