COPASI enables researchers to construct biochemical models that help them understand how a system works. Model parameters can be adjusted as necessary to reproduce experimental results.
DMEAS is the first user-friendly tool dedicated to analyze methylation entropy for the quantification of epigenetic variation. The DMEAS program, user guide, and all the testing data are freely available.
DSI:DC is an educational adventure game where players take on the role of a public health agent asked to solve a growing crisis resulting from a disease outbreak. The game focuses on the science and mathematics of infectious disease, the application of computational modeling for decision-making, and the civic and health implications of these actions.
ENteric Immune Simulator (ENISI), a multiscale modeling tool for modeling the mucosal immune responses. ENISI can simulate in silico experiments from signaling pathways to tissue level events. ENISI’s architecture integrates multiple modeling technologies. During the development of ENISI, 3 versions were released; ENISE HPC, ENISI Visual, ENISI MSM.
Users can view Ebola (or Flu) activity for the past four weeks and view forecast predictions for the next two weeks. They can also view forecast trends and compare them to surveillance data. EpiCaster allows users to see what impact various strategies, such as vaccines and social distancing, have on disease spread.
HBS analyzer is the first command-line-based open-source tool to process genome-wide hairpin bisulfite sequencing data. It accepts Illumina paired-end sequencing reads as input, performs alignment to recover the original (pre-bisulfite-converted) DNA sequences, and calls methylation status for cytosines on both DNA strands.
My4Sight uses human computation to enhance disease forecasting. Similar to games like Foldit, this web application allows users to assist computational models by performing tasks that humans are uniquely good at, in this case pattern matching.
PATRIC is the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools.
PlantSimLab is a virtual laboratory, allowing biologists to interrogate a computational model as they would an experimental one.
SysGenSIM is a bioinformatics toolbox for MATLAB to create artificial gene expression datasets by simulating Systems Genetics experiments.
The VBI Genome Browser allows viewing of genomic data that adheres to the Genomics Unified Schema (GUSDB) data storage standard.
Virus Tracker simulates the spread of a virus and demonstrates the critical role of vaccinations in combating a disease outbreak. Designed to show how disease spreads, players can "infect" others with the “Zombie Virus" and can then return to a ‘Human’ state by getting vaccinated from other players.