[upstream-sync] README.md from ai-boost/awesome-ai-for-science@e0557705 [catalogue]

2026-08-23 22:47:01 +00:00
6 changed files with 158 additions and 909 deletions
@@ -2,9 +2,9 @@
 title: "Readme"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/ai-boost/awesome-ai-for-science/blob/ec6f3650/README.md
-upstream_sha: ec6f3650
-imported_at: 2026-08-21
+upstream_source: https://github.com/ai-boost/awesome-ai-for-science/blob/e0557705/README.md
+upstream_sha: e0557705
+imported_at: 2026-08-23
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -307,6 +307,7 @@ validated: false
 - [Scholar Loop](https://github.com/renee-jia/scholar-loop) - Autonomous multi-agent AI scientist that mirrors a PhD workflow: literature review → grounded hypothesis → real ML experiments → self-critique → write-up; features a deterministic harness with frozen-metric scoring, edit allowlists, and a verified registry to make reward-hacking and hallucination impossible, plus 108 unit tests runnable without API keys or GPUs (461+ stars, MIT License, 2026)
 - [ResearchStudio (Microsoft)](https://github.com/microsoft/ResearchStudio) - AI co-author covering the entire research lifecycle — from an under-specified research direction to a published paper; includes ResearchStudio-Idea for evidence-grounded research ideation and ResearchStudio-Reel for turning finished papers into posters, narrated videos, blogs, and interactive reels; runs as skills on Claude Code and Codex (1.2K+ stars, MIT License, 2026)
 - [Principia](https://github.com/pzqpzq/Principia) - Principle-first scientific idea discovery framework that extracts reusable principles from public literature and private research materials, composes them into traceable Idea Cards with prior-art comparisons, and exports validation-ready research packs; emphasizes inspectable scientific objects, risk disclosure, and falsification paths (ICML 2026, 411+ stars, MIT License)
+- [Imbue Catalyst](https://github.com/imbue-ai/catalyst) - Semi-autonomous AI scientist for scientific theory discovery and verifiable goal solving, using adversarial review-refinement loops and evolution-inspired candidate populations; integrates with Claude Code, Gemini CLI, Antigravity, and Codex harnesses (Imbue, 31+ stars, AGPL-3.0, 2026)

 ### Evaluation & Benchmarking
 - [ScienceAgentBench (ICLR 2025)](https://github.com/OSU-NLP-Group/ScienceAgentBench) - 102 executable tasks from 44 peer-reviewed papers across 4 disciplines with containerized evaluation
@@ -706,6 +707,7 @@ validated: false
 #### Materials Discovery
 - [GNoME](https://github.com/google-deepmind/materials_discovery) - DeepMind's graph neural network for materials exploration, discovering 2.2M new crystal structures (380K most stable) equivalent to 800 years of traditional research, with 520K+ materials dataset open-sourced (Nature 2023)
 - [FAIRChem (OMat24)](https://github.com/FAIR-Chem/fairchem) - Meta's comprehensive ML ecosystem for materials/chemistry with 118M+ DFT calculations, EquiformerV2 models achieving top Matbench Discovery performance
+- [Skala 1.1 (Microsoft Research, 2026)](https://github.com/microsoft/skala) - Neural network-based exchange-correlation functional for density functional theory (DFT) that surpasses state-of-the-art hybrid functionals in accuracy for main-group thermochemistry, kinetics, and non-covalent interactions at semi-local DFT cost; includes PySCF/GPU4PySCF/ASE bindings and C++/Fortran integrations (248+ stars, MIT License)
 - [All-atom Diffusion Transformers (ADiT)](https://github.com/facebookresearch/all-atom-diffusion-transformer) - Unified latent diffusion transformer that jointly generates periodic crystals and non-periodic molecules, scaling to 500M parameters with SOTA results on QM9, MP20, and GEOM-DRUGS (Meta FAIR, ICML 2025, 310+ stars)
 - [JARVIS](https://github.com/usnistgov/jarvis) - NIST's open-source platform for data-driven atomistic materials design, integrating DFT datasets (JARVIS-DFT), machine learning property prediction (JARVIS-ML), and a comprehensive leaderboard for benchmarking materials AI methods across the periodic table (384+ stars)
