Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Training of Crisis Mappers and Map Production from Multi-sensor Data: Vernazza Case Study (Cinque Terre National Park, Italy)

This aim of paper is to presents the development of a multidisciplinary project carried out by the cooperation between Politecnico di Torino and ITHACA (Information Technology for Humanitarian Assistance, Cooperation and Action). The goal of the project was the training in geospatial data acquiring and processing for students attending Architecture and Engineering Courses, in order to start up a team of "volunteer mappers". Indeed, the project is aimed to document the environmental and built heritage subject to disaster; the purpose is to improve the capabilities of the actors involved in the activities connected in geospatial data collection, integration and sharing. The proposed area for testing the training activities is the Cinque Terre National Park, registered in the World Heritage List since 1997. The area was affected by flood on the 25th of October 2011. According to other international experiences, the group is expected to be active after emergencies in order to upgrade maps, using data acquired by typical geomatic methods and techniques such as terrestrial and aerial Lidar, close-range and aerial photogrammetry, topographic and GNSS instruments etc.; or by non conventional systems and instruments such us UAV, mobile mapping etc. The ultimate goal is to implement a WebGIS platform to share all the data collected with local authorities and the Civil Protectio

Nexus between nature-based solutions, ecosystem services and urban challenges

Nature-based Solutions (NBS) are increasingly promoted to support sustainable and resilient urban planning. However, design and planning urban NBS targeted at the needs of the local context require knowledge about the causal relationships between NBS, ecosystem services (ES) and urban challenges (UC) This paper aims at contributing to this knowledge, by systematically identifying nexuses (i.e. qualitative links) between UC, ES and NBS, and describing plausible causal relationships. A conceptual UC-ES-NBS criteria framework was built, and used to guide a two-step systematic literature review on current UC and on the supply of ES by urban NBS. This was followed by a non-systematic literature review, which complemented the previous one by unveiling knowledge gaps on the biophysical and social processes and attributes on which specific ES classes depend. The non-systematic review was also used to identify additional NBS. The UC review identified 18 UC and 58 sub-challenges, and illustrated which UC were more studied, according to the type of literature and environmental and socio-economic attributes of urban contexts. The ES review led to the development of an urban NBS classification, and supported the identification of UC-ES and ES-NBS nexuses, which were analysed and classified into four groups of causal relationship. For the nexuses identified as direct plausible causal relationship, the main processes and attributes on which the supply of specific ES depend were pointed out. Relationships between UC, ES, NBS, processes, and attributes were represented in the form of network diagrams. Our results can be used to support urban policies aimed at mainstreaming NBS and as a basis to further understand UC-ES-NBS relationships