Systems biology
Reactome
Curated, peer-reviewed pathway database covering signaling, metabolism, transport, and more.
Why it matters
Provides graph-structured pathway priors for hybrid models. Treat as a prior, not as truth.
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Open 05 · Resource Library
Datasets, tools, priors.
A starter library. Treat each entry as a prior, not as truth — and add your own URLs as you find better ones.
Intermediate
Drug discovery
Open Targets
Target–disease evidence platform integrating genetics, omics, and literature.
Why it matters
Anchors target choice in real evidence and disease relevance.
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Open Datasets
DepMap
Cancer cell line dependency and vulnerability data from CRISPR and RNAi screens.
Why it matters
Large-scale loss-of-function perturbation data across hundreds of cell lines.
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Open Single-cell omics
CELLxGENE
Portal for exploring and downloading published single-cell datasets.
Why it matters
Quick access to curated single-cell data without re-downloading raw files.
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Open Single-cell omics
Human Cell Atlas
Reference maps of all human cells across tissues and developmental stages.
Why it matters
A reference for cell identity and tissue context.
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Open Perturbation data
LINCS / Connectivity Map
Perturbational signatures across cell lines for drugs, gene knockdowns, and overexpression.
Why it matters
Foundational dataset for connectivity-based reversal search.
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Protein structure
RCSB PDB
Repository of experimentally determined biomolecular structures.
Why it matters
The canonical source of real protein structures and ligand complexes.
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Open Protein structure
AlphaFold resources
Predicted protein structures across most known proteins.
Why it matters
Structure coverage for targets without experimental structures.
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Open Perturbation data
JUMP Cell Painting
Morphology-based perturbation profiles across thousands of compounds and gene perturbations.
Why it matters
Image-based phenotypic readout, complementary to transcriptomic perturbation data.
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Single-cell omics
scRNA-seq tutorials
Best-practices tutorials for single-cell analysis (QC, normalization, embedding, DE).
Why it matters
Avoids the common pitfalls before you start modeling.
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Systems biology
Systems biology textbooks
Foundational textbooks on pathway modeling, networks, and dynamics.
Why it matters
Builds the mechanistic vocabulary you need to read pathway literature.
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Pharmacology
Pharmacology references
References on PK/PD, ADMET, dose-response, and toxicity.
Why it matters
Connects molecular potency to in vivo therapeutic feasibility.
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Drug discovery
Peptiter · DiscoveryLab
A peptide discovery workbench combining condition-first targeting, receptor/pathway mapping, structure-aware design, and Lean 4 mechanism audits before wet-lab handoff.
Why it matters
A working example of the course's thesis: biology as a constrained search problem with formally checked, falsifiable mechanism claims.
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Open