 - [NVIDIA ALCHEMI Toolkit](https://github.com/NVIDIA/nvalchemi-toolkit) - Developer toolkit for accelerating training and inference for AI in chemistry and material science, providing optimized GPU-accelerated workflows for molecular and materials machine learning (NVIDIA, 2026)
@@ -744,6 +746,7 @@ validated: false
 - [Neural ODEs](https://github.com/rtqichen/torchdiffeq) - Differential equations with neural networks
 - [Physics-Informed Neural Networks](https://github.com/maziarraissi/PINNs) - Physics-constrained ML
 - [EquiformerV2](https://github.com/atomicarchitects/equiformer_v2) - Improved equivariant Transformer for 3D atomic graphs (ICLR2024)
+- [EquiformerV3](https://github.com/atomicarchitects/equiformer_v3) - Scaling efficient, expressive, and general SE(3)-equivariant graph attention transformers for atomic systems and machine-learned interatomic potentials (MIT License, 2026)
 - [Equiformer](https://github.com/atomicarchitects/equiformer) - Equivariant graph attention Transformer (ICLR2023)
 - [TORAX](https://github.com/google-deepmind/torax) - Differentiable tokamak core transport simulator for fusion energy research, coupling PDE solvers with JAX auto-differentiation and neural-network surrogates for fast forward modelling, pulse-design, and trajectory optimization (Google DeepMind, Apache 2.0)
 - [DiffPhysDrone (Nature Machine Intelligence 2025)](https://github.com/HenryHuYu/DiffPhysDrone) - First real quadrotor robot trained end-to-end with differentiable physics for vision-based agile flight, bridging simulation-based learning and real-world deployment with physics-informed neural network controllers (558+ stars)
@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/README.md
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/README.md
+upstream_sha: 7a064bf0
+imported_at: 2026-08-08
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -75,7 +75,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
      - [Drug Target Interaction](#drug-target-interaction)
      - [Compound-Protein Interaction](#compound-protein-interaction)
      - [Molecular Generation](#molecular-generation)
-    - [Protein Property Prediction](#protein-property-prediction)
    - [LLM for Biology](#llm-for-biology)
    - [Foundation Models](#foundation-models)
      - [Single-cell Foundation Models](#single-cell-foundation-models)
@@ -160,7 +159,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GenBank](https://www.ncbi.nlm.nih.gov/genbank/) — NCBI's database of genetic sequences.
 - [UCSC Genome Browser](https://genome.ucsc.edu/) — UCSC's genome browser.
 - [cBioPortal](https://www.cbioportal.org/) — Cancer genomics database; aggregating many patient datasets.
- [OncoKB](https://www.oncokb.org/) — Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.
 - [10x Genomics Dataset](https://www.10xgenomics.com/resources/datasets) — Collection of single-cell datasets.
 - [The Genotype-Tissue Expression (GTEx)](https://gtexportal.org/home/) — Human gene expression and regulation resource.
 - [Dependency Map (DepMap)](https://depmap.org/portal/) — CRISPR-Cas9 screens in cancer cell lines.
@@ -318,7 +316,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [CellCharter](https://github.com/CSOgroup/cellcharter) — Identification and characterization of spatial cell niches from spatial transcriptomics using VAEs and Gaussian mixture models.
 - [STAGATE](https://github.com/RucDongLab/STAGATE) — Adaptive graph attention auto-encoder for spatial domain identification in spatial transcriptomics.
 - [NCEM](https://github.com/theislab/ncem) — GNN-based model for learning intercellular communication from spatial graphs of cells.
- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics.
+- [DeepTalk](https://github.com/JiangBioLab/DeepTalk) — Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.
 - [COMMOT](https://github.com/zcang/COMMOT) — Optimal transport-based framework for screening cell-cell communication in spatial transcriptomics.
 - [TIGON](https://github.com/yutongo/TIGON) — Neural optimal transport method for reconstructing growth and dynamic trajectories from single-cell transcriptomics.
 - [LINGER](https://github.com/Durenlab/LINGER) — Neural network for gene regulatory network inference from single-cell multiome (RNA+ATAC-seq) data with bulk data pretraining.
