Our research team website

a modeling environment tailored to parameter estimation in dynamical systems

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.

Picotti lab data analysis package.

Galaxy wrappers of SynBioCAD tools suite

Multi-condensate state as a functional strategy to optimize the cell signaling output

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Finite State Projection algorithms for chemical reaction networks

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

PyBioPAX: A python implementation of the BioPAX object model

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

PySCeS biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.

eBCSgen - BioChemical Space Language support tool.

The consensus GEM for Saccharomyces cerevisiae

SyBValS: Systems Biology Validation Service

LibSBML is a native library for reading, writing and manipulating files and data streams containing the Systems Biology Markup Language (SBML). It offers language bindings for C, C++, C#, Java, JavaScript, MATLAB, Perl, PHP, Python, R and Ruby.

Spatial bio-chemical reaction model editor and simulator

Dynamical modeling of biological systems in 1, 2 and 3D - incl. diffusion, reactions & compartments (Python, JupyterLab, Plotly)