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.
Dynamic Behavior Visualizer (DBV) is an interactive visualization of people, a group of people, or a family used to help understand behaviors and movements over time during a natural or man-made disaster. DBV is used to study the resilience of critical infrastructures such as transportation, communication, and public health.
Dynamics on networked populations are useful in understanding social processes on networked populations. Contagion dynamics can take various forms such as epidemics, social protest, smoking and drug use, use of social media, etc. EDISON utilizes big data and data mining to perform social dynamics on networks.
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.
EpiViewer is a data repository for epidemiologists. Users can upload and compare Ebola forecasts and surveillance data from a variety of sources and see how forecasts change over time. Users can also load and share their own forecasting predictions.
EpiViz is a highly dynamic system that provides a platform to track and study subjects’ decision making and information search strategies, under controlled and repeatable conditions using simulated disease outbreaks. Data visualization supports a multiple views environment and parallel simulation runs.
Road conditions can be variable in some of the rural areas in Western Africa. Eyes on the Ground allows people in affected areas to report their road conditions. Other travelers can then view these reports and plan their trips accordingly. This is especially useful when planning the delivery of patients and supplies between cities.
Agent-based simulations are used to understand disease transmission, the spread of social unrest, and the propagation a host of other contagions such as fads, rumors, and influence. Contagions may be spread, for example, by face-to-face interaction and/or electronic means (e.g., social media). Simulation is an effective way to study these dynamics of contagion spread.
This tool contains network analysis libraries to compute structural characteristics of networks. The libraries are GaLib, NetworkX, and SNAP.
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.
SIBEL allows bioinformatics researchers to design experiments and create analysis for epidemiological disease studies based on realistic social network simulations. It enables improved readiness, planning, and decision making in the domains of public safety and national security by delivering sophisticated modeling and simulation capabilities directly into the hands of the analyst.
Synthetic Information Viewer (SIV) is a synthetic population visualization tool that allows users to explore demographic information at several levels of resolution - from national to individual. It supports our 2009 version of U.S. data and all international countries NDSSL has constructed, total population of 800+ million.
SysGenSIM is a bioinformatics toolbox for MATLAB to create artificial gene expression datasets by simulating Systems Genetics experiments.
The TRansportation ANalysis SIMulation System is a transportation planning and decision support tool capable of simulating second-by-second movements of every person and every vehicle through the transportation network of a large urban environment. TRANSIMS was the first successful example of high performance computational social sciences and policy informatics.
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.