Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
An Artificial Life simulator for Investigating Noogenesis
Modular cloning simulation with the MoClo framework in Python
Integration of pathway-related information from Reactome in BEL
LLM based multi agent system for automated MorpheusML model generation from scientific papers using Model Context Protocol (MCP).
Convert proteomics data from ppm to cellular concentrations (g/gDCW) for enzyme constrained modeling
A state-driven Multi-Agent framework for automated genetic circuit design. Combines RAG, ODE simulations, and Human-in-the-Loop verification to compile natural language into Cello Verilog netlists.
A Python simulator for modeling gene expression perturbations using a recursive, depth-limited path summation model.
Repository for our paper "When Does Gene Regulatory Network Inference Break? A Controlled Diagnostic Study of Causal and Correlational Methods on Single-Cell Data"
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