Integrative Bioinformatics Laboratory

Translational solutions at the data-driven crossroads of Computational Statistics, Computer Science, and Systems Biomedicine.

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.


Projects

Published

ImageJS

ImageJS is a browser-based image analysis environment inspired by ImageJ and reimagined using HTML5 and JavaScript.

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QMachine

QMachine is a web service that can incorporate ordinary browsers into a World Wide Computer — without installing anything.

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S3DB

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.

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TCGA Roadmap

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.

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USM

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.

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In-Progress

EvalSpace

A WebRTC experiment to find out the feasibility of assembly "evaluation spaces" aggregating multiple browsers.

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Formalin

Formalin (formerly HPath) is a browser-based, user-extensible report generator for clinical environments.

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Kinomics Quality Control

Kinomics Quality Control is a toolbox for working with Pamgene-generated kinomics data.

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MinervaJS

MinervaJS is a tool for publishing and finding Javascript libraries, and weaving them together.

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Ming

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.

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TCGA Toolbox

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.

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wApps

A wApp is a web application in a hurry to be part of a webApp ecosystem.

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People

Current

Jonas Almeida, PhD

Homepage Publications GitHub

Professor, Group Leader

Alex Dussaq

Homepage GitHub

MD/PhD student, Medical Scientist Training Program

Research interests: Kinomics

Alexander Gr√ľneberg

Publications GitHub

Visiting Scientist

Research interests: Web Application Architectures

David Robbins, PhD

GitHub Publications

Research Associate, Pathology Informatics

Research interests: Software Ecosystems, Software Engineering, Analysis Ecosystems, The Cancer Genome Atlas

Sean Wilkinson

Homepage Publications GitHub

PhD student, Biomedical Engineering

Research interests: Distributed Computing, Web Science

Alumni

Matthew D. Cain, MD

GitHub

Pathology Resident Rotation, 2013

Robert Gish

GitHub

Summer student from UAB Medical School

Henrique Goncalves

GitHub

Summer student from Columbia University (Computer Science undergraduate)

James R. Hackney, MD

GitHub

Neuropathology Fellowship research year, 2011-2012

Benjamin C. Hill, MD

GitHub

Pathology Resident Rotation, 2012

Vincent Laufer

MD/PhD student, Medical Scientist Training Program

Giuliana Pirovani

GitHub

Summer student from Universidade Presbiteriana Mackenzie (Computer Science undergraduate)

Young Soo Song, MD, PhD

GitHub

Postdoctoral researcher, 2011-2012



Calendar


Contact

Division of Informatics, Department of Pathology
P220 West Pavilion
615 18th Street South
Birmingham, AL 35294-7331
P: (205) 934-0533
informatics@mathbiol.org