Open Source Software & Tools

Neural Decoding & Analysis

• Neural_Decoding - Comprehensive Python package for decoding neural activity using modern machine learning methods including LSTMs, neural networks, and gradient boosting
• Spykes (Documentation) - Python tools for spike data analysis and visualization
• pyglmnet - Python implementation of elastic-net regularized generalized linear models (Paper)
• SpykesML - Machine learning algorithms for spike prediction
• DAD (Distribution Alignment Decoder) - Novel decoder for neural data that aligns distributions

Educational & Teaching Resources

• Lab Teaching Materials - Repository of materials and codes from Kording lab teachings
• Kording Lab Projects - Full collection of 38+ repositories from our lab

Datasets

Movement & Motor Control

• DREAM Database - Database for Reaching Experiments And Models, containing standardized reaching movement data from multiple labs
  • Requires CRCNS login for download
  • Includes MATLAB tools and documentation
  • Overview paper

Neural Recordings

• Neural Decoding Datasets - Three datasets available with our Neural_Decoding package:
  • Motor cortex recordings
  • Somatosensory cortex recordings
  • Hippocampus recordings
  • Available in both MATLAB and Python formats

Open Science Framework

• Bayesian Models of Behavior Datasets - Datasets accompanying the book by Ma, Kording, and Goldreich
• Konrad Kording OSF Profile - Additional datasets and materials

Educational Initiatives

Neuromatch Academy

Neuromatch Academy - Free, online computational neuroscience summer school co-founded by Konrad Kording

• Course Materials - Complete curriculum as interactive Jupyter notebooks
• GitHub Repository - All course content and tutorials
• Topics include: modeling, machine learning, dynamics, causality, and deep learning
• Over 10,000 students trained globally since 2020

Community for Rigor (C4R)

Community for Rigor - NIH/NINDS-funded initiative for teaching scientific rigor at scale

• GitHub Organization - Educational tools and materials
• Free online modules covering:
  • Confirmation bias and cognitive errors
  • Causation vs correlation
  • Research question formulation
  • Experimental design and randomization
  • Statistical analysis best practices

Neuro4Pros

Neuro4Pros Summer School - Training for young computational neuroscience professors

• Co-organized with Gunnar Blohm
• Focus on rigorous science, mentoring, and lab management

Key Publications & Methods

Recent Methods Papers

• Machine Learning for Neural Decoding (eNeuro 2020)
• Three Aspects of Representation in Neuroscience (Trends in Cognitive Sciences 2022)
• Distribution Alignment Decoder (Nature Biomedical Engineering 2017)

Theory & Perspectives

• Nothing Makes Sense in Deep Learning, Except in the Light of Evolution (2022)
• Toward a Neuroscience of Natural Behavior (Nature Communications 2023)
• The Credit Assignment Problem (2019)

Collaborations & Networks

Data Sharing Initiatives

• CRCNS - Collaborative Research in Computational Neuroscience
  • Multiple shared datasets and models
  • Focus on open science and reproducibility

Community Platforms

• Twitter/X: @KordingLab - Lab updates and discussions
• GitHub: KordingLab - All our open source projects

For Researchers

Getting Started with Our Tools

1. Neural Decoding: pip install neural_decoding or clone from GitHub
2. Spykes: pip install spykes for spike analysis
3. Data Access: Register at CRCNS for movement datasets

Contributing

• Most repositories accept pull requests
• Issues and bug reports welcome on GitHub
• Contact lab members for collaboration opportunities

For Students

Learning Resources

• Start with Neuromatch Academy materials for computational neuroscience fundamentals
• Explore C4R modules for research methods training
• Check our lab teachings repository for specialized topics

Tools for Projects

• Use our project planner app for structuring research
• Access example notebooks in each repository for implementation guidance

Contact & Support

For questions about specific resources:

• Software issues: Open an issue on the relevant GitHub repository
• Dataset access: Contact CRCNS for database-specific questions
• Educational materials: Visit Neuromatch or C4R websites
• General inquiries: kording@upenn.edu

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Last updated: September 2025