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Error exporting to SBML when compartment size is an Expression

Status: Open.

#604 In pysb/pysb;

· blakeaw opened on Aug 6, 2025

sympy dependency issue: sympy<1.12,>=1.6

Status: Open.

#598 In pysb/pysb;

· fbergmann opened on Aug 14, 2024

Fails to simulate an SBML model (Species does not have a compartment attribute!)

Status: Open.

#592 In pysb/pysb;

· TorkelE opened on Mar 12, 2024

Exception: The program BioNetGen was not found in the default search path(s)

Status: Open.

#578 In pysb/pysb;

· CNelias opened on Jul 3, 2023

test_bng_boolean_multiply_number fails with SymPy 1.12

Status: Open.

#577 In pysb/pysb;

· himoto opened on Jun 13, 2023

SBML export annotations

Status: Open.

#573 In pysb/pysb;

· pcarlip opened on Mar 17, 2023

Odd behavior when modeling second order reaction with one species

Status: Open.

#572 In pysb/pysb;

· jadeshi opened on Mar 13, 2023

Add units to model parameters, expressions, species

Status: Open.

#571 In pysb/pysb;

· ortega2247 opened on Jan 4, 2023

Error at tutorial visualization step

Status: Open.

#568 In pysb/pysb;

· lhdp0110 opened on Sep 23, 2022

Problems with reactions where two monomers form another monomer VS two monomers form a dimer

Status: Open.

#561 In pysb/pysb;

· Quim98 opened on Jul 14, 2022

Model component concentration as an explicit function

Status: Open.

#556 In pysb/pysb;

· melkonyan opened on Dec 2, 2021

top-level export function does not accept extra exporter-specific kwargs

Status: Open.

#547 In pysb/pysb;

· jmuhlich opened on Jun 13, 2021