aipoch
aipoch / paper-narrative
4.9kJudge and reshape the story told by an entire paper figure deck
aipoch / skill-creator
4.9kCreate, revise, evaluate, publish, and improve Open-Science Skills through the native JavaScript host.skills composer
aipoch / ColabFold MSA server (api.colabfold.com)
4.9kPredict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021).
aipoch / ColabFold MSA server (api.colabfold.com)
4.9kStructure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz).
aipoch / Borzoi (PyTorch port)
4.9kPredict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted t…
aipoch / ColabFold MSA server (api.colabfold.com)
4.9kStructure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab).
aipoch / compute-env-setup
4.9kPrepare reproducible setup instructions and validate a user-managed named software environment on an Open-Science SSH Compute Host, including direct SSH and Slurm hosts
aipoch / customize
4.9kUse when the user wants to create or manage a Specialist agent or create, revise, publish, or delete a Skill through the conversational `/Customize` entry. Routes Skill work to the internal skill-creator and handles Specialist work through the JavaScript host.agents SDK.
aipoch / DiffDock-L
4.9kPredict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model.
aipoch / env-management
4.9kUse when a notebook run fails on a missing package (ImportError, ModuleNotFoundError, "there is no package called"), when you need to inspect an installed package version, or when you need to install, add, or manage Python or R packages for the notebook runtime.
aipoch / esmfold2
4.9kBiohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass.
aipoch / Evo 2
4.9kScore, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a pre…
aipoch / ESM-2
4.9kEmbed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.
aipoch / figure-composer
4.9kCompose one publication-grade multi-panel figure. Start from a one-line claim plus immutable data Artifact Version references, or inspect an existing figure and draft its outline directly.
aipoch / figure-style
4.9kPublication-grade correctness and legibility rules for final-deliverable scientific figures, not exploratory plots. Use for a figure that will ship in a report, paper, export, or kept artifact.
aipoch / indication-dossier
4.9kGenerate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.
aipoch / LigandMPNN
4.9kInverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN).
aipoch / OpenAlex
4.9kFind, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. Covers grounding claims in real retrieved sources, avoiding fabricated citations, handling retractions, and calibrating confidence to evidence strength.
aipoch / ColabFold MSA server (api.colabfold.com)
4.9kStructure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use this skill when predicting protein/nucleic-acid/ligand complex structures with an Apache-2.0-licensed AF3 reimplementation.
aipoch / ProteinMPNN
4.9kInverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN).
aipoch / remote-compute-ssh
4.9kEvaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote commands and asynchronous jobs with automatic harvest and analysis.
aipoch / scGPT
4.9kEmbed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN t…
aipoch / scvi-tools
4.9kProbabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression.
aipoch / self-awareness
4.9kInspect Open-Science's JavaScript control REPL, discover managed Project files, Sessions, and Agent Frames, and safely feature-gate host.* calls with host.capabilities()
aipoch / SolubleMPNN
4.9kInverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation.