E-cyanobacterium.org is an online platform providing tools for public sharing, annotation, analysis, and visualization of dynamical models and wet-lab experiments related to cyanobacteria. The platform is unique in integrating abstract mathematical models with a precise consortium-agreed biochemical description provided in a rule-based formalism. The general aim is to stimulate collaboration between experimental and computational systems biologists to achieve better understanding of cyanobacteria.

Biochemical Space is developed as a part of Comprehensive Modeling Platform – a web-based platform for modeling and analysis of biological processes. In the context of the platform, Biochemical Space glues together complicated quantitative models with an easy-to-understand, yet formal and compact qualitative description. It allows to specify formal and well-annotated reaction networks of chemical entities and elemental reactions onto which the mathematical models are projected. Biochemical Space is supported by a Biochemical Space Language that combines state-of-the-art rule-based techniques with meta-data formats developed in well-known annotation databases.

The general goal of the tool is to provide environment suitable for editing and maintenance of the Biochemical Space Language models and provide functionality to analyse the models. The tool is developed in Python language (version 2.7) as open-source desktop software build under GPL-3.0 license. The source code, a short tutorial for usage and installation, and current stable version are available on GitHub.