NVIDIA-BioNeMo/bionemo-recipes

bionemo-phage-design-adapt-execution

Use when a phage-design workflow must discover or adapt to local GPU, SSH, Slurm, Lepton, manual, or unfamiliar execution infrastructure and produce durable launch, monitoring, resume, or handoff commands.

bionemo-phage-design-calibrate-rl-sampling

Use after selecting an Evo 2 phage SFT checkpoint and defining RL objectives to calibrate prompt serialization, temperature, prefix-length distribution, and fixed validation sampling.

bionemo-phage-design-collect-genomes

Use when an Evo 2 phage SFT project needs a reproducible Microviridae or new phage genome collection from NCBI, paper-linked repositories, supplements, or other public biological databases.

bionemo-phage-design-generate-and-screen

Use when producing, deduplicating, hard-QC screening, clustering, ranking, or selecting final phage designs from a chosen RL checkpoint.

bionemo-phage-design-implement-rl-objectives

Use when adding or changing Evo2 phage RL metrics, reward functions, filter logic, or validation criteria after an objective plan has been approved.

bionemo-phage-design-operate-mbridge-sft

Use when launching, monitoring, stopping, resuming, or relaunching Evo 2 phage SFT with Megatron Bridge, or when selecting its best validation-loss checkpoint across local, SSH, scheduler, or cloud execution.

bionemo-phage-design-operate-nemo-rl

Use when launching, monitoring, resuming, relaunching, or selecting checkpoints from a NeMo-RL Evo2 phage optimization run.

bionemo-phage-design-plan-rl-objectives

Use when converting a phage-design goal into target-specific RL rewards, validation criteria, and final QC filters, especially for a new reference phage or altered objective.

bionemo-phage-design-prepare-sft

Use when phage genomes must be deduplicated, clustered, split without near-duplicate leakage, and converted into explicit train, validation, and test inputs for Evo 2 supervised fine-tuning.

bionemo-phage-design-publish-stage-artifacts

Use when a phage-design user requests publication, backup, or an intermediate snapshot of selected checkpoints, validation generations, logs, results, or final deliverables to object, cloud, mounted, or network storage.

bionemo-phage-design-research-evidence

Use when a phage-design decision needs literature, database, dataset, gene-essentiality, synteny, viability, bootability, host, threshold, or model evidence.

bionemo-phage-design

Use when planning or running an Evo 2 bacteriophage genome-design project for phage therapy research, including host-specific candidates for antibiotic-resistant infections and antimicrobial resistance (AMR); coordinates evidence review, genome collection,…

bionemo-phage-generation

Use when starting, planning, or resuming BioNeMo and Evo 2 bacteriophage genome generation or design for phage therapy research, including host-specific candidates for antibiotic-resistant infections and antimicrobial resistance (AMR); locates or acquires a…