key: cord-0168294-7m55c6u0 authors: Arias-Carrasco, Ra'ul; Giddaluru, Jeevan; Cardozo, Lucas E.; Martins, Felipe; Maracaja-Coutinho, Vinicius; Nakaya, Helder I. title: OUTBREAK: A user-friendly georeferencing online tool for disease surveillance date: 2020-04-22 journal: nan DOI: nan sha: e9d88308ee1cfddf51c0c3d9028f1b16aa4d2a6e doc_id: 168294 cord_uid: 7m55c6u0 The current COVID-19 pandemic has already claimed more than 100,000 victims and it will cause more deaths in the coming months. Tools that can track the number and locations of cases are critical for surveillance and can help in making policy decisions for controlling the outbreak. The current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We present a new tool (OUTBREAK) for studying and visualizing epidemiological data. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. This tool has the potential to guide and help health authorities to intervene and minimize the effects of the outbreaks. It is freely available at http://outbreak.sysbio.tools/. The current COVID-19 pandemic has already claimed more than 100,000 victims and it will cause more deaths in the coming months. Tools that can track the number and locations of cases are critical for surveillance and can help in making policy decisions for controlling the outbreak. The current surveillance web-based dashboards run on proprietary platforms, which are often expensive and require specific computational knowledge. We present a new tool (OUTBREAK) for studying and visualizing epidemiological data. It permits even non-specialist users to input data most conveniently and track outbreaks in real-time. This tool has the potential to guide and help health authorities to intervene and minimize the effects of the outbreaks. It is freely available at http://outbreak.sysbio.tools/. Effective epidemiological surveillance is essential to ensure that the response to infectious disease outbreaks is timely and adequate. Communicable disease surveillance provides the essential information to monitor, evaluate, and model the impact of preventive and control activities; to detect and track the spread of the epidemic and emerging diseases and other threats to public health and to geographically locate communicable diseases in countries, regions, and across the globe. Integrated surveillance enables health authorities to (i) identify populations at risk, (ii) implement prevention and control strategies, (iii) detect unusual disease patterns, and (iv) contain the re-emergence or emergence of communicable diseases [1] . [3] . The current SARS-COV-2 pandemic has already claimed more than 100,000 victims and it will cause more deaths in the coming months [4] . Coronaviruses spread through human contact and also through objects contaminated by respiratory droplets exhaled by the infected persons [5] . Because of its rapid spread and high rate of infection [6] , by infecting a large proportion of the population it can cause the collapse of the health system of a country [7] . Tools that track and update the number and locations of cases are critical for surveillance of an epidemic and can help the decision-makers to fashion effective policies for controlling the spread of the disease. Although most of these epidemic dashboards use open-source data, they run on Esir ARCGIS web-services which are often expensive and hard to build and require specific knowledge on GIS-based programs. These dashboards are limited in monitoring the outbreak from a spatial epidemiological perspective, are without a time axis to track the evolution of the epidemic, and they do not allow the user to input data. To overcome these issues, we developed a new webbased tool for studying and visualizing epidemiological data, allowing the user to input data in the most convenient way for non-specialists to track outbreaks in real time and in a user-friendly manner. OUTBREAK online tool is freely available at http://outbreak.sysbio.tools/. The software includes a text and video tutorial with a detailed description of how to use it. OUTBREAK was developed using Python, through the Flask environment [9] . The interface was implemented using JavaScript through the React.js (reactjs.org) with the Node.js library [10] . The map for georeferencing was implemented using the MapBox service through the React.js library "reactmap-gl". An up-to-date version of the tool is available for downloading at Docker Hub (https://hub.docker.com/r/integrativebioinformatics/outbreak) together with the information on how to install and run the software locally. OUTBREAK input file requires geographical (latitude and longitude pairs) and temporal (date) information. Users are required to provide this information in a tab-delimited text file. The file can be generated as an Excel sheet that has at least four fixed columns for geographical (Label, Latitude, Longitude) and temporal (Date) data ( Table 1 ). The other three optional columns representing the colors, size, and the number of occurrences for each point can also be included in this file (Table 1) . This file can be uploaded at the "Run" page ( Figure 1A ), after filling a form with the title and a brief description to be shown on the interactive map ( Figure 1B) . The optional columns in the input file are useful to differentiate datasets of interest to be visualized in the interactive map. For instance, in Figure 1B the reported cases for the COVID-19 outbreak are represented in orange, whereas the associated deaths are represented in red. The tool accepts as input any file containing georeferenced and dated information. Users can specify the dates from a calendar to visualize the outbreak evolution throughout a particular period (Figure 2A ) Finally, we hope that the ease of use and the availability of interactive and dynamic maps that make exploration of the data easy will guide and help health authorities and decision-makers in making effective interventions to minimize the undesirable impacts of the current and future outbreaks. Latitude value (Decimal Degrees) Longitude value (Decimal Degrees) Optional columns: The names of user-defined colors for representing data on the interactive map. One color to be assigned to each set of data. Size of the points displayed on the interactive map. represented, such as the use of different colors to show the studied cases, and the use of zoom to investigate particular cases and retrieve the information at a neighborhood, street or even at a single building level. Global infectious disease surveillance Responding to global infectious disease outbreaks: lessons from SARS on the role of risk perception, communication and management Risks of Death and Severe Disease in Patients With Middle East Respiratory Syndrome Coronavirus Coronavirus disease 2019 The SARS, MERS and novel coronavirus epidemics, the newest and biggest global health threats: what lessons have we learned? Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia Critical Care Utilization for the COVID-19 Outbreak in Lombardy, Italy: Early Experience and Forecast During an Emergency Response An interactive web-based dashboard to track COVID-19 in real time Efficient Way Of Web Development Using Python And Flask Node.js: Using JavaScript to Build High Performance Network Programs We would like to thanks Lucas Fleig for his technical assistance in the