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A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.

Interaction Fingerprints for protein-ligand complexes and more.

Foundation model for universal prompt-driven medical image segmentation extending SAM3 to clinical imaging, supporting 2D public benchmarks and 3D training/evaluation with text and box prompts; pretrained weights available on HuggingFace (189+ stars)

Numerical differential equation solving in JAX

Fudan University's cascade machine learning forecasting system for 15-day global weather prediction, employing a 3D Earth-specific transformer with hard-constraint techniques to achieve state-of-the-art accuracy against traditional NWP and AI baselines

Diffusion-based document OCR framework replacing autoregressive decoding with block-level parallel diffusion decoding, enabling high-accuracy text recognition in scientific PDFs (613+ stars, MIT License)

Cross-platform system optimizations for accelerating AlphaFold3 training with 1.73x speedup and 1.23x memory reduction

Minimalist, batteries-included repository for training video world models with diffusion-forcing, supporting long-horizon rollouts, 3D point-cloud generation, and model-predictive control with pretrained checkpoints (Simchowitz Lab, 700+ stars, MIT License, 2026)

Learning the language of protein-protein interactions

Genomic foundation model for metagenomic and genome annotation, featuring an 8k base-pair context and 500M parameters trained on 386B base pairs of eukaryotic DNA; provides expert models and a unified CLI for prokaryotic/eukaryotic coding-sequence annotation with strong performance on Genomic Benchmarks, Nucleotide Transformer tasks, and custom Gener tasks (GenerTeam, 314+ stars, MIT License)

Automatic atomic model building program for cryo-EM maps using deep learning, enabling rapid de novo protein structure determination from electron density with high accuracy (3DEM/EMBL, 169+ stars)

Performs laboratory unit conversions across molarity, OD600 cell density, C₁V₁ dilution, and related dimensional pairs from mass, volume, molecular weight, and organism-specific OD factors. A browser calculator combines four modes in one tabbed workspace with compound MW lookup, species-aware OD uncertainty ranges, cross-tab chaining, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits conversion inputs and returns structured results and shareable run identifiers.

Translates spectrophotometer and NanoDrop readings into mass and molar concentrations for dsDNA, ssDNA, ssRNA, and protein from a single anchor input, with optional sequence-specific nearest-neighbor extinction coefficients. A browser calculator supports bidirectional unit conversion, batch processing of up to ninety-six NanoDrop export rows, and A260/A280 purity interpretation with plain-language warnings; a REST API exposes converter, batch, and purity modes for scripted use. Calculator arithmetic is hosted remotely; API clients transmit parameters and return structured result fields and shareable run identifiers.

Calculates sequence-derived molecular properties and related laboratory planning outputs from FASTA and assay setup inputs. The tool supports sequence analysis for DNA, RNA, and protein entries, plus dilution and ligation calculation modes through one API-backed workflow. Programmatic use is available through a Python library and command-line interface that submit run payloads and return structured result objects.

Translates between centrifuge RPM and relative centrifugal force using rotor geometry, reporting g-force or speed at rmin, ravg, and rmax. Convert mode handles rpm_to_rcf and rcf_to_rpm with rotor presets or manual radii in mm; transfer mode maps a source RPM on one rotor to an equivalent target RPM at matched rmax RCF; batch mode processes multiple spin steps from CSV or row arrays. A browser calculator and a Python library with command-line interface submit the same parameters to the Pepkio Tools API and return structured results with optional methods text and safety warnings.

Derives cells per well and suspension pipette volumes for standard 6-, 12-, 24-, 48-, 96-, and 384-well plates from a hemocytometer stock count, trypan blue viability, and target seeding confluency, with QC flags for low viability and impractical transfers. A browser calculator supports interactive planning with cell-line presets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured plate tables and shareable run identifiers.

Constructs Punnett squares and offspring genotype and phenotype ratios for complete, incomplete, codominant, ABO multiple-allele, and sex-linked Mendelian crosses from parent genotypes, with step-by-step walkthroughs and reduced ratio output. A browser calculator provides live grids, textbook presets, PNG and SVG export, and shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits cross inputs and returns structured grids, ratios, walkthroughs, and shareable run identifiers.

Evaluates Hardy-Weinberg equilibrium for diploid loci with two to six alleles using chi-square and Guo-Thompson exact tests, inbreeding coefficient F, and plain-language verdicts from observed genotype counts, allele frequencies, or biallelic disease incidence. A browser calculator provides De Finetti plots, export, and Wright-Fisher simulation under selection, drift, mutation, and migration; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted use. Calculator arithmetic for the API client is hosted remotely; the client transmits genotype or simulation inputs and returns structured results and shareable run identifiers.

Performs batch four-parameter and five-parameter logistic regression on multi-compound concentration–response screens to estimate IC50, EC50, pIC50, Hill slope, and related potency metrics with per-compound QC grades. A browser calculator supports CSV upload, curve review, and figure export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits concentration–response data and returns structured fit results and shareable run identifiers.

Processes 96-well plate absorbance data through blank subtraction, regression fitting, and dilution correction to report sample concentrations with QC flags for BCA, Bradford, and ELISA workflows. A browser calculator supports interactive grid entry with CSV and PDF export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits plate layout and absorbance values and returns model comparison, per-sample concentrations, and shareable run identifiers.

Generalist deep learning algorithm for cell and nucleus segmentation across diverse image types, with human-in-the-loop training (2.0) and one-click image restoration (3.0), 70K+ training objects (Nature Methods 2021/2022/2025)

Python library to train, interpret, and apply deep learning models to DNA sequences, providing a unified framework for regulatory genomics with support for CNN and transformer architectures, variant effect prediction, and attribution analysis (325+ stars)

General-purpose deep learning backbone for molecular modeling

Access to Biological Web Services from Python.

