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Software

Research software I lead or maintain. Everything here is open source; issues and pull requests are welcome.

CeDNe

Python · MIT · 2024–present · lead developer

Connectome-embedded Dynamical Networks. A graph-based framework that integrates the C. elegans connectome, neuron identities, transcriptomes, neuropeptide maps and calcium imaging into one model, with tools for motif and pathway analysis and for fitting and simulating neural dynamics on the wiring diagram.

GitHub Docs Web app Preprint Research page
SWITCHES

Web resource · 2021 · with G. V. HarshaRani, N. Ramakrishnan and U. S. Bhalla

Searchable Web Interface for Topologies of CHEmical Switches. A database of bistable chemical reaction network topologies and the parameter regimes in which they switch, from an exhaustive enumeration of small networks.

Website Paper
LHSMDU

Python · 2020 · on PyPI

Latin Hypercube Sampling with Multi-Dimensional Uniformity. A small library for sampling high-dimensional parameter spaces evenly, written for large model-exploration runs and used across the chemical-switch work.

GitHub PyPI Zenodo
RD → SBML

NeuroRD-SBML

Python · 2022

Translates NeuroRD reaction–diffusion models into SBML with units, so biophysical signaling models can be shared, validated and reused across simulators.

GitHub