@@ -385,10 +383,6 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [ReLeaSE](https://github.com/isayev/ReLeaSE) — Deep reinforcement learning framework for de novo drug design combining a generative and predictive model.
 - [PaccMannRL](https://github.com/PaccMann/paccmann_generator) — Reinforcement learning-based generative model for de novo hit-like anticancer molecule design from transcriptomic data.

-### Protein Property Prediction
-
- [NbBayesLM](https://github.com/FairuzShadmaniShishir/NbBayesLM) — Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)
-
 ### LLM for Biology

 - [AI4Chem/ChemLLM-7B-Chat](https://huggingface.co/AI4Chem/ChemLLM-7B-Chat) — LLM for chemical & molecular science.
@@ -445,7 +439,7 @@ Browse and search the resources via the [GitHub Pages UI](https://inoue0426.gith
 - [GeneCompass](https://github.com/xCompass-AI/GeneCompass) — Large-scale foundation model integrating DNA regulatory sequences and single-cell transcriptomics from 120M+ cells across multiple species for gene regulation prediction.
 - [UnitedNet](https://github.com/LiuLab-Bioelectronics-Harvard/UnitedNet) — Interpretable multi-task deep neural network for single-cell multi-omics integration spanning transcriptomics, chromatin accessibility, and proteomics.
 - [SpatialGlue](https://github.com/zhanglabtools/SpatialGlue) — Graph attention network for spatial multi-omics integration jointly embedding spatial transcriptomics with chromatin accessibility or proteomics.
- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
+- [MIDAS](https://github.com/labomics/midas) — Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
 - [Concerto](https://github.com/melobio/Concerto-reproducibility) — Contrastive self-supervised learning framework for single-cell multimodal data integration, batch correction, and reference-query mapping.
 - [scButterfly](https://github.com/BioX-NKU/scButterfly) — Dual-aligned variational autoencoder for single-cell cross-modality translation between paired and unpaired multiomics data.
 - [JAMIE](https://github.com/Oafish1/JAMIE) — Joint variational autoencoder for multimodal single-cell data imputation and embedding.
@@ -527,7 +521,6 @@ If you use this list in papers, slides, or documentation, please cite this repos
 To keep quality high, additions should meet all of the following:

 - The resource is trustworthy and relevant to computational biology.
- The resource has clear value to the scope and audience of this collection; highly specialized resources with limited relevance beyond a narrow application context may be declined even when technically sound.
 - The primary link points to an official source (official docs, organization site, maintained repository, or official dataset page).
 - The resource has evidence of technical substance: ideally a peer-reviewed paper; at minimum a preprint or official technical documentation.
 - The description is factual and concise (no marketing copy).
@@ -2,9 +2,9 @@
 title: "Cspell"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/cspell.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/cspell.json
+upstream_sha: 7a064bf0
+imported_at: 2026-08-08
 prompt_class: unknown
 upstream_changes: accepted
 author: upstream
@@ -59,7 +59,6 @@ validated: false
    "eukaryotic",
    "metabolites",
    "OMIM",
-    "OncoKB",
    "Mendelian",
    "DisGeNET",
    "GWAS",
@@ -172,9 +171,7 @@ validated: false
    "bowang",
    "ctheodoris",
    "OpenAI",
-    "GPT",
-    "nanobody",
-    "thermostability"
+    "GPT"
  ],
  "ignorePaths": [
    "node_modules/**"
@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.json
+upstream_sha: 7a064bf0
+imported_at: 2026-08-08
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -899,20 +899,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "documentation": "https://www.10xgenomics.com/resources/datasets",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.10xgenomics.com/resources/datasets"
-    ]
+    "api": false
  },
  {
    "id": "alphafold_protein_structure_database",
@@ -925,20 +915,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://alphafold.ebi.ac.uk/",
-      "https://alphafold.ebi.ac.uk/api-docs"
-    ]
+    "api": false
  },
  {
    "id": "bindingdb",
@@ -952,20 +932,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
+      "Protein",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.bindingdb.org/rwd/bind/index.jsp"
-    ]
+    "api": false
  },
  {
    "id": "biocyc",
@@ -978,20 +949,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Pathway"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "pathway",
-      "organism"
-    ],
-    "documentation": "https://biocyc.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://biocyc.org/"
-    ]
+    "api": false
  },
  {
    "id": "biogrid",
@@ -1008,16 +969,7 @@ validated: false
      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "documentation": "https://thebiogrid.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://thebiogrid.org/"
