PORGY: a Visual Analytics Platform for System Modelling and Analysis Based on Graph Rewriting

PORGY is a visual environment for rule-based modelling based on port graphs and port graph rewrite rules whose application is steered by rewriting strategies. The focus of this demonstration is the visual and interactive features offered by PORGY, which facilitate an exploratory approach to model, simu- late and analyse different ways of applying the rules while recording the model evolution, as well as tracking and plotting system parameters

Semantic Social Networks: A Mixed Methods Approach to Digital Ethnography

International audienc

Labelled Graph Strategic Rewriting for Social Networks

We develop an algebraic approach, based on labelled-graph strategic rewriting , for the study of social networks, specifically network generation and propagation mechanisms. This approach sheds a new light on these problems, and leads to new or improved generation and propagation algorithms. We argue that relevant concepts are provided by three ingredients: labelled graphs to represent networks of data or users, rewrite rules to describe concurrent local transformations, and strategies to express control. We show how these techniques can be used to generate random networks that are suitable for social network analysis, simulate different propagation mechanisms, and analyse and compare propagation models by extracting common rules and differences, thus leading to improved algorithms. We illustrate with examples the flexibility of the approach

Labelled Graph Strategic Rewriting for Social Networks

International audienceWe propose an algebraic and logical approach to the study of social networks, where network components and processes are directly defined by labelled port graph strategic rewriting. Data structures attached to graph elements (nodes, ports and edges) model local and global knowledge in the network, rewrite rules express elementary and local transformations , and strategies control the global evolution of the network. We show how this approach can be used to generate random networks, simulate existing propagation and dissemination mechanisms, and design new, improved algorithms

TULIP 4

Tulip is an information visualization framework dedicated to the analysis and visualization of relational data. Based on more than 15 years of research and development, Tulip is built on a suite of tools and techniques , that can be used to address a large variety of domain-specific problems. With Tulip, we aim to provide Python and/or C++ developers a complete library, supporting the design of interactive information visualization applications for relational data, that can be customized to address a wide range of visualization problems. In its current iteration, Tulip enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. This development pipeline makes the framework efficient for creating research prototypes as well as developing end-user applications. The recent addition of a complete Python programming layer wraps up Tulip as an ideal tool for fast prototyping and treatment automation, allowing to focus on problem solving, and as a great system for teaching purposes at all education levels

Porgy Strategy Language: User Manual

This document provides concrete syntax illustrated with ex-amples for the Porgy’s strategy language and the language for rulealgorithm and conditions. Porgy is a visual, interactive modelling tool based on port graph rewriting. In Porgy, system states are represented by port graphs, and the dynamic evolution of the system is defined via port graph rewrite rules. Strategy expressions are used to control the application of rules, more precisely, strategy expressions indicate both the rule to be applied at each step in a rewriting derivation, and the position in the graph where the rule is applied (the latter is done via focusing constructs). Some of the strategy constructs are strongly inspired from term rewriting languages such as Elan [Borovansk´yBorovansk´y et al., 1998], Stratego [Visser, 2001] and Tom [Balland et al., 2007]. Focusing operators are not present in term rewriting languages (although they rely on implicit traversal strategies). The direct management of positions in strategy expressions, via the distinguished position and banned subgraphs in the target graph and in a located port graph rewrite rule are original features of the language and are managed using positioning constructs. This document describes the concrete syntax of strategy expressions, explains how the different kinds of constructs are used, and provides examples

PORGY : a Visual Analytics Platform for System Modelling and Analysis Based on Graph Rewriting

Atelier Visualisation d'informations, interaction et fouille de données, Conférence EGC2017We propose PORGY 1 a visual modelling framework (Fig. 1) designed for specifying, simulating , and analysing complex systems. PORGY is built on top of the open-source visualisation framework TULIP 2. PORGY is based on the use of port graphs with attributes to represent system states. In a port graph, edges connect to nodes at specific points, called ports. Nodes, ports and edges describe the system components and their relationships, while attributes encapsulate the data values associated with entity. We use graph transformations based on port graph rewrite rules to describe the evolution of the system. FIG. 1 – Overview of PORGY: (1) editing a graph; (2) editing a rule; (3) all available rules; (4) the derivation tree, a complete trace of the computing history; (5) editing a strategy

A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces

Article Authors Metrics Comments Related Content Abstract Author summary Introduction Results and discussion Conclusions Methods Supporting information Acknowledgments References Reader Comments (0) Media Coverage (0) Figures Abstract Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants. However, the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form. During a random T-DNA mutagenesis screen performed on the pleomorphic wheat (Triticum aestivum) pathogen Zymoseptoria tritici, we acquired a mutant unable to extend hyphae specifically when on solid surfaces. In contrast “yeast-like” growth, and all other growth forms, were unaffected. The inability to extend surface hyphae resulted in a complete loss of virulence on plants. The affected gene encoded a predicted type 2 glycosyltransferase (ZtGT2). Analysis of >800 genomes from taxonomically diverse fungi highlighted a generally widespread, but discontinuous, distribution of ZtGT2 orthologues, and a complete absence of any similar proteins in non-filamentous ascomycete yeasts. Deletion mutants of the ZtGT2 orthologue in the taxonomically un-related fungus Fusarium graminearum were also severely impaired in hyphal growth and non-pathogenic on wheat ears. ZtGT2 expression increased during filamentous growth and electron microscopy on deletion mutants (ΔZtGT2) suggested the protein functions to maintain the outermost surface of the fungal cell wall. Despite this, adhesion to leaf surfaces was unaffected in ΔZtGT2 mutants and global RNAseq-based gene expression profiling highlighted that surface-sensing and protein secretion was also largely unaffected. However, ΔZtGT2 mutants constitutively overexpressed several transmembrane and secreted proteins, including an important LysM-domain chitin-binding virulence effector, Zt3LysM. ZtGT2 likely functions in the synthesis of a currently unknown, potentially minor but widespread, extracellular or outer cell wall polysaccharide which plays a key role in facilitating many interactions between plants and fungi by enabling hyphal growth on solid matrices

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

TULIP 5

International audienceTulip is an information visualization framework dedicated to the analysis and visualization of relational data. Based on more than 16 years of research and development, Tulip is built on a suite of tools and techniques, that can be used to address a large variety of domain-specific problems. With \tulip, we aim to provide Python and/or C++ developers a complete library, supporting the design of interactive information visualization applications for relational data, that can be customized to address a wide range of visualization problems. In its current iteration, \tulip enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. This development pipeline makes the framework efficient for creating research prototypes as well as developing end-user applications. The recent addition of a complete Python programming layer wraps up Tulip as an ideal tool for fast prototyping and treatment automation, allowing to focus on problem solving, and as a great system for teaching purposes at all education levels