Integrated Exploration of Biomedical Literature and Data
The PubAnatomy 3D project is NOT an extension of the original PubAnatomy.
Total Funding: $373,200 from NIH and possible more other public funding.
This application is one man, 3 years(10/2011-08/2014) project to learn from scratch, re-architecture and re-implementation!
The complexity of the structure and function of brain makes text- or even 2D-graphics based exploration of high throughput data sets and literature related to brain ineffective. We hope to build a web-based system to facilitate the understanding of brain structures, circuits, gene expression levels and disease by taking advantage of large data sets in a centralized database. We choose to use the Adobe Flash Platform for 3D development due to its cross browser/platform support. The newly released Adobe released Flash Player and AIR support the Stage3D API, which is a set of low-level GPU-accelerated APIs enabling advanced 2D and 3D capabilities.
We build brain 3D structure models using voxel-level data provided by the Allen Brain Institute. When requested by users, 3D models will be loaded from server to the Flash player in users' browser. We believe this is the first implementation of interactive 3D biological structure display in Flash and we plan to integrate this implementation with gene expression, function annotation and literature data to help the understanding of high throughput neurobiology data in the context of brain structure and functions.
PubAnatomy3D is no longer under development after Aug/2014. Please send your questions and comments to contacts in NIH project page
These following videos are just memory and proof of my 3 years of hard work on $55k/yr!