-    ]
+    "api": false
  },
  {
    "id": "cancer_cell_line_encyclopedia",
@@ -1031,22 +983,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "transcriptomics"
+      "Gene Expression",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://sites.broadinstitute.org/ccle/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://sites.broadinstitute.org/ccle/"
-    ]
+    "api": false
  },
  {
    "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1059,20 +1000,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "documentation": "https://cancer.sanger.ac.uk/cosmic",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cancer.sanger.ac.uk/cosmic"
-    ]
+    "api": false
  },
  {
    "id": "cath_database",
@@ -1085,19 +1016,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.cathdb.info/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cathdb.info/"
-    ]
+    "api": false
  },
  {
    "id": "cbioportal",
@@ -1110,23 +1032,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "clinical"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "github": "https://github.com/cBioPortal/cbioportal",
-    "documentation": "https://www.cbioportal.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cbioportal.org/",
-      "https://github.com/cBioPortal/cbioportal"
-    ]
+    "api": false
  },
  {
    "id": "cellminer_cross_database_cellminercdb",
@@ -1183,20 +1092,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.ebi.ac.uk/chembl/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.ebi.ac.uk/chembl/"
-    ]
+    "api": false
  },
  {
    "id": "chemspider",
@@ -1225,19 +1124,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "clinical"
+      "Clinical"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://clinicaltrials.gov/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://clinicaltrials.gov/"
-    ]
+    "api": false
  },
  {
    "id": "comparative_toxicogenomics_database",
@@ -1251,20 +1141,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "gene",
-      "disease"
-    ],
-    "documentation": "https://ctdbase.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://ctdbase.org/"
-    ]
+    "api": false
  },
  {
    "id": "critical_assessment_of_structure_prediction_casp",
@@ -1293,21 +1174,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "transcriptomics"
+      "Single Cell"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "tissue"
-    ],
-    "documentation": "https://cellxgene.cziscience.com/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cellxgene.cziscience.com/"
-    ]
+    "api": false
  },
  {
    "id": "davis_kinase_inhibitors_db",
@@ -1338,21 +1208,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://depmap.org/portal/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://depmap.org/portal/"
-    ]
+    "api": false
  },
  {
    "id": "dgidb",
@@ -1366,19 +1225,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "gene"
-    ],
-    "documentation": "https://www.dgidb.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.dgidb.org/"
-    ]
+    "api": false
  },
  {
    "id": "diseases",
@@ -1441,21 +1292,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Knowledge Graph"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "disease",
-      "gene",
-      "pathway"
-    ],
-    "github": "https://github.com/SuLab/DrugMechDB",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/SuLab/DrugMechDB"
-    ]
+    "api": false
  },
  {
    "id": "drug_repurposing_hub",
@@ -1468,20 +1308,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://repo-hub.broadinstitute.org/repurposing"
-    ]
+    "api": false
  },
  {
    "id": "drugbank",
@@ -1519,20 +1349,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://drugcentral.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugcentral.org/"
-    ]
+    "api": false
  },
  {
    "id": "drugtargetcommons",
@@ -1545,19 +1365,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein"
-    ],
-    "documentation": "https://drugtargetcommons.fimm.fi/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugtargetcommons.fimm.fi/"
-    ]
+    "api": false
  },
  {
    "id": "encode",
@@ -2125,22 +1936,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "oncokb",
-    "name": "OncoKB",
-    "type": "database",
-    "url": "https://www.oncokb.org/",
-    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
-    "tags": [
-      "genome"
-    ],
-    "tasks": [],
-    "modalities": [
-      "Genomics"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "open_targets_platform",
    "name": "Open Targets Platform",
@@ -2588,18 +2383,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.uniprot.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.uniprot.org/"
-    ]
+    "api": false
  },
  {
    "id": "uniref",
@@ -4208,7 +3995,7 @@ validated: false
    "name": "MIDAS",
    "type": "model",
    "url": "https://github.com/labomics/midas",
