CSML

This document summarizes release notes of each version of CSML.

Cell System Markup Language 3.0 (CSML 3.0)

Currently, some XML formats are proposed to be a standard format for biopathways. However all formats provide only a partial solution for the storage and integration of biological data. The aim of CSML3.0 is to create a really usable XML format for visualizing, modeling and simulating biopathways.

For many cases, in vivo/vitro biological experimental results and in silico analyzed results are useful information for biopathway analysis. A successful application is Cytoscape, which can combine in vivo/vitro and in silico analyses into one graphical network. The core application supports a text-based and a GML formats. Plugins for importing XML format are developed, however, the functionality is limited. In addition, the application just visualizes the biopathway related data but dynamic simulation part is missing.

Other XML formats, SBML L2 and CellML1.1 are proposed and developed for dynamic simulation. These formats have become popular for chemical reactions and many applications support them as data exchanging formats. However, these formats do not define any graphical elements, which causes a difficulty to be a powerful data exchange format among biopathway applications.

Here, CSML3.0 is proposed as an integrated data exchange format which covers widely used data formats and applications, e.g. CellML1.1, SBML L2, BioPAX, and Cytoscape. In CSML1.9 and CSML2.0, the main focus was to support Hybrid Functional Petri net (HFPN) based visualization and simulation. CSML3.0 has focused on HFPNe architecture, extended HFPN with object notion, for more advanced biopathway representation. In short, objects that construct biopathways are treated as "generic entity" of HFPNe architecture and any relations among objects are treated as "generic process" on the HFPNe architecture.

Cell System Markup Language 2.0 (CSML 2.0)

CSML2.0 are developing as one of XML formats for biopathway modeling and simulation. This version add many features from CSML1.9. The document can obtain from Download page. However, the format is internal one, so stable version CSML1.9 is recommended at now.

Cell System Markup Language 1.9 (CSML 1.9)

CSML1.9 are developing as one of XML formats for biopathway modeling and simulation. The format mainly consists of five parts.

  1. The format for biopathway static network representation, e.g. graph structure.
  2. The format for biopathway dynamic network representation, e.g. Kinetics.
  3. The format for biological graphical representation of elements in (1).
  4. The format for representing relationships between each element of (1) and other biological public databases, e.g. GO, UnigeneID.
  5. The format for dynamic network simulation logging format for feature biopathway analyses.

Cell System Markup Language 1.0 (CSML 1.0)

CSML1.0 was released at Aug/2005 as one of XML formats for biopathway modeling and simulation. The format mainly consists of three parts.

  1. Petri net based static network representation, e.g. graph structure.
  2. Petri net based dynamic network representation, e.g. Kinetics.
  3. Graphical representation for (1).