Biomedical Knowledge Engineering Group

BMKEG Software

We gratefully acknowledge the support of ej-technologies, who provide us with an open-source license for their excellent install4j and JProfiler tools.  We find that these systems are an essential part of our development cycle, providing an easy, robust deployment methodology and a system that supports our development of top-quality software.

We enthusiastically base our development work within the creative coding environment of GitHub. All code is de-facto open source and we see our role principally as one of facilitation and support of researchers engaged in their work. We are here to help, and both recognize and actively support other like-minded developers and researchers in the field.

The View Primitive Data Model framework (VPDMf)
The VPDMf is a scaffolding framework for building knowledge engineering applications. It uses code-generation based on a UML-based model coupled with a representation of 'Views' over the underlying schema that encapsultate objects in a similar way to 'named graphs' in RDF-based representations. Using code-generation based on this underlying generic object-oriented conceptual design allows us to build software systems tailored for different applications rapidly and robustly using components based in a variety of implementation languages. The VPDMf builds MySQL databases, Java services, Flex clients, OWL ontologies and SOLR indexes that all know how to talk to each other because they all use the same underlying conceptual design. This provides a strong agile development framework that permits all our other systems to interoperate. 
BMKEG Project Page:  VPDMf
Wiki-based documentation:  Documentation on BIRN Wiki
Latest Installers (Beta):  [mac][win][unix]
BioScholar is a practical Knowledge Management application for use by a domain scientist in a lab. The system is supposed to act as a local knowledge base for an individual PI to build a curated database for published material pertaining to their in-house research. This is now a fully developed (Beta) software application for download by the community. It's primary technical contribution is the realization of a practical software system that instantiates the KEfED model.
System Demo:  Neural Connectivity Demo
Google Code Project:  Google Code Page
Installers:  Google Code Downloads Page
Source Code for Releases:  Google Code SVN Page
Layout-Aware PDF Text Extraction  
The Portable Document Format (PDF) is the almost universally used file format for online scientific publications. It is also notoriously difficult to read and handle computationally, presenting challenges for developers of biomedical text mining or biocuration informatics systems that use the published literature as an information source. To facilitate the effective use of scientific literature in such systems we have developed  Layout-Aware PDF Text Extraction (LA-PDFText).
Google Code Project:  Google Code Page
Installers:  Google Code Downloads Page
The 'NeuARt' Neuroanatomical Mapping System  
The neuroanatomical maps of Dr Larry Swanson's laboratory beautifully illustrate the organization of neural connectivity in the Rat Brain. The work needed to generate these maps requires that researchers draw each relevant map over atlas plates to register the distribution of fibers in the context of a brain atlas. These data are valuable and require tools to present them to users within the community. The NeuARt software provides a web-based atlas-viewing tool that provides access to these maps (Note that at present, NeuARt is only available as an online demo with password protection due to copyright restrictions).
Demo system (password protected):  Demo
Google Code Project:  Google Code Page
INCF Project Page:  INCF Software Page