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

RACS: Rapid Analysis of ChIP-Seq data for contig based genomes

Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of data which can be difficult to process and analyse, particularly for organisms with contig based genomes. Contig-based genomes often have poor annotations for cis-elements, for example enhancers, that are important for gene expression. Poorly annotated genomes make a comprehensive analysis of ChIP-Seq data difficult and as such standardized analysis pipelines are lacking. Methods: We report a computational pipeline that utilizes traditional High-Performance Computing techniques and open source tools for processing and analysing data obtained from ChIP-Seq. We applied our computational pipeline "Rapid Analysis of ChIP-Seq data" (RACS) to ChIP-Seq data that was generated in the model organism Tetrahymena thermophila, an example of an organism with a genome that is available in contigs. Results: To test the performance and efficiency of RACs, we performed control ChIP-Seq experiments allowing us to rapidly eliminate false positives when analyzing our previously published data set. Our pipeline segregates the found read accumulations between genic and intergenic regions and is highly efficient for rapid downstream analyses. Conclusions: Altogether, the computational pipeline presented in this report is an efficient and highly reliable tool to analyze genome-wide ChIP-Seq data generated in model organisms with contig-based genomes. RACS is an open source computational pipeline available to download from: https://bitbucket.org/mjponce/racs --or-- https://gitrepos.scinet.utoronto.ca/public/?a=summary&p=RACSComment: Submitted to BMC Bioinformatics. Computational pipeline available at https://bitbucket.org/mjponce/rac

Seafloor characterization using airborne hyperspectral co-registration procedures independent from attitude and positioning sensors

The advance of remote-sensing technology and data-storage capabilities has progressed in the last decade to commercial multi-sensor data collection. There is a constant need to characterize, quantify and monitor the coastal areas for habitat research and coastal management. In this paper, we present work on seafloor characterization that uses hyperspectral imagery (HSI). The HSI data allows the operator to extend seafloor characterization from multibeam backscatter towards land and thus creates a seamless ocean-to-land characterization of the littoral zone

Veni Vidi Vici, A Three-Phase Scenario For Parameter Space Analysis in Image Analysis and Visualization

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization

Sense and symbolic objects: Strategic sensemaking through design

This paper reports on an ongoing investigation into one aspect of the design thinking phenomenon, namely the use of designed artifacts — sketches, renderings, graphics, models and prototypes — as symbolic objects in strategy making and implementation. It examines the conceptual overlap between design and the strategic cognition perspective, which considers cognitive processes and structures involved in strategic decision making, particularly the phenomenon of sensemaking. It is primarily a theoretical exploration, but draws on two short testimonies from designers. The specific conceptual connection between design practice and strategic cognition theory is potentially valuable to business leaders and managers involved with innovation, design management and strategic decisions. Preliminary findings suggest sensemaking activities by designers generate innovative future concepts with far-reaching strategic implications; designed artifacts aid sensemaking and sensegiving by management in exploring new business opportunities and directions. This paper is an early draft of a fuller account to be published in 2013 (AIEDAM Special Issue, Spring 2013, Vol.27, No.2, Studying and Supporting Design Communication, Edited by: Maaike Kleinsmann & Anja Maier)

Skills and Knowledge for Data-Intensive Environmental Research.

The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap