Biosurveillance Tools and Applications
List of tools and applications
Analytics for Investigation of Disease Outbreaks (AIDO)
AIDO is a tool designed to enhance situational awareness of an unfolding disease event. This capability is accomplished by providing context and a frame of reference for disease surveillance information through matching of user input to a library of global historical disease outbreaks.
This tool was previously known as the Surveillance Window Application (SWAP).
Points of contact: Geoffrey Fairchild and Alina Deshpande
Biosurveillance Resource Directory (BRD)
The BRD is a tool to facilitate obtaining disease surveillance information. It contains disease surveillance resources, epidemiological models (previously known as the "BARD"), and a disease ontology.
In prototype testing
Point of contact: Alina Deshpande
Empowering the Development of Genomics Expertise (EDGE)
Genomic EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
The bioinformatics platform allows users to address a wide range of use cases, including assay validation and the characterization of novel biological threats, clinical samples, and complex environmental samples.
Point of contact: Patrick Chain
Epi Archive
Epi Archive is a web-based tool that automatically collects, stores, and visualizes global epidemiological data for any country, region, and disease.
Point of contact: Hari S. Khalsa
Flu Forecasts
Flu Forecasts are based on a model for probabilistic forecast of flu season. Percentage chance of flu peaking at a certain time is provided at national and regional level.
Point of contact: Sara del Valle
Genomic Origin Through Taxonomic Challenge (GOTTCHA)
GOTTCHA is an application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly smaller false discovery rates (FDR) that is also laptop deployable.
Point of contact: Patrick Chain
Pathogen Databases
The pathogen databases suite comprises three databases that contain genomic sequence, drug resistance, and immunological data for Human Immunodeficiency Virus (HIV), Hemorrhagic Fever Viruses (HFV), and Hepatitis C Virus (HCV).
Point of contact: Bette Korber
pyda
Open-source software for data assimilation in Python; implementations of the Ensemble Kalman Filter (EnKF), Ensemble Kalman Smoother (EnKS), Particle Filter (PF), and Kernel Particle Filter (kPF); contains examples using an SIR disease model.
Point of contact: Kyle Hickmann
pyHarmonySearch
Open-source software that enables python implementation of the harmony search (HS) global optimization algorithm
Point of contact: Geoffrey Fairchild
pyxDamerauLevenshtein
Open-source software to reconcile misspellings of tweets
Point of contact: Geoffrey Fairchild
Quantitative Analysis of Chatter (QUAC)
QUAC is open-source software for acquiring and analyzing social Internet content.
Point of contact: Reid Priedhorsky
Quick Urban and Industrial Complex (QUIC)
The QUIC Dispersion Modeling System is a fast response urban dispersion model that runs on a laptop.
Point of contact: Michael Brown
Re-Emerging Infectious Disease Alert (RED Alert)
RED Alert is an analysis tool to provide early warning or detection of the re-emergence of an infectious disease—at the global level but through a regional lens—in order to facilitate long-term public health planning.
Points of contact: Geoffrey Fairchild and Alina Deshpande
Sequedex
Sequedex is a tool that classifies DNA sequences by analyzing collections of sequences in new ways up to ~250,000 times faster than BLAST.
Point of contact: Ben McMahon
