13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable
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$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill pytorch-lightning --agent claude-code
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Gemini CLI
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name: pytorch-lightning description: Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training. allowed-tools: Read Write Edit Bash license: Apache-2.0 license compatibility: Requires Python 3.10+ with lightning 2.6.6 and compatible PyTorch. CPU examples need no network after installation. CUDA/DDP/FSDP/DeepSpeed need suitable hardware; optional loggers require separate packages and online services need credentials/network. metadata: version: "1.4" last-reviewed: "2026-10-01" skill-author: K-Dense Inc.
PyTorch Lightning is a deep learning framework that organizes PyTorch code to eliminate boilerplate while maintaining full flexibility. Automate training workflows, multi-device orchestration, and implement best practices for neural network training and scaling across multiple GPUs/TPUs.
**Reviewed release:** [Lightning 2.6.6](https://github.com/Lightning-AI/pytorch-lightning/releases/tag/2.6.6), including its checkpoint-loading security fixes. CPU tests use Python 3.11, Torch 2.14.1 and Lightning 2.6.6. Use `import lightning as L` with the `lightning` distribution. The alternative `pytorch-lightning` distribution exposes `import pytorch_lightning as pl`; do not mix class namespaces within one application. GPU, TPU, multi-node and online logger examples are source-verified illustrations, not executed training validation.
uv pip install "lightning==2.6.6"
Optional extras:
uv pip install "lightning[extra]==2.6.6" # loggers, strategies, etc. uv pip install wandb mlflow # specific loggers as needed
This skill should be used when:
Organize PyTorch models into six logical sections:
1. **Initialization** - `__init__()` and `setup()` 2. **Training Loop** - `training_step(batch, batch_idx)` 3. **Validation Loop** - `validation_step(batch, batch_idx)` 4. **Test Loop** - `test_step(batch, batch_idx)` 5. **Prediction** - `predict_step(batch, batch_idx)` 6. **Optimizer Configuration** - `configure_optimizers()`
**Quick template reference:** See `scripts/template_lightning_module.py` for a complete boilerplate.
**Detailed documentation:** Read `references/lightning_module.md` for comprehensive method documentation, hooks, properties, and best practices.
The Trainer automates the training loop, device management, gradient operations, and callbacks. Key features:
**Quick setup reference:** See `scripts/quick_trainer_setup.py` for common Trainer configurations.
**Detailed documentation:** Read `references/trainer.md` for all parameters, methods, and configuration options.
Encapsulate all data processing steps in a reusable class:
1. `prepare_data()` - Download/cache on local rank zero per node by default; use global rank zero with shared storage when configured 2. `setup()` - Create datasets and apply transforms (per-GPU) 3. `train_dataloader()` - Return training DataLoader 4. `val_dataloader()` - Return validation DataLoader 5. `test_dataloader()` - Return test DataLoader
**Quick template reference:** See `scripts/template_datamodule.py` for a complete boilerplate.
**Detailed documentation:** Read `references/data_module.md` for method details and usage patterns.
Add custom functionality at specific training hooks without modifying your LightningModule. Built-in callbacks include:
**Detailed documentation:** Read `references/callbacks.md` for built-in callbacks and custom callback creation.
Integrate with multiple logging platforms:
`NeptuneLogger` was removed in Lightning 2.6.4; the Neptune service shut down March 5, 2026. The bundled helpers use local CSV logging; cloud tracking and model artifact uploads require an intentional choice.
Log metrics with `self.log("metric_name", value)` in supported LightningModule hooks; specify epoch/step reduction and batch size when they matter.
**Detailed documentation:** Read `references/logging.md` for logger setup and configuration.
Choose the right strategy based on model size:
Choose from peak memory and throughput measurements, not a fixed parameter-count threshold.
Configure with: `Trainer(strategy="ddp", accelerator="gpu", devices=4)`
**Detailed documentation:** Rea
๐ Claude Scientific Skills is now Scientific Agent Skills. Same skills, broader compatibility โ now works with any AI agent that supports the open Agent Skills standard, not just Claude.
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