Open source code for AlphaFold 2.
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Efficiently computes derivatives of NumPy code.
- autograd
- automatic-differentiation
- numpy
- python
Mesa is an open-source Python library for agent-based modeling, ideal for simulating complex systems and exploring emergent behaviors.
- mesa
- agent-based-modeling
- agent-based-simulation
- simulation-framework
Python Toolkit for Causal and Probabilistic Reasoning
- python
- bayesian-networks
- causal-inference
- causal-discovery
Visualize and compare datasets, target values and associations, with one line of code.
- pandas-dataframe
- eda
- pandas
- data-exploration
Open-source, end-to-end platform for evaluating, observing, and improving LLM and AI agent applications. Tracing · Evals · Simulations · Datasets · Gateway · Guardrails. Self-hostable. Apache 2.0.
- ai-gateway
- observability
- simulation
- ai-agents
Source code of PyGAD, a Python 3 library for building the genetic algorithm and training machine learning algorithms (Keras & PyTorch).
- python
- genetic-algorithm
- optimization
- numpy
Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining
A full spaCy pipeline and models for scientific/biomedical documents.
- scientific-documents
- spacy
- custom-pipes
- nlp
MarS: a Financial Market Simulation Engine Powered by Generative Foundation Model
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
- diffusion-models
- docking
- binding
- computational-biology
Biological foundation modeling from molecular to genome scale
Unknown Horizons official code repository
- game
- python
- strategy
- simulation
Brian is a free, open source simulator for spiking neural networks.
- python
- neuroscience
- science
- differential-equations
[CONTRIBUTORS WELCOME] Generalized Additive Models in Python
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
- machine-learning
- generative-models
- drug-discovery
- benchmark
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
⚗ A package useful for chemistry written in Python
- chemistry
- physical-chemistry
- chemical-kinetics
- chemical-formulas
FiPy is a Finite Volume PDE solver written in Python
- scientific-computing
- scientific-computing-with-python
- phase-field
- materials-science
Module for statistical learning, with a particular emphasis on time-dependent modelling
- machine-learning
- python
- point-process
- optimization
Universal SKILL.md catalog for research workflows: literature review, research design, project memory, manuscript writing, and cross-agent delegation for Claude Code, Codex, Gemini, Cursor, OpenClaw, and generic AI clients.
- academic-writing
- ai-skills
- notebooklm
- obsidian
Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
A Python native dynamical system simulation framework in the block diagram paradigm.
- blockdiagram
- control-systems
- hierarchical-modeling
- nonlinear-dynamics
Unmanned Surface Vehicle simulation on Gazebo with water current and winds
- usv
- boat
- gazebo
- water-surface