Outbreak science: recent progress in the detection and response to outbreaks of infectious diseases.

The frequency of reported outbreaks of infectious diseases has increased over the past 3 decades, with predictions that this rise will continue. Outbreak response continues to follow nine basic principles: establish the presence of an outbreak, verify the diagnosis, make a case definition, find cases and contacts, conduct basic epidemiology, test hypotheses, institute control measures, communicate the situation and establish ongoing surveillance. Within each of these areas, significant advances have been made over the past 5 years using progress in digital, laboratory, epidemiology and anthropological equipment or techniques. Irrespective of these, future outbreaks of high-consequence are inevitable, and vigilance and preparation must continue in order to prevent significant mortality, morbidity and socio-economic crisis

Un Modèle basé sur les Grammaires Attribuées Gardées pour les Processus Dynamiques, Centrés sur l’Utilisateur, Distribués et Collaboratifs: Cas de la Surveillance Epidémiologique

Dynamic processes in which users need to work together and collaborate in myriad ways on process models defined on-the-fly are fast becoming the rule rather than the exception. This thesis presents the design of a purely declarative modelling approach for dynamic, collaborative, user-centred, and data-driven processes. First, we organize the work of a user into task hierarchies which we model as mindmaps, which are trees used to visualize, organize, and log information about tasks in which the user is involved. We introduce the model of guarded attribute grammars, or GAG, to help the automation of updating such maps. A GAG consists of an underlying grammar, that specifies the logical structure of the map, with semantic rules which are used both to govern the evolution of the tree structure (how an open node may be rened to a sub-tree) and to compute the values of some of its attributes. The map enriched with this extra information and with high-level constructs for task dependencies; collaborationand user-interactions is termed an active workspace or AW. Communication between AWs is essentially through the exchange of messages without a shared memory thus enabling convenient distribution on an asynchronous architecture. Lastly, we introduce a language syntax for GAG specification and design a prototype that includes an internal domain specific language (in Haskell) for their specification and a graphical user interface to simulate its execution in a distributed environment. We motivate our approach and illustrate its language syntax and features on a case study for a disease surveillance system.De plus en plus, les utilisateurs collaborent de multiples façons sur des processus dynamiques construit de manière progressive. Dans cette thèse, nous concevons une nouvelle approche d´déclarative de modélisation des processus dynamiques, centrés sur l’utilisateur et dirigés par les données. Tout d’abord, nous organisons le travail d’un utilisateur par des hiérarchies des taches, représentées par des cartes heuristiques (arbre de taches). Ces derniers sont utilisés pour visualiser, organiser, et sauvegarder les informations sur les tâches menés par l’utilisateur. Nous introduisons ensuite le modèle des grammaires attribuées gardées, ou GAG, pour faciliter l’automatisation de la manipulation de telles cartes. Une GAG consiste en une grammaire sous-jacente, qui spécifie la structure logique de la carte, avec des règles sémantiques qui servent à la fois a` gouverner l’évolution de l’arbre des taches (raffinement des nœuds ouverts) et a` calculer les valeurs de certains de ses attributs. La carte enrichie de ces informations supplémentaires et d’autres concepts de haut niveau pour les d´dépendances entre les taches, la collaboration et les interactions utilisateur est appelée Active Workspace ou AW. La communication entre AWs est essentiellement par échange des messages permettant ainsi une implémentation commode sur une architecture distribuée et asynchrone. Enfin, nous décrivons une syntaxe de langage pour la spécification des processus en utilisant les GAGs et concevons un prototype qui inclut un langage spécifique au domaine, interne `a Haskell, pour leur spécification et une interface utilisateur graphique pour la simulation de l’exécution dans un environnement distribué. Nous motivons notre approche et illustrons sa syntaxe et ses caractéristiques sur une étude de cas portant sur le processus de surveillance épidémiologique

Towards One Health Knowledge Networks: A Southern African Centre of Infectious Disease Surveillance case study

The dynamic nature of new information and/or knowledge is a big challenge for information systems. Early knowledge management systems focused entirely on technologies for storing, searching and retrieving data; these systems have proved a failure. Juirsica and Mylopoulos1 suggested that in order to build effective technologies for knowledge management, we need to further our understanding of how individuals, groups and organisations use knowledge. As the focus on knowledge management for organisations and consortia alike is moving towards a keen appreciation of how deeply knowledge is embedded in people’s experiences, there is a general realisation that knowledge cannot be stored or captured digitally. This puts more emphasis in creating enabling environments for interactions that stimulate knowledge sharing. Our work aims at developing an un-obtrusive intelligent system that glues together effective contemporary and traditional technologies to aid these interactions and manage the information captured. In addition this system will include tools to aid propagating a repository of scientific information relevant to surveillance of infectious diseases to complement knowledge shared and/or acts as a point of reference. This work is ongoing and based on experiences in developing a knowledge network management system for the Southern African Centre of Infectious Disease Surveillance (SACIDS), A One Health consortium of southern African academic and research institutions involved with infectious diseases of humans and animals in partnership with world-renowned centres of research in industrialised countries