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subspace-identification

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charlesdavid / JED

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JED is a program for performing Essential Dynamics of protein trajectories written in Java. JED is a powerful tool for examining the dynamics of proteins from trajectories derived from MD or Geometric simulations. Currently, there are two types of PCA: distance-pair and Cartesian, and three models: COV, CORR, and PCORR.

pymol pca-analysis free-energy covariance-matrix principal-components dynamical-modeling kernel-density-estimation correlation-measures essentialmode correlation-matrices eigen-vector-decomposition subspace-identification
  • Updated May 18, 2018
  • HTML

ICSAC / internal-dynamics-of-decisions

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Analysis code, result files and both pre-registrations for "The Internal Dynamics of Decisions: From rats and primates to AI" (Thornhill 2026). Reanalysis of public rat, primate and AI-model recordings with an input-aware dynamical demix. Preprint: doi.org/10.20944/preprints202608.1095.v1

reproducible-research neuroscience electrophysiology dynamical-systems system-identification preregistration consciousness subspace-identification n4sid neural-dynamics
  • Updated Aug 21, 2026
  • Python

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