-    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
+    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
    "tags": [
      "foundation-models",
      "multi-omics-foundation-models",
@@ -4479,24 +4266,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "nbbayeslm",
-    "name": "NbBayesLM",
-    "type": "model",
-    "url": "https://github.com/FairuzShadmaniShishir/NbBayesLM",
-    "description": "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)",
-    "tags": [
-      "protein-property-prediction"
-    ],
-    "tasks": [
-      "Protein Property Prediction"
-    ],
-    "modalities": [
-      "Protein"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "neodti",
    "name": "NeoDTI",
@@ -5675,23 +5444,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "dna-sequence",
-      "protein-sequence"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "github": "https://github.com/biopython/biopython",
-    "documentation": "https://biopython.org/wiki/Documentation",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/biopython/biopython",
-      "https://biopython.org/"
-    ]
+    "api": false
  },
  {
    "id": "casper",
@@ -5721,22 +5476,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/CSOgroup/cellcharter",
-    "documentation": "https://cellcharter.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/CSOgroup/cellcharter",
-      "https://cellcharter.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "cellchat",
@@ -5750,20 +5492,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/sqjin/CellChat",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/sqjin/CellChat"
-    ]
+    "api": false
  },
  {
    "id": "celltypist",
@@ -5775,24 +5506,11 @@ validated: false
      "preprocessing-tools"
    ],
    "tasks": [
-      "cell-type-annotation"
-    ],
-    "modalities": [
-      "single-cell-rna-seq"
+      "Preprocessing"
    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/Teichlab/celltypist",
-    "documentation": "https://celltypist.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/Teichlab/celltypist",
-      "https://celltypist.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "chatspatial",
@@ -5854,30 +5572,16 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "github": "https://github.com/deepchem/deepchem",
-    "documentation": "https://deepchem.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/deepchem/deepchem",
-      "https://deepchem.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "deeptalk",
    "name": "DeepTalk",
    "type": "toolkit",
    "url": "https://github.com/JiangBioLab/DeepTalk",
-    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics.",
+    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.",
    "tags": [
      "preprocessing-tools"
    ],
@@ -6092,21 +5796,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule"
-    ],
-    "github": "https://github.com/rdkit/rdkit",
-    "documentation": "https://www.rdkit.org/docs/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/rdkit/rdkit",
-      "https://www.rdkit.org/docs/"
-    ]
+    "api": false
  },
  {
    "id": "scanpy",
@@ -6120,22 +5812,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scanpy",
-    "documentation": "https://scanpy.readthedocs.io/en/stable/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scanpy",
-      "https://scanpy.readthedocs.io/en/stable/"
-    ]
+    "api": false
  },
  {
    "id": "scenic",
@@ -6197,23 +5876,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq",
-      "multi-omics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scvi-tools",
-    "documentation": "https://docs.scvi-tools.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scvi-tools",
-      "https://docs.scvi-tools.org/"
-    ]
+    "api": false
  },
  {
    "id": "seqbench",
@@ -6243,22 +5908,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/satijalab/seurat",
-    "documentation": "https://satijalab.org/seurat/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/satijalab/seurat",
-      "https://satijalab.org/seurat/"
-    ]
+    "api": false
  },
  {
    "id": "squidpy",
@@ -6272,22 +5924,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/scverse/squidpy",
-    "documentation": "https://squidpy.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/squidpy",
-      "https://squidpy.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "stagate",
@@ -2,9 +2,9 @@
 title: "Awesome Computational Biology - machine-readable resource list"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/data/resources.yml
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/data/resources.yml
+upstream_sha: 7a064bf0
+imported_at: 2026-08-08
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -1183,17 +1183,6 @@ resources:
    organism: []
    api: false

-  - id: oncokb
-    name: "OncoKB"
-    type: database
-    url: https://www.oncokb.org/
-    description: "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications."
