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Papers by Renato Giovanni
Darwin Core standard release 2014-11-08.
Frontiers of Biogeography, 2012
Biodiversity Informatics, 2015
Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed... more Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed. Such tasks may consume a significant amount of computing resources and take a long time to complete, especially when using personal computers. OMWS is a Web service interface that allows more powerful computing back-ends to be remotely exploited by other applications to carry out ENM tasks. Its latest version includes a new operation that can be used to specify complex workflows in a single request, adding the possibility of using workflow management systems on parallel computing back-end. In this paper we describe the OMWS protocol and compare its most recent version with the previous one by running the same ENM experiment using two functionally equivalent clients, each designed for one of the OMWS interface versions. Different back-end configurations were used to investigate how the performance scales for each protocol version when more processing power is made available. Results sho...
2013 27th International Conference on Advanced Information Networking and Applications Workshops, 2013
GeoInformatica, 2009
Species’ potential distribution modelling is the process of building a representation of the fund... more Species’ potential distribution modelling is the process of building a representation of the fundamental ecological requirements for a species and extrapolating these requirements into a geographical region. The importance of being able to predict the distribution of species is currently highlighted by issues like global climate change, public health problems caused by disease vectors, anthropogenic impacts that can lead to
Computers in Agriculture and Natural Resources, 23-25 July 2006, Orlando Florida, 2006
ABSTRACT Ecological niche models play an import role in species distribution prediction. They pro... more ABSTRACT Ecological niche models play an import role in species distribution prediction. They provide ways to study biodiversity distribution, past and present, to understand its causes, and to propose scenarios and strategies for sustainable use and for preservation initiatives. Ecological niche modeling usually involves many algorithms, environmental variables, data types and formats, and both pre and post analysis work. That complexity forces modeling experts to know and to use many software packages and to manually solve technical issues. openModeller was conceived as a framework to provide an open, standardized and integrated infrastructure for accommodating geo-referencing issues, environmental data and algorithms deployment, allowing researchers to focus on the modeling problem and on other high-level analysis. This paper presents an analysis of openModeller describing its main use cases and interactions. It also suggests improvements in the current software to reduce its learning curve and to increase system usability through a set of modifications. The set of changes adds the following features: (1) new storage component for species, geographic and environmental data, (2) new data import mechanisms, (3) graphical user interface improvements, and (4) new documentation about installing and using the software. These recommendations result from a first analysis of openModeller as part of a major project concerned with species occurrence data, environmental data, dataset preparation, modeling algorithms, pre and postanalysis, component-based software development, high performance computing, web services, and multiple interfaces in order to make the framework accessible to a larger range of users.
Osgeo Journal, Mar 19, 2007
Biodiversity Informatics, 2015
Ecography, 2015
ABSTRACT Ecological Niche Modelling (ENM) Components are a set of reusable workflow components sp... more ABSTRACT Ecological Niche Modelling (ENM) Components are a set of reusable workflow components specialized for performing ENM tasks within the Taverna workflow management system. Each component encapsulates specific functionality and can be combined with other components to facilitate the creation of larger and more complex workflows. One key distinguishing feature of ENM Components is that most tasks are performed remotely by calling web services, simplifying software setup and maintenance on the client side and allowing more powerful computing resources to be exploited. This paper presents the current set of ENM Components in the context of the Taverna family of tools for creating, publishing and sharing workflows. An example is included showing how the components can be used in a preliminary investigation of the effects of mixing different spatial resolutions in ENM experiments.This article is protected by copyright. All rights reserved.
Journal of biogeography, 2015
The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterize... more The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterized by many special features, including endemic species that may be particularly threatened by climate change. We mapped potential distribution patterns under present and future conditions for a community with three trophic levels. We analysed climate-induced changes in the species' distribution patterns and examined possible consequences for the chosen food web. Baltic Sea and northern Europe. We developed two open-source workflow-based analytical tools: one for ecological niche modelling and another for raster layer comparison to compute the extent and intensity of change in species' potential distributions. Individual ecological niche models were generated under present conditions and then projected into a future climate change scenario (2050) for a food web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesiculosus and Fucus radicans) and their fis...
Natureza & Conservação, 2012
Darwin Core standard release 2014-11-08.
