Pathway Pioneer: A Web-Based Graphical Tool for the Organization and Flux Analysis of Metabolic Networks

As stoichiometric metabolic models increase in complexity and fidelity, design and reconstruction tools are urgently needed to increase the productivity of this time-consuming process. Engineers require software for the exploration, evaluation, and rapid analysis of model alternatives within an intuitive visualization and data management framework. This thesis introduces such a tool: Pathway Pioneer (www.pathwaypioneer.org), a web based system built as a front-end graphical user interface to the flux balance analysis tool COBRA. Pathway Pioneer adds additional functionality for customized network layout and model-engineering collaboration through shared models and model version control. Pathway Pioneer is a dynamic, clickable, browser-based visualization system for metabolic network models retrieved from databases such as BiGG or developed in-house as SBML or XLS compliant files. The user can customize the network layout to visually organize the metabolites and reactions into functional modules. The tool supports zooming and panning, level-of-detail control, flux visualization, keyword searching, and hierarchical subsystem organization. A reaction may be knocked out, set as an objective, looked up in a database or many other operations by a single click on the visualized network. Following each operation the visualization is refreshed with the new flux values. The system supports model revision control to manage alternative network configurations and supports sharing of models and layouts to the broader community. By moving the computationally intensive model analysis from the user computer to remote servers, Pathway Pioneer enables the application of high performance cloud-based resources for greater efficiency and scalability. I demonstrate the utility of Pathway Pioneer through application in model reconstruction and analysis of many standard models and also two new models under development: Eukaryotic multicompartment Chinese Hamster Ovary (Cho) cells and in a large-scale Escherichia coli system for bio-manufacturing

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool

MuxViz: A Tool for Multilayer Analysis and Visualization of Networks

Multilayer relationships among entities and information about entities must be accompanied by the means to analyze, visualize, and obtain insights from such data. We present open-source software (muxViz) that contains a collection of algorithms for the analysis of multilayer networks, which are an important way to represent a large variety of complex systems throughout science and engineering. We demonstrate the ability of muxViz to analyze and interactively visualize multilayer data using empirical genetic, neuronal, and transportation networks. Our software is available at https://github.com/manlius/muxViz.Comment: 18 pages, 10 figures (text of the accepted manuscript

Fine-grained traffic state estimation and visualisation

Tools for visualising the current traffic state are used by local authorities for strategic monitoring of the traffic network and by everyday users for planning their journey. Popular visualisations include those provided by Google Maps and by Inrix. Both employ a traffic lights colour-coding system, where roads on a map are coloured green if traffic is flowing normally and red or black if there is congestion. New sensor technology, especially from wireless sources, is allowing resolution down to lane level. A case study is reported in which a traffic micro-simulation test bed is used to generate high-resolution estimates. An interactive visualisation of the fine-grained traffic state is presented. The visualisation is demonstrated using Google Earth and affords the user a detailed three-dimensional view of the traffic state down to lane level in real time

Updates in metabolomics tools and resources: 2014-2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources—in the form of tools, software, and databases—is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table

Analyzing the solutions of DEA through information visualization and data mining techniques: SmartDEA framework

Data envelopment analysis (DEA) has proven to be a useful tool for assessing efficiency or productivity of organizations, which is of vital practical importance in managerial decision making. DEA provides a significant amount of information from which analysts and managers derive insights and guidelines to promote their existing performances. Regarding to this fact, effective and methodologic analysis and interpretation of DEA solutions are very critical. The main objective of this study is then to develop a general decision support system (DSS) framework to analyze the solutions of basic DEA models. The paper formally shows how the solutions of DEA models should be structured so that these solutions can be examined and interpreted by analysts through information visualization and data mining techniques effectively. An innovative and convenient DEA solver, SmartDEA, is designed and developed in accordance with the proposed analysis framework. The developed software provides a DEA solution which is consistent with the framework and is ready-to-analyze with data mining tools, through a table-based structure. The developed framework is tested and applied in a real world project for benchmarking the vendors of a leading Turkish automotive company. The results show the effectiveness and the efficacy of the proposed framework

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3) Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.Comment: 72 page

Obvious: a meta-toolkit to encapsulate information visualization toolkits. One toolkit to bind them all

This article describes “Obvious”: a meta-toolkit that abstracts and encapsulates information visualization toolkits implemented in the Java language. It intends to unify their use and postpone the choice of which concrete toolkit(s) to use later-on in the development of visual analytics applications. We also report on the lessons we have learned when wrapping popular toolkits with Obvious, namely Prefuse, the InfoVis Toolkit, partly Improvise, JUNG and other data management libraries. We show several examples on the uses of Obvious, how the different toolkits can be combined, for instance sharing their data models. We also show how Weka and RapidMiner, two popular machine-learning toolkits, have been wrapped with Obvious and can be used directly with all the other wrapped toolkits. We expect Obvious to start a co-evolution process: Obvious is meant to evolve when more components of Information Visualization systems will become consensual. It is also designed to help information visualization systems adhere to the best practices to provide a higher level of interoperability and leverage the domain of visual analytics