-    tags: [genome]
-    tasks: []
-    modalities: [Genomics]
-    organism: []
-    api: false
-
  - id: open_targets_platform
    name: "Open Targets Platform"
    type: database
@@ -2254,7 +2243,7 @@ resources:
    name: "MIDAS"
    type: model
    url: https://github.com/labomics/midas
-    description: "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics."
+    description: "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics."
    tags: [foundation-models, multi-omics-foundation-models, single-cell-foundation-models]
    tasks: [Foundation Model]
    modalities: [Multi-Omics, Single Cell]
@@ -2393,17 +2382,6 @@ resources:
    organism: []
    api: false

-  - id: nbbayeslm
-    name: "NbBayesLM"
-    type: model
-    url: https://github.com/FairuzShadmaniShishir/NbBayesLM
-    description: "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)"
-    tags: [protein-property-prediction]
-    tasks: [Protein Property Prediction]
-    modalities: [Protein]
-    organism: []
-    api: false
-
  - id: neodti
    name: "NeoDTI"
    type: model
@@ -3002,7 +2980,7 @@ resources:
    name: "DeepTalk"
    type: toolkit
    url: https://github.com/JiangBioLab/DeepTalk
-    description: "Graph attention network for deciphering cell-cell communication from spatial transcriptomics."
+    description: "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data."
    tags: [preprocessing-tools]
    tasks: [Preprocessing]
    modalities: []
@@ -2,9 +2,9 @@
 title: "Resources"
 task: ""
 lineage_type: import
-upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/c6f07d90/docs/data/resources.json
-upstream_sha: c6f07d90
-imported_at: 2026-08-31
+upstream_source: https://github.com/inoue0426/awesome-computational-biology/blob/7a064bf0/docs/data/resources.json
+upstream_sha: 7a064bf0
+imported_at: 2026-08-08
 prompt_class: catalogue
 upstream_changes: accepted
 author: upstream
@@ -899,20 +899,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "documentation": "https://www.10xgenomics.com/resources/datasets",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.10xgenomics.com/resources/datasets"
-    ]
+    "api": false
  },
  {
    "id": "alphafold_protein_structure_database",
@@ -925,20 +915,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://alphafold.ebi.ac.uk/api-docs",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://alphafold.ebi.ac.uk/",
-      "https://alphafold.ebi.ac.uk/api-docs"
-    ]
+    "api": false
  },
  {
    "id": "bindingdb",
@@ -952,20 +932,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
+      "Protein",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.bindingdb.org/rwd/bind/index.jsp",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.bindingdb.org/rwd/bind/index.jsp"
-    ]
+    "api": false
  },
  {
    "id": "biocyc",
@@ -978,20 +949,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Pathway"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "pathway",
-      "organism"
-    ],
-    "documentation": "https://biocyc.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://biocyc.org/"
-    ]
+    "api": false
  },
  {
    "id": "biogrid",
@@ -1008,16 +969,7 @@ validated: false
      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "documentation": "https://thebiogrid.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://thebiogrid.org/"
-    ]
+    "api": false
  },
  {
    "id": "cancer_cell_line_encyclopedia",
@@ -1031,22 +983,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "transcriptomics"
+      "Gene Expression",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://sites.broadinstitute.org/ccle/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://sites.broadinstitute.org/ccle/"
-    ]
+    "api": false
  },
  {
    "id": "catalogue_of_somatic_mutations_in_cancer_cosmic",
@@ -1059,20 +1000,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "documentation": "https://cancer.sanger.ac.uk/cosmic",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cancer.sanger.ac.uk/cosmic"
-    ]
+    "api": false
  },
  {
    "id": "cath_database",
@@ -1085,19 +1016,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "molecular-structure",
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.cathdb.info/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cathdb.info/"
-    ]
+    "api": false
  },
  {
    "id": "cbioportal",
@@ -1110,23 +1032,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics",
-      "clinical"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "gene",
-      "variant"
-    ],
-    "github": "https://github.com/cBioPortal/cbioportal",
-    "documentation": "https://www.cbioportal.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.cbioportal.org/",
-      "https://github.com/cBioPortal/cbioportal"
-    ]
+    "api": false
  },
  {
    "id": "cellminer_cross_database_cellminercdb",
