Agentic-SpliceAI Documentation¶
Central documentation hub for Agentic-SpliceAI — Context-Aware Novel Isoform Discovery for Drug Target Identification.
📁 Topic Index¶
Getting Started¶
| Document | Description |
|---|---|
| QUICKSTART.md | Get running in 5 minutes |
| SETUP.md | Full environment setup |
| getting_started/RUNPODS_SETUP.md | Cloud GPU (RunPods) workflow |
| getting_started/LATEX_SETUP.md | LaTeX / PDF generation setup |
Architecture¶
| Document | Description |
|---|---|
| architecture/README.md | System architecture overview |
| architecture/STRUCTURE.md | Full project directory structure |
| architecture/PACKAGE_ORGANIZATION.md | Package organization guide |
System Design¶
| Document | Description |
|---|---|
| system_design/README.md | System design overview |
| system_design/resource_management.md | Genomic resource registry |
| system_design/output_management.md | Output & artifact management |
| system_design/configuration_system.md | Configuration (Pydantic) |
| system_design/base_layer_architecture.md | Base layer architecture |
Base Layer¶
| Document | Description |
|---|---|
| base_layer/DATA_PREPARATION_CLI.md | Data preparation CLI |
| base_layer/PROCESSING_ARCHITECTURE.md | Chunking & processing architecture |
| base_layer/POSITION_COORDINATE_SYSTEMS.md | Position / coordinate system reference |
Multimodal Feature Engineering¶
| Document | Description |
|---|---|
| multimodal_feature_engineering/feature_catalog.md | Complete 9-modality, 100-column feature reference |
| Epigenetic marks tutorial | H3K36me3/H3K4me3 ChIP-seq modality |
| RBP eCLIP tutorial | ENCODE RBP binding modality |
| Chromatin accessibility tutorial | ENCODE ATAC-seq modality |
Meta Layer¶
| Document | Description |
|---|---|
| meta_layer/README.md | Meta layer overview |
| meta_layer/ARCHITECTURE.md | Foundation-Adaptor architecture |
| M1-M4 model variants | Four meta-layer model variants for splice prediction |
| meta_layer/methods/README.md | Methods overview |
| meta_layer/methods/ROADMAP.md | Development roadmap |
| meta_layer/methods/PAIRED_DELTA_PREDICTION.md | Paired delta prediction method |
| meta_layer/methods/VALIDATED_DELTA_PREDICTION.md | Validated delta prediction method |
| meta_layer/experiments/README.md | Experiments index |
Compute Resources¶
| Document | Description |
|---|---|
| compute/README.md | Compute resource management overview |
| compute/remote_training_options.md | Modal vs SkyPilot vs RunPods comparison |
| getting_started/RUNPODS_SETUP.md | RunPods first-time setup guide |
Foundation Models¶
| Document | Description |
|---|---|
| foundation_models/README.md | Foundation models overview |
| foundation_models/evo2/junction_support_labels.md | Evo2 junction support labels |
| foundation_models/training/deepspeed_training.md | DeepSpeed training guide |
Applications & Use Cases¶
| Document | Description |
|---|---|
| applications/README.md | Domain-specific application workflows |
| isoform_discovery/README.md | Novel isoform discovery overview |
| variant_analysis/README.md | Variant analysis overview |
Agentic Workflows¶
| Document | Description |
|---|---|
| agency/README.md | Agentic workflow overview |
| agency/AGENTIC_MEMORY_TUTORIAL.md | Memory system tutorial |
| agency/MEMORY_PATTERNS.md | Memory design patterns |
Tutorials & Workflows¶
| Document | Description |
|---|---|
| tutorials/README.md | Tutorials overview |
| tutorials/SPLICE_PREDICTION_GUIDE.md | Splice site prediction guide |
| workflows/README.md | Analysis workflows |
Domain Knowledge¶
| Document | Description |
|---|---|
| biology/README.md | Splice site biology background |
| bioinformatics/README.md | Bioinformatics methods |
API Reference¶
| Document | Description |
|---|---|
| api/README.md | REST & Python API reference |
| api/ENDPOINTS.md | API endpoints, configuration, and data format |
Project¶
| Document | Description |
|---|---|
| ROADMAP.md | Development roadmap (Phases 1-10+) |
📖 Documentation Conventions¶
docs/— Official, centralized documentation (mkdocs + Obsidian). All new tutorial and reference notes go here.- Package-level
docs/(e.g.,src/agentic_spliceai/docs/) — Temporary working notes close to the code. Promoted todocs/<topic>/when mature. dev/— Private development notes, session logs, refactoring plans. Not in mkdocs or Obsidian.
🎯 Find What You Need¶
| I want to... | Go to |
|---|---|
| Get running fast | QUICKSTART.md |
| Understand the pipeline | architecture/README.md |
| Learn about the base layer | base_layer/ |
| Understand meta-learning | meta_layer/ |
| Work with foundation models | foundation_models/ |
| Discover novel isoforms | isoform_discovery/README.md |
| Use agentic validation | agency/README.md |
| Follow a tutorial | tutorials/SPLICE_PREDICTION_GUIDE.md |
| Read splice biology | biology/README.md |
| Use the API | api/ENDPOINTS.md |
| Explore multimodal features | multimodal_feature_engineering/feature_catalog.md |
| See the roadmap | ROADMAP.md |
| Find application workflows | applications/README.md |
Last Updated: March 2026