BACKGROUND: Gene set enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) plays an important role in bioinformatics focused on diseases of genetic basis. To facilitate phenotype-oriented gene set analysis, we developed PhenoExam, a freely available R package for tool developers and a web interface for users, which performs: (1) phenotype and disease enrichment analysis on a gene set; (2) measures statistically significant phenotype similarities between gene sets and (3) detects significant differential phenotypes or disease terms across different databases. RESULTS: PhenoExam generates sensitive and accurate phenotype enrichment analyses. It is also effective in segregating gene sets or Mendelian diseases with very similar phenotypes. We tested the tool with two similar diseases (Parkinson and dystonia), to show phenotype-level similarities but also potentially interesting differences. Moreover, we used PhenoExam to validate computationally predicted new genes potentially associated with epilepsy. CONCLUSIONS: We developed PhenoExam, a freely available R package and Web application, which performs phenotype enrichment and disease enrichment analysis on gene set G, measures statistically significant phenotype similarities between pairs of gene sets G and G' and detects statistically significant exclusive phenotypes or disease terms, across different databases. We proved with simulations and real cases that it is useful to distinguish between gene sets or diseases with very similar phenotypes. Github R package URL is https://github.com/alexcis95/PhenoExam . Shiny App URL is https://alejandrocisterna.shinyapps.io/phenoexamweb/ .

MOTIVATION: Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behavior for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks. RESULTS: We applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets by 46.73%. Moreover, GMSCA predicts that the SNCA gene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes. AVAILABILITYAND IMPLEMENTATION: The tool is available at GitHub, https://github.com/drlaguna/GMSCA as open-source software. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine. This review cuts across the boundaries between genomics, transcriptomics and proteomics, summarizing how omics data are generated, analysed and shared, and provides an overview of the current strengths and weaknesses of this global approach. This work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research.

Physical data representations, or data physicalizations, are a promising new medium to represent and communicate data. Previous work mostly studied passive physicalizations which require humans to perform all interactions manually. Dynamic shape-changing displays address this limitation and facilitate data exploration tasks such as sorting, navigating in data sets which exceed the fixed size of a given physical display, or preparing "views" to communicate insights about data. However, it is currently unclear how people approach and interact with such data representations. We ran an exploratory study to investigate how non-experts made use of a dynamic physical bar chart for an open-ended data exploration and presentation task. We asked 16 participants to explore a data set on European values and to prepare a short presentation of their insights using a physical display. We analyze: (1) users' body movements to understand how they approach and react to the physicalization, (2) their hand-gestures to understand how they interact with physical data, (3) system interactions to understand which subsets of the data they explored and which features they used in the process, and (4) strategies used to explore the data and present observations. We discuss the implications of our findings for the use of dynamic data physicalizations and avenues for future work.

This paper presents ShapeClip: a modular tool capable of transforming any computer screen into a z-actuating shape-changing display. This enables designers to produce dynamic physical forms by "clipping" actuators onto screens. ShapeClip displays are portable, scalable, fault-tolerant, and support runtime re-arrangement. Users are not required to have knowledge of electronics or programming, and can develop motion designs with presentation software, image editors, or web-technologies. To evaluate ShapeClip we carried out a full-day workshop with expert designers. Participants were asked to generate shape-changing designs and then construct them using ShapeClip. ShapeClip enabled participants to rapidly and successfully transform their ideas into functional systems.

Visualizations such as bar charts help users reason about data, but are mostly screen-based, rarely physical, and almost never physical and dynamic. This paper investigates the role of physically dynamic bar charts and evaluates new interactions for exploring and working with datasets rendered in dynamic physical form. To facilitate our exploration we constructed a 10x10 interactive bar chart and designed interactions that supported fundamental visualisation tasks, specifically; annotation, filtering, organization, and navigation. The interactions were evaluated in a user study with 17 participants. Our findings identify the preferred methods of working with the data for each task i.e. directly tapping rows to hide bars, highlight the strengths and limitations of working with physical data, and discuss the challenges of integrating the proposed interactions together into a larger data exploration system. In general, physical interactions were intuitive, informative, and enjoyable, paving the way for new explorations in physical data visualizations.

