- CellDesigner is a software suite for systems biology which enables grpahical editing of biological networks, simulation. It comply with SBML and SBGN, and can connect to SBW to utlize analysis packages.
- NetBuilder is an interactive graphical tool for representing and simulating genetic regulatory networks in multicellular organisms. Developed by Maria Schilstra, Mark Robinson, and Chrystopher Nehaniv at University of Hartfordshare. SBML Compliant and SBW Enabled.
- CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in the format compatible to a simulator. It has been developed by H. Kurata at the Kyushu Institute of Technology together with staffs at Mitsui Knowledge Industry Co., Ltd.
- Bio Sketch Pad
- Bio sketch Pad is an interactive tool for modeling and designing biomolecular and cellular networks with a simple, easy-to-use, graphical front end, leveraging powerful tools from control theory, hybrid systems, and software engineering.
- BioTapestry is an interactive tool for building, visualizing, and simulating genetic regulatory networks. It is designed around the concept of a developmental network model, and is intended to deal with large scale models with consistency and clarity. It is capable of representing systems that exhibit increasing complexity over time, such as the genetic regulatory network controlling endomesoderm development in sea urchin embryos.
- BioUML is Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.
- JDesigner is a graphical network editing tool developed by H. Sauro. It is tightly connected with Jarnac.
- PaVESy is a pathway visualization and editing system.
- SRS Pathway Editor
- A pathway eduitor tool by Lion Bioscience AG.