IBL is a research group working on transdisciplinary problems that span computational statistics, computer science, and systems biomedicine. The projects IBL pursues seek translational validation in applications to precision medicine for novel ideas traversing these fields.
In addition to the graduate research level projects, IBL also hosts Pathology Informatics rotations for residents and fellows.
This combination of fields and career tracks is integrated through immersive problem solving venues including weekly hackathons and software development bootcamps.
IBL is a research group in the Division of Informatics of the UAB Department of Pathology.
ImageJS is a browser-based image analysis environment inspired by ImageJ and reimagined using HTML5 and JavaScript.
QMachine is a web service that can incorporate ordinary browsers into a World Wide Computer — without installing anything.
S3DB (Simple Sloppy Semantic Database) is a way to represent information on the Semantic Web without the rigidness of relational/XML schema while avoiding the "spaghetti" of unconstrained RDF stores.
The TCGA Roadmap is a linked data resource indexing the TCGA Open Access HTTP Repository. Queried using SPARQL, the TCGA Roadmap enables the discovery of subsets of data files within the TCGA.
Universal Sequence Maps (USM) is an iterated procedure that maps symbolic sequences into numeric spaces where alignment-free sequence analysis can be performed. For a review see Almeida JS (2013) Sequence analysis by iterated maps, a review." Briefings in bioinformatics. bbt072 Epub Oct 25 PMID:24162172.
A WebRTC experiment to find out the feasibility of assembly "evaluation spaces" aggregating multiple browsers.
Formalin (formerly HPath) is a browser-based, user-extensible report generator for clinical environments.
Kinomics Quality Control is a toolbox for working with Pamgene-generated kinomics data.
MinervaJS is a tool for publishing and finding Javascript libraries, and weaving them together.
Ming is a quasi-RESTful and CORS-enabled web service that allows reads, writes, and queries to one or more instances of MongoDB over the HTTP protocol.
TCGA Toolbox provides a scripting environment to retrieve, store, and analyze data from The Cancer Genome Atlas (TCGA) in the browser. It can be extended by loading modules and/or used interactively from the browser's JavaScript console.
Professor, Group Leader
MD/PhD student, Medical Scientist Training Program
Research interests: Kinomics
Visiting Scientist
Research interests: Web Application Architectures
Research Associate, Pathology Informatics
Research interests: Software Ecosystems, Software Engineering, Analysis Ecosystems, The Cancer Genome Atlas
PhD student, Biomedical Engineering
Research interests: Distributed Computing, Web Science
Pathology Resident Rotation, 2013
Summer student from UAB Medical School
Summer student from Columbia University (Computer Science undergraduate)
Neuropathology Fellowship research year, 2011-2012
Pathology Resident Rotation, 2012
MD/PhD student, Medical Scientist Training Program
Summer student from Universidade Presbiteriana Mackenzie (Computer Science undergraduate)
Postdoctoral researcher, 2011-2012