Digital fabrication machines such as 3D printers and laser-cutters allow users to produce physical objects based on virtual models. The creation process is currently unidirectional: once an object is fabricated it is separated from its originating virtual model. Consequently, users are tied into digital modeling tools, the virtual design must be completed before fabrication, and once fabricated, re-shaping the physical object no longer influences the digital model. To provide a more flexible design process that allows objects to iteratively evolve through both digital and physical input, we introduce bidirectional fabrication. To demonstrate the concept, we built ReForm, a system that integrates digital modeling with shape input, shape output, annotation for machine commands, and visual output. By continually synchronizing the physical object and digital model it supports object versioning to allow physical changes to be undone. Through application examples, we demonstrate the benefits of ReForm to the digital fabrication process.

The author has spent a year living and working with an interactive office desk based on a modified desktop computer. This paper recounts these experiences as a post-hoc, reflective case study that investigates the effects that ergonomics, input devices and user interface elements have on work patterns, task organisation, collaboration and personal habits. In addition to covering usability questions such as why the mouse and keyboard remained the dominant input method, it illustrates how new workflow processes formed around hardware constraints and the roles that separate visual planes played in the management and perception of subtasks. This study explores the meeting of the virtual and physical workspace in terms of clutter, personal expression and aesthetics and concludes by discussing the future of interactive office desks and outlining the key findings from the year.

Trends such as the increasing adoption of smartphones, the development of the service-oriented internet, and diffusion of sensing technologies into cities have the potential to combine in order to form a ubiquitous computing infrastructure. At the same time, as the computer diffuses into the physical world, it loses its location-neutrality, exposing the urgent need for a debate of design choices in ubiquitous computing. In this paper, we discuss the process of urban development as a source of inspiration for such design choices. Looking from the ground up, of particular interest is the opportunity to localize and democratize an emerging ubiquitous computing infrastructure. The design choices we negotiate today will determine the society in which we will live in the future.

Many global internet services today can be thought of as being managed 'top-down' without much appreciation or requirement for local control. New services such as location-based data stores implemented in cities around the world suggest opportunities for novel forms of management of data with relevance to a local context. We argue that such localization of ubiquitous system management provides an opportunity in supporting local off-line interaction and 'community building' and that urban development, which requires interaction between members of different communities, presents an interesting case where such systems could be realised.

This paper presents a software toolkit designed to enable the rapid development of multimedia-rich, multi-touch enabled, and interactive projection-based displays. For instance: door displays, floor displays, wall displays, and interactive tables. Despite recent technological advances and the commercialization of hardware required to achieve this at a relatively low cost, creating and deploying such displays remains a difficult task, even for those with the essential technical skills and experience. We assert that greater accessibility of toolkits like the one presented in this paper will reduce these barriers and allow people (not necessarily from the ubiquitous computing domain) to apply the technology to their own fields. To assess this toolkit's suitability for this role, we present a system and usability evaluation. We observed that participants were able to quickly create their own novel display deployments. Our findings offer insights for potential toolkit users and those considering how to write programs for future ubiquitous projected display environments.

Software engineering is a team activity yet the programmer's key tool, the IDE, is still largely that of a soloist. This paper describes the vision, implementation and initial evaluation of CoffeeTable - a fully featured research prototype resulting from our reflections on the software design process. CoffeeTable exchanges the traditional IDE for one built around a shared interactive desk. The proposed solution encourages smooth transitions between agile and traditional modes of working whilst helping to create a shared vision and common reference frame - key to sustaining a good design. This paper also presents early results from the evaluation of CoffeeTable and offers some insights from the lessons learned. In particular, it highlights the role of developer tools and the software constructions that are shaped by them.

Today, one does not have to travel far to find examples of digital signage, yet the adoption of interactive gesture based public displays remains quite rare. Subsequently, not much is known about them despite a large array of potential advantages. This paper contributes to our understanding of how people perceive, respond to and interact with such displays outside the controlled environment of a research lab. Unlike other works which have focused on isolated aspects of in-lab interaction, we present a detailed examination that addresses a wide range of responses to such a display - including those who ignore them completely. To facilitate our study we created an experimental coarse gesture based software suite and then deployed the system along with associated applications as part of an existing large scale public display network. Using this as a base, we executed four studies designed to passively observe the reactions of passers-by and followed these up with a fifth controlled experiment that compared the effectiveness of two different kinds of gesture in the context of menu item selection. To conclude, we present our key-findings and highlight possible avenues of further study for the future of gesture based digital signage.