Extract text from CYS files
To convert your CYS file to another format, you need Cytoscape or other Data software.
To convert other file formats to the "Network Visualization Session" file type, you need software like Cytoscape or a similar tool.
The .CYS file extension is primarily associated with Cytoscape, the industry-standard software for visualizing complex networks and biological pathways. These files serve as "Session" containers, preserving your entire workspace - including imported networks, node/edge attributes, and visual styles - exactly as you left them.
While .CYS files are essential for saving progress, they present significant friction for sharing and publishing. Because the format is proprietary to Cytoscape, you cannot simply double-click a .CYS file to view the graph in a web browser, nor can you open it in Microsoft Excel to analyze the underlying data tables. The file is actually a compressed archive (similar to ZIP) containing XML metadata and internal ontologies, making it unreadable to standard image editors like Adobe Photoshop.
To use your network data elsewhere, conversion is mandatory. For high-quality academic publishing or printing, users should convert the active network view to vector formats like PDF or SVG. For including the network in a presentation, a raster PNG or JPG is preferred. If you need to analyze the graph structure in other tools (like Python's NetworkX or Gephi), the internal data must be exported to standard exchange formats like GraphML, SIF, or XGMML. Rarely, a .CYS file may be an architectural symbol file from the discontinued Data Becker Cyber-House, which is incompatible with modern CAD tools.
Convert.Guru analyzes your CYS file, detects the exact format, and lets you read the text inside.
Users also converted CX, FPK and WAD files.
If you want to convert CYS file to CSV, JSON, XML, YAML, YML, TOML, INI, CFG, CONF, DAT, DB or SQL, you can use Cytoscape or similar software from the "Biological Network Visualization" category. In the File menu, look for Save As… or Export….
To convert DBF, XML, SQLITE, XLSX, SQL, TSV, ACCDB, YAML, MDB, CSV, ODS or JSON files to CYS, try Cytoscape or another comparable tool in the "Biological Network Visualization" category.
The history of Convert.Guru began over 25 years ago in California with Tom Simondi’s file-format database. A former contributor to Space Shuttle development and a software pioneer of the 1980s, Simondi established a trusted resource for file type analysis that was even referenced by Microsoft Windows XP. Today, we use modern technology to process and convert thousands of file formats while continually improving our CYS converter.