Scientists’ sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support

Abstract A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists’ analytical workflows and their implications for tool design.http://deepblue.lib.umich.edu/bitstream/2027.42/109495/1/12859_2012_Article_6377.pd

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

Flexibility in MDE for scaling up from simple applications to real case studies: illustration on a Nuclear Power Plant

International audienceModel Driven Engineering provides powerful solutions for the development of User Interfaces. However, concepts and techniques are difficult to master and to apply: the threshold of use is said to be high, making designers and developers reluctant to use it. This paper investigates process model flexibility as a solution. We present three kinds of flexibility for improving design and development process models: (1) variability for equivalent choices, (2) granularability for several levels of details, (3) completeness for possibly optional and pre-defined reusable components. Flexibility decreases the threshold of use by reusability of knowledge, know-how and pieces of code. We illustrate these forms of flexibility on an industrial case study from the nuclear power plant domain. We explain how they are implemented in FlexiLab, a running prototype based on OSGi. The innovation is twofold: on one hand, the operationalization of flexibility; on the other hand, the jump from simple applications to real case studies thanks to flexibility

Firm Transformation: Advancing a Darwinian Perspective

Purpose of the paper: The paper advocates a Darwinian explanation of the process of firm transformation. Existing, but generally opposing views related to the selection-adaptation debates are united to consider the dialogic nature of both approaches. It is argued that a Darwinian approach, as opposed to a neo-Darwinian or Lamarckian approach provides the means to scale the sides of a debate that has for too long divided scholars interested in firm and industry transformation. Approach: The paper addresses three specific issues to develop its Darwinian argument. Firstly, the various work of Geoff Hodgson that have for many years advanced Darwin's evolutionary ideas are used to argue the nature and application of Darwinism in the socio-economic domain. Secondly, the nature of what constitutes the elements of firm-environment interaction is considered to establish basic areas of focus through which the process of firm transformation is more understandable. Lastly, the construct absorptive capacity is likened to a mechanism of transmission through which the learning processes associated with the acquisition of favoured variations can be reconciled with the generic evolutionary processes of variation, selection, and retention. Findings: To understand the process of firm learning, the role of habits and routines must be outlined in specific detail. They cannot be assumed to perform interacting and replicating roles simultaneously. To do so, undermines the fundamental qualities of an evolutionary theory. What is the original/value of paper: The preliminary framework advanced takes us beyond the Darwinian - Lamarckian debate and provides elements of focus from which a greater understanding of the process of firm/industry transformation is possible

The Body Social: An Enactive Approach to the Self

This paper takes a new look at an old question: what is the human self? It offers a proposal for theorizing the self from an enactive perspective as an autonomous system that is constituted through interpersonal relations. It addresses a prevalent issue in the philosophy of cognitive science: the body-social problem. Embodied and social approaches to cognitive identity are in mutual tension. On the one hand, embodied cognitive science risks a new form of methodological individualism, implying a dichotomy not between the outside world of objects and the brain-bound individual but rather between body-bound individuals and the outside social world. On the other hand, approaches that emphasize the constitutive relevance of social interaction processes for cognitive identity run the risk of losing the individual in the interaction dynamics and of downplaying the role of embodiment. This paper adopts a middle way and outlines an enactive approach to individuation that is neither individualistic nor disembodied but integrates both approaches. Elaborating on Jonas’ notion of needful freedom it outlines an enactive proposal to understanding the self as co-generated in interactions and relations with others. I argue that the human self is a social existence that is organized in terms of a back and forth between social distinction and participation processes. On this view, the body, rather than being identical with the social self, becomes its mediator

Applying modern Omic technologies to the Neuronal Ceroid Lipofuscinoses

The Neuronal Ceroid Lipofuscinoses are a group of severe and progressive neurodegenerative disorders, which generally present during childhood. With new treatments emerging on the horizon, there is a growing need to understand the specific disease mechanisms as well as identify prospective biomarkers for use to stratify patients and monitor treatment. The use of Omics technologies to NCLs has the potential to address this need. We discuss the recent use and outcomes of Omics to various forms of NCL including identification of interactomes, affected biological pathways and potential biomarker candidates. We also identify common pathways affected in NCL across the reviewed studies

INDCOR white paper 3: Interactive Digital Narratives and Interaction

The nature of interaction within Interactive Digital Narrative (IDN) is inherently complex. This is due, in part, to the wide range of potential interaction modes through which IDNs can be conceptualised, produced and deployed and the complex dynamics this might entail. The purpose of this whitepaper is to provide IDN practitioners with the essential knowledge on the nature of interaction in IDNs and allow them to make informed design decisions that lead to the incorporation of complexity thinking throughout the design pipeline, the implementation of the work, and the ways its audience perceives it. This white paper is concerned with the complexities of authoring, delivering and processing dynamic interactive contents from the perspectives of both creators and audiences. This white paper is part of a series of publications by the INDCOR COST Action 18230 (Interactive Narrative Design for Complexity Representations), which all clarify how IDNs representing complexity can be understood and applied (INDCOR WP 0 - 5, 2023).Comment: 17 pages, 1 figur

Organizational Darwinism and research methodology

I argue that research methodologies in organizational studies provide an example of cultural evolution but that the resulting dominant logic impedes understanding by militating against realistic inductive research. I examine major 'schools' in organizational Darwinism / cultural evolution and identify overlap between those who use evolutionary dynamics as a relativist lens, the more classically positivist thinking derived from Evolutionary Economics and Darwin's original (1871) conceptual or constructive cultural evolution I then take Darwin's inductive assembly of facts and test existing research that has used an evolutionary perspective against the various strands of his "one long argument

ARL3 mutations cause Joubert syndrome by disrupting ciliary protein composition

Joubert syndrome (JBTS) is a genetically heterogeneous autosomal recessive neurodevelopmental ciliopathy. We investigated further the underlying genetic etiology of Joubert syndrome by studying two unrelated families in whom JBTS was not associated with pathogenic variants in known JBTSrelated genes. Combined autozygosity mapping of both families highlighted a candidate locus on chromosome 10 (chr10: 101569997-109106128 (hg 19)), and exome sequencing revealed two missense variants in ARL3 within the candidate locus. The encoded protein, ADP Ribosylation Factor-Like GTPase 3, ARL3, is a small GTP-binding protein that is involved in directing lipid-modified proteins into the cilium in a GTP-dependent manner. Both missense variants replace the highly conserved Arg149 residue, which we show to be necessary for the interaction with its guanine nucleotide exchange factor ARL13B, such that the mutant protein is associated with reduced INPP5E and NPHP3 localisation in cilia. We propose that ARL3 provides a potential hub in the network of encoded ciliopathy genes, whereby perturbation of ARL3 results in the mislocalisation of multiple ciliary proteins due to abnormal displacement of lipidated protein cargo