Universal foundation model for grounded biomedical image interpretation, enabling comprehensive visual understanding, reasoning, and grounding across diverse biomedical imaging modalities with strong zero-shot generalization (55+ stars, Apache 2.0, 2025-2026)

A tool and library for creating quantum chemistry input files.

Sparse identification of nonlinear dynamics

Closed-loop multi-agent system from hypothesis to verification across 12 scientific tasks, #1 on MLE-Bench (36.44%)

A swiss army knife for manipulating and editing PDB files.

Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.

Programmatic data labeling and weak supervision

Multi-agent system with Parser-Planner-Painter architecture converting `paper.pdf` to editable `poster.pptx`, outperforms GPT-4o with 87% fewer tokens

Estimates PCR primer melting temperatures and polymerase-specific annealing temperatures from sequence and buffer inputs, with per-pair QC for hairpins, dimers, and Tm balance. A browser calculator supports interactive single-pair and batch entry (up to 200 pairs) with method comparison and export; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic for the API client is hosted remotely; sequences are transmitted for programmatic runs while the web interface performs calculations in the browser.

Computes weighed laboratory buffer recipes from target pH, concentration, and volume, accounting for separate preparation and working temperatures when pKa shifts with temperature. Supports calculator mode from dry reagents and stock dilution mode, returning acid and base masses, ionic strength estimates, optional NaCl adjustment, gravimetric and titration routes, and stepwise protocols. A browser calculator supports interactive recipe entry with shareable links; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured recipe tables, compatibility warnings, and shareable run identifiers.

Plans PCR and qPCR master-mix reagent volumes from stock and final concentrations, reaction counts, and pipetting overage, with consolidated totals when several assays are prepared together. A browser calculator supports interactive recipe entry with printable bench sheets; a Python library and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured volume tables, dilution warnings, and shareable run identifiers.

Computes laboratory solution preparation parameters—powder mass to weigh, stock and diluent volumes for single dilutions, and multi-step serial concentration tables—with correction for hydrated salts and supplier purity. A browser calculator supports interactive prep planning with saved recipes and shareable links; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured protocol steps and shareable run identifiers.

Family of causal genomic foundation models trained on 1T tokens (~6T DNA base pairs) from the Carbon Pretraining Corpus, combining eukaryote genes, mRNA transcripts, and prokaryote genomes with a hybrid text/6-mer tokenizer; Carbon-3B matches or beats Evo2-7B on zero-shot DNA evaluations including sequence recovery, variant effect prediction, and perturbations (Apache 2.0, 201+ stars)

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.

Plans geometric serial dilution series for molecular biology and biochemistry workflows, rounding transfer volumes to declared pipette ranges and optional 96- or 384-well plate layouts. A browser calculator supports interactive protocol design; a Python client and command-line tool submit the same parameters to the Pepkio Tools API for scripted and pipeline use. Calculator arithmetic is hosted remotely; the client transmits parameters and returns structured step tables and shareable run identifiers.

State-of-the-art RNA 3D folding model developed with Stanford Das Lab and Kaggle competition winners, featuring a 488M-parameter AF3-like architecture with MSA and template-based modeling, enabling structure-driven drug discovery and RNA therapeutics design (NVIDIA-Digital-Bio, Apache 2.0)

LLM-native molecular language that represents molecules as explicit graph-based code, enabling LLMs to operate and reason on chemistry directly with 5× lower token cost and ~76-80% accuracy on novel molecules vs ~20% for SMILES; supports small molecules, polymers, and Markush structures with lossless RDKit interconversion and Claude Code/Codex agent skills (AtomFlow, arXiv:2605.16480, 281+ stars, MIT License, 2026)

Foundation model for universal cell segmentation achieving state-of-the-art performance across bacteria, tissue, yeast, cell culture, and diverse imaging modalities (brightfield, fluorescence, phase), with pip-installable inference and Napari plugin (vanvalenlab/Caltech, bioRxiv 2024)

Apache 2.0 single-cell foundation model family scaling to 3B parameters, pretrained on 266M cell profiles including perturbation data and released with training, embedding, and downstream benchmarking workflows for disease-relevant single-cell tasks (2025)

End-to-end composable multi-agent framework for automating OpenFOAM-based CFD simulations from natural language prompts, managing meshing, case setup, execution, error correction, and post-processing; achieves 100% success rate on 110 FoamBench tasks with Claude Opus 4.6 through Architect-Input Writer-Runner-Reviewer agent collaboration with RAG-enhanced generation and MCP tool integration (RPI CSML, 242+ stars, MIT License)

Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.

Programmatic framework for designing state-switching proteins via backpropagation through compositional design constraints parameterized by structure prediction models; enables de novo design of allosteric regulators and fluorescent biosensors for arbitrary small-molecule analytes (79+ stars, MIT License, ICML 2026)

High-throughput PubChem client for batch queries with caching, validation, rate-limit-aware retries, and a simple CLI.

First fully open-source model achieving AlphaFold3-level accuracy with 1000x faster binding affinity prediction (MIT)

Highly scalable equivariant deep learning interatomic potentials enabling million-atom molecular dynamics simulations with ab initio accuracy, building on E(3)-equivariant architectures for large-scale atomistic modeling (mir-group, MIT License, 480+ stars)

Foundational auto-research agent framework for agentic science at scale, providing modular agent construction, run-level self-evolution, and multiple SciMaster domain agents (ML-Master, X-Master, Browse-Master); outperforms general-purpose agents across authoritative benchmarks including the OpenAI Frontier Science Benchmark (206+ stars, Apache 2.0, 2026)