Software (original) (raw)
Software support
- Editors
- Visualizers and Formats Converters
- Tools using SBGN
- Databases and collections of SBGN maps
- File formats
- Archive of old tools
This page summarises what we know about software support for SBGN languages. This knowledge comes from a variety of sources, and is not necessarily complete. If your software and/or database is not listed below, or if you know of another effort, please post a message to sbgn-discuss.
The following are lists of software packages known to provide support for editing and visualising in SBGN Process Description (PD), Entity Relationship (ER) and Activity Flow (AF) with and without SBGN-ML file format support.
Editors
| Software | PD | ER | AF | SBGN-ML support | Availability |
|---|---|---|---|---|---|
| CellDesigner* | ☑ | ☐ | ☐ | ☑ | Installers for Win/Mac/Lin |
| Krayon for SBGN | ☑ | ☐ | ☐ | ☑ | IDE or Win installer |
| Newt Editor | ☑ | ☐ | ☑ | ☑ | In-browser |
| Omix | ☑ | ☐ | ☐ | ☑ | Commercial/free trial |
| PathVisio | ☑ | ☑ | ☑ | ☐ | Web start/binary |
| SBGN-ED | ☑ | ☑ | ☑ | ☑ | VANTED plugin |
| yEd** | ☑ | ☐ | ☐ | ☐ | Installers for Win/Mac/Lin |
* The cd2sbgnml converter enables bidirectional convertsion to/from SBGN-ML.
** The ySBGN converter enables bidirectional convertsion to/from SBGN-ML.
Visualisers and Formats Converters
| Software | PD | ER | AF | Formats | Availability |
|---|---|---|---|---|---|
| CySBGN | ☑ | ☑ | ☑ | SBML → SBGN | Cytoscape plugin |
| EscherConverter | ☑ | ☐ | ☐ | Esher JSON → SBGN | JAR file |
| KEGGtranslator | ☑ | ☐ | ☐ | KEGG-ML → SBGN | JAR file |
| SBML Layout Viewer | ☑ | ☐ | ☐ | SBML → SBGN | NET library |
| ChiBE | ☑ | ☐ | ☐ | BioPAX → SBGN | Istallers for Win/Mac/Linux |
| SBGNTikZ | ☑ | ☑ | ☑ | LaTex → SBGN | TeX package |
| stonpy | ☑ | ☐ | ☐ | SBGN-ML → Neo4j | Library for Neo4j |
| SBGNViz | ☑ | ☐ | ☐ | SBGN-ML → image | In-browser |
| ySBGN | ☑ | ☐ | ☑ | GraphML ↔ SBGN-ML | Maven install |
| cd2sbgnml | ☑ | ☐ | ☐ | CellDesigner ↔ SBGN-ML | Maven install |
| CaSQ | ☑ | ☐ | ☐ | CellDesigner → SBML-qual | Python package |
| Software | PD | ER | AF | Type of a tool |
|---|---|---|---|---|
| BIOCHAM | ☑ | ☐ | ☐ | Modeling |
| BioUML | ☑ | ☐ | ☐ | Modeling & Bioinformatics |
| COPASI | ☑ | ☐ | ☐ | Modeling |
| JWS Online | ☑ | ☐ | ☐ | Modeling |
| geneXplain platform | ☑ | ☐ | ☐ | Modeling & Bioinformatics |
| NaviCell | ☑ | ☐ | ☐ | Server supporting CellDesigner maps |
| MINERVA | ☑ | ☐ | ☐ | Server supporting SBGN maps |
Databases and collections of SBGN maps
| Database | PD | ER | AF | SBGN-ML export | Type of maps |
|---|---|---|---|---|---|
| AlzPathway | ☑ | ☐ | ☐ | ☐ | CellDesigner generated |
| AsthmaMap | ☑ | ☐ | ☑ | ☑ | yEd/CellDesigner generated, based on MINERVA platform |
| Atlas of Cancer Signalling Networks | ☑ | ☐ | ☐ | ☑ | CellDesigner generated |
| BioModels Database | ☑ | ☐ | ☐ | ☐ | JWS generated |
| COVID-19 Disease Map | ☑ | ☐ | ☐ | ☐ | Based on MINERVA platform |
| Metabolism Regulation Maps | ☑ | ☐ | ☐ | ☑ | yEd generated |
| MetaCrop | ☑ | ☐ | ☐ | ☑ | SBGN-ED generated |
| PANTHER Pathway | ☑ | ☐ | ☐ | ☑ | CellDesigner generated |
| Parkinson's disease map | ☑ | ☐ | ☐ | ☐ | CellDesigner generated, based on MINERVA platform |
| Path2Models* | ☑ | ☐ | ☐ | ☑ | PathVisio and SBGN-ED generated |
| Pathway Commons | ☑ | ☐ | ☐ | ☑ | |
| PathWhiz | ☑ | ☐ | ☐ | ☑ | SBGN-ML export |
| Reactome | ☑ | ☐ | ☐ | ☑ | Diagram JS or GWT |
| Rheumatoid Arthritis Map | ☑ | ☐ | ☐ | ☑ | CellDesigner generated, based on MINERVA platform |
| RIMAS | ☑ | ☐ | ☐ | ☐ | SBGN-ED generated |
| SubtiPathways | ☑ | ☐ | ☐ | ☐ | CellDesigner generated |
| Virtual Metabolic Human ReconMaps | ☑ | ☐ | ☐ | ☐ | CellDesigner generated |
* Path2Models is part of the BioModels Database.
File formats
SBGN-ML
The implementation of SBGN support in software packages may be facilitated by the use of the XML-based file format SBGN-ML. SBGN-ML can be processed and generated by the standard library LibSBGN. LibSBGN is a community project and everyone is welcome to participate.
Discussions around SBGN-ML and LibSBGN take place on sbgn-libsbgn-discuss.
One can compare the rendering of SBGN-ML by different software packages on the LibSBGN Render Comparison site.
BioPAX-SBGN Mapping
Biological Pathways Exchange (BioPAX) is a standard that aims to provide integration, exchange, visualization and analysis of biological pathway data. A substantial amount of BioPAX Level 3 concepts can be represented in SBGN PD via BioPAX-SBGN Mapping.
Biological Connection Markup Language (BCML)
The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML can be automatically converted into a SBGN-compliant graphical representation. More information regarding BCML software can be found here.
| Software | PD | ER | AF | Active |
|---|---|---|---|---|
| Arcadia | ☑ | ☐ | ☐ | |
| Athena | ☑ | ☐ | ☐ | |
| Beacon Pathway Editor | ☐ | ☐ | ☑ | |
| Biographer | ☑ | ☑ | ☑ | |
| Dunnart | ☑ | ☐ | ☐ | |
| Edinburgh Pathway Editor | ☑ | ☑ | ☑ | 2007 - 2011 |
| Netbuilder' | ☑ | ☐ | ☐ | |
| iPathways | ☑ | ☐ | ☐ | 2011 - 2017 |
| Mayday MGV | ☑ | ☐ | ☐ | |
| Mimoza | ☑ | ☐ | ☐ | |
| PathwayLab | ☑ | ☐ | ☐ | |
| SBMM assistant | ☑ | ☐ | ☐ | |
| STON | ☑ | ☐ | ☑ | |
| iPAVS | ☑ | ☐ | ☐ | |
| VISIBIOweb | ☑ | ☐ | ☐ | 2002 |