BioFabric is an open-source network visualization tool that uses a new approach: nodes are represented as horizontal lines instead of as points:
Work on Version 2.0 is continuing (June 2019). It is currently available as Version 2.0 Beta Release 2, and bug fixing continues with frequent merges into the master branch.
Version 2 contains a number of new features, many of which are dedicated to handling very large networks. While there are still bugs being addressed, this new version is the only practical way to deal with large networks with over a million links.
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Significant performance improvements. The 280K node, 2.3M edge test network now loads in a couple minutes, in a memory footprint of under 8 GB.
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Long-running operations are tracked with frequent progress reports and cancel options.
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If a long running operation is canceled, the previous network can be restored. This feature uses a copy written to a cached file, thus reducing memory requirements.
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To handle very large networks, where e.g. there may be hundreds or thousands of node or link lines per pixel, a special bucket renderer has been written. This renderer does not draw lines, but simply counts the nodes and links per pixel to shade each pixel accordingly.
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Object creation has been kept to a minimum, to minimize garbage collection while processing large networks. The images, byte arrays, and integer arrays used for the tiling renderer are tightly managed and efficiently reused.
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Intersection testing uses a new quadtree data structure, resulting in massive improvements in mouse responsiveness with huge networks.
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The navigation pane on the bottom of the window can be resized or hidden entirely.
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There is a new plugin architecture to allow developers to write extensions to the core program.
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There is a new batch mode that allows the code to write out a PNG in headless mode, allowing renderings on e.g. cloud machines with huge amounts of physical memory.
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Node and Link Annotations have been implemented. This allows the user to label blocks of links and nodes with shaded rectangles, to add semantic information to networks.
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Five new layouts have been added; some of these use the new node and link annotation feature to e.g. label clusters.
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Shadow links can be toggled from a button on the toolbar.
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NEW in Beta release 2 The mouse scroll wheel now zooms the main view, and scrolling can be accomplished by pressing the left mouse button and dragging.
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NEW in Beta release 2 Java heap limit for all three platform executables has been increased to 8 GB. It can be tweaked most easily on the Linux version, which sets the value in a shell script.
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Basic GW files can be imported, link groups can be either gathered per node or per network, and multiple node zones per node can be labeled (hat tip to Rishi Desai for these features).
This Version 2.0 Beta Release 2 replaces Version 2.0 Beta Release 1.
The current stable production release (Version 1, released 2012) is available as the V1.0 tag.