@@ -1183,20 +1092,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "molecule",
-      "protein"
-    ],
-    "documentation": "https://www.ebi.ac.uk/chembl/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.ebi.ac.uk/chembl/"
-    ]
+    "api": false
  },
  {
    "id": "chemspider",
@@ -1225,19 +1124,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "clinical"
+      "Clinical"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://clinicaltrials.gov/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://clinicaltrials.gov/"
-    ]
+    "api": false
  },
  {
    "id": "comparative_toxicogenomics_database",
@@ -1251,20 +1141,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "compound",
-      "gene",
-      "disease"
-    ],
-    "documentation": "https://ctdbase.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://ctdbase.org/"
-    ]
+    "api": false
  },
  {
    "id": "critical_assessment_of_structure_prediction_casp",
@@ -1293,21 +1174,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "single-cell-rna-seq",
-      "transcriptomics"
+      "Single Cell"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "tissue"
-    ],
-    "documentation": "https://cellxgene.cziscience.com/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://cellxgene.cziscience.com/"
-    ]
+    "api": false
  },
  {
    "id": "davis_kinase_inhibitors_db",
@@ -1338,21 +1208,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "genomics"
+      "Genomics"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene",
-      "disease",
-      "drug"
-    ],
-    "documentation": "https://depmap.org/portal/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://depmap.org/portal/"
-    ]
+    "api": false
  },
  {
    "id": "dgidb",
@@ -1366,19 +1225,11 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Gene",
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "gene"
-    ],
-    "documentation": "https://www.dgidb.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.dgidb.org/"
-    ]
+    "api": false
  },
  {
    "id": "diseases",
@@ -1441,21 +1292,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "knowledge-graph"
+      "Knowledge Graph"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "disease",
-      "gene",
-      "pathway"
-    ],
-    "github": "https://github.com/SuLab/DrugMechDB",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/SuLab/DrugMechDB"
-    ]
+    "api": false
  },
  {
    "id": "drug_repurposing_hub",
@@ -1468,20 +1308,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://repo-hub.broadinstitute.org/repurposing",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://repo-hub.broadinstitute.org/repurposing"
-    ]
+    "api": false
  },
  {
    "id": "drugbank",
@@ -1519,20 +1349,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein",
-      "disease"
-    ],
-    "documentation": "https://drugcentral.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugcentral.org/"
-    ]
+    "api": false
  },
  {
    "id": "drugtargetcommons",
@@ -1545,19 +1365,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "chemical-structure"
+      "Small Molecule"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "drug",
-      "protein"
-    ],
-    "documentation": "https://drugtargetcommons.fimm.fi/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://drugtargetcommons.fimm.fi/"
-    ]
+    "api": false
  },
  {
    "id": "encode",
@@ -2125,22 +1936,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "oncokb",
-    "name": "OncoKB",
-    "type": "database",
-    "url": "https://www.oncokb.org/",
-    "description": "Precision oncology knowledge base of cancer genes, variants, and therapeutic implications.",
-    "tags": [
-      "genome"
-    ],
-    "tasks": [],
-    "modalities": [
-      "Genomics"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "open_targets_platform",
    "name": "Open Targets Platform",
@@ -2588,18 +2383,10 @@ validated: false
    ],
    "tasks": [],
    "modalities": [
-      "protein-sequence"
+      "Protein"
    ],
    "organism": [],
-    "api": false,
-    "entities": [
-      "protein"
-    ],
-    "documentation": "https://www.uniprot.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://www.uniprot.org/"
-    ]
+    "api": false
  },
  {
    "id": "uniref",
@@ -4208,7 +3995,7 @@ validated: false
    "name": "MIDAS",
    "type": "model",
    "url": "https://github.com/labomics/midas",
-    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
+    "description": "Mosaic integration and differential accessibility model for single-cell multi-omics data that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.",
    "tags": [
      "foundation-models",
      "multi-omics-foundation-models",
@@ -4479,24 +4266,6 @@ validated: false
    "organism": [],
    "api": false
  },
-  {
-    "id": "nbbayeslm",
-    "name": "NbBayesLM",
-    "type": "model",