Frontiers of Biogeography, 2012
Biodiversity Informatics, 2015
Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed... more Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed. Such tasks may consume a significant amount of computing resources and take a long time to complete, especially when using personal computers. OMWS is a Web service interface that allows more powerful computing back-ends to be remotely exploited by other applications to carry out ENM tasks. Its latest version includes a new operation that can be used to specify complex workflows in a single request, adding the possibility of using workflow management systems on parallel computing back-end. In this paper we describe the OMWS protocol and compare its most recent version with the previous one by running the same ENM experiment using two functionally equivalent clients, each designed for one of the OMWS interface versions. Different back-end configurations were used to investigate how the performance scales for each protocol version when more processing power is made available. Results sho...
2013 27th International Conference on Advanced Information Networking and Applications Workshops, 2013
GeoInformatica, 2009
Species’ potential distribution modelling is the process of building a representation of the fund... more Species’ potential distribution modelling is the process of building a representation of the fundamental ecological requirements for a species and extrapolating these requirements into a geographical region. The importance of being able to predict the distribution of species is currently highlighted by issues like global climate change, public health problems caused by disease vectors, anthropogenic impacts that can lead to
Computers in Agriculture and Natural Resources, 23-25 July 2006, Orlando Florida, 2006
ABSTRACT Ecological niche models play an import role in species distribution prediction. They pro... more ABSTRACT Ecological niche models play an import role in species distribution prediction. They provide ways to study biodiversity distribution, past and present, to understand its causes, and to propose scenarios and strategies for sustainable use and for preservation initiatives. Ecological niche modeling usually involves many algorithms, environmental variables, data types and formats, and both pre and post analysis work. That complexity forces modeling experts to know and to use many software packages and to manually solve technical issues. openModeller was conceived as a framework to provide an open, standardized and integrated infrastructure for accommodating geo-referencing issues, environmental data and algorithms deployment, allowing researchers to focus on the modeling problem and on other high-level analysis. This paper presents an analysis of openModeller describing its main use cases and interactions. It also suggests improvements in the current software to reduce its learning curve and to increase system usability through a set of modifications. The set of changes adds the following features: (1) new storage component for species, geographic and environmental data, (2) new data import mechanisms, (3) graphical user interface improvements, and (4) new documentation about installing and using the software. These recommendations result from a first analysis of openModeller as part of a major project concerned with species occurrence data, environmental data, dataset preparation, modeling algorithms, pre and postanalysis, component-based software development, high performance computing, web services, and multiple interfaces in order to make the framework accessible to a larger range of users.
Osgeo Journal, Mar 19, 2007
Biodiversity Informatics, 2015
Ecography, 2015
ABSTRACT Ecological Niche Modelling (ENM) Components are a set of reusable workflow components sp... more ABSTRACT Ecological Niche Modelling (ENM) Components are a set of reusable workflow components specialized for performing ENM tasks within the Taverna workflow management system. Each component encapsulates specific functionality and can be combined with other components to facilitate the creation of larger and more complex workflows. One key distinguishing feature of ENM Components is that most tasks are performed remotely by calling web services, simplifying software setup and maintenance on the client side and allowing more powerful computing resources to be exploited. This paper presents the current set of ENM Components in the context of the Taverna family of tools for creating, publishing and sharing workflows. An example is included showing how the components can be used in a preliminary investigation of the effects of mixing different spatial resolutions in ENM experiments.This article is protected by copyright. All rights reserved.
Journal of biogeography, 2015
The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterize... more The Baltic Sea is one of the world's largest semi-enclosed brackish water bodies characterized by many special features, including endemic species that may be particularly threatened by climate change. We mapped potential distribution patterns under present and future conditions for a community with three trophic levels. We analysed climate-induced changes in the species' distribution patterns and examined possible consequences for the chosen food web. Baltic Sea and northern Europe. We developed two open-source workflow-based analytical tools: one for ecological niche modelling and another for raster layer comparison to compute the extent and intensity of change in species' potential distributions. Individual ecological niche models were generated under present conditions and then projected into a future climate change scenario (2050) for a food web consisting of a guild of meso-grazers (Idotea spp.), their host algae (Fucus vesiculosus and Fucus radicans) and their fis...
Natureza & Conservação, 2012