-    "url": "https://github.com/FairuzShadmaniShishir/NbBayesLM",
-    "description": "Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. [Paper](https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2026.1832968/full)",
-    "tags": [
-      "protein-property-prediction"
-    ],
-    "tasks": [
-      "Protein Property Prediction"
-    ],
-    "modalities": [
-      "Protein"
-    ],
-    "organism": [],
-    "api": false
-  },
  {
    "id": "neodti",
    "name": "NeoDTI",
@@ -5675,23 +5444,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "dna-sequence",
-      "protein-sequence"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "gene",
-      "protein"
-    ],
-    "github": "https://github.com/biopython/biopython",
-    "documentation": "https://biopython.org/wiki/Documentation",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/biopython/biopython",
-      "https://biopython.org/"
-    ]
+    "api": false
  },
  {
    "id": "casper",
@@ -5721,22 +5476,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/CSOgroup/cellcharter",
-    "documentation": "https://cellcharter.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/CSOgroup/cellcharter",
-      "https://cellcharter.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "cellchat",
@@ -5750,20 +5492,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/sqjin/CellChat",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/sqjin/CellChat"
-    ]
+    "api": false
  },
  {
    "id": "celltypist",
@@ -5775,24 +5506,11 @@ validated: false
      "preprocessing-tools"
    ],
    "tasks": [
-      "cell-type-annotation"
-    ],
-    "modalities": [
-      "single-cell-rna-seq"
+      "Preprocessing"
    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/Teichlab/celltypist",
-    "documentation": "https://celltypist.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/Teichlab/celltypist",
-      "https://celltypist.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "chatspatial",
@@ -5854,30 +5572,16 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure",
-      "molecular-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule",
-      "protein"
-    ],
-    "github": "https://github.com/deepchem/deepchem",
-    "documentation": "https://deepchem.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/deepchem/deepchem",
-      "https://deepchem.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "deeptalk",
    "name": "DeepTalk",
    "type": "toolkit",
    "url": "https://github.com/JiangBioLab/DeepTalk",
-    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics.",
+    "description": "Graph attention network for deciphering cell-cell communication from spatial transcriptomics data.",
    "tags": [
      "preprocessing-tools"
    ],
@@ -6092,21 +5796,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "chemical-structure"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "molecule"
-    ],
-    "github": "https://github.com/rdkit/rdkit",
-    "documentation": "https://www.rdkit.org/docs/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/rdkit/rdkit",
-      "https://www.rdkit.org/docs/"
-    ]
+    "api": false
  },
  {
    "id": "scanpy",
@@ -6120,22 +5812,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scanpy",
-    "documentation": "https://scanpy.readthedocs.io/en/stable/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scanpy",
-      "https://scanpy.readthedocs.io/en/stable/"
-    ]
+    "api": false
  },
  {
    "id": "scenic",
@@ -6197,23 +5876,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq",
-      "multi-omics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/scverse/scvi-tools",
-    "documentation": "https://docs.scvi-tools.org/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/scvi-tools",
-      "https://docs.scvi-tools.org/"
-    ]
+    "api": false
  },
  {
    "id": "seqbench",
@@ -6243,22 +5908,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "single-cell-rna-seq"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "gene"
-    ],
-    "github": "https://github.com/satijalab/seurat",
-    "documentation": "https://satijalab.org/seurat/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/satijalab/seurat",
-      "https://satijalab.org/seurat/"
-    ]
+    "api": false
  },
  {
    "id": "squidpy",
@@ -6272,22 +5924,9 @@ validated: false
    "tasks": [
      "Preprocessing"
    ],
-    "modalities": [
-      "spatial-transcriptomics"
-    ],
+    "modalities": [],
    "organism": [],
-    "api": false,
-    "entities": [
-      "cell",
-      "tissue"
-    ],
-    "github": "https://github.com/scverse/squidpy",
-    "documentation": "https://squidpy.readthedocs.io/",
-    "last_checked": "2026-08-08",
-    "metadata_sources": [
-      "https://github.com/scverse/squidpy",
-      "https://squidpy.readthedocs.io/"
-    ]
+    "api": false
  },
  {
    "id": "stagate",