MOTIVATION: A common experimental output in biomedical science is a list of genes implicated in a given biological process or disease. The gene lists resulting from a group of studies answering the same, or similar, questions can be combined by ranking aggregation methods to find a consensus or a more reliable answer. Evaluating a ranking aggregation method on a specific type of data before using it is required to support the reliability since the property of a dataset can influence the performance of an algorithm. Such evaluation on gene lists is usually based on a simulated database because of the lack of a known truth for real data. However, simulated datasets tend to be too small compared to experimental data and neglect key features, including heterogeneity of quality, relevance and the inclusion of unranked lists. RESULTS: In this study, a group of existing methods and their variations that are suitable for meta-analysis of gene lists are compared using simulated and real data. Simulated data were used to explore the performance of the aggregation methods as a function of emulating the common scenarios of real genomic data, with various heterogeneity of quality, noise level and a mix of unranked and ranked data using 20 000 possible entities. In addition to the evaluation with simulated data, a comparison using real genomic data on the SARS-CoV-2 virus, cancer (non-small cell lung cancer) and bacteria (macrophage apoptosis) was performed. We summarize the results of our evaluation in a simple flowchart to select a ranking aggregation method, and in an automated implementation using the meta-analysis by information content algorithm to infer heterogeneity of data quality across input datasets. AVAILABILITY AND IMPLEMENTATION: The code for simulated data generation and running edited version of algorithms: https://github.com/baillielab/comparison_of_RA_methods. Code to perform an optimal selection of methods based on the results of this review, using the MAIC algorithm to infer the characteristics of an input dataset, can be downloaded here: https://github.com/baillielab/maic. An online service for running MAIC: https://baillielab.net/maic. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Graphia is an open-source platform created for the graph-based analysis of the huge amounts of quantitative and qualitative data currently being generated from the study of genomes, genes, proteins metabolites and cells. Core to Graphia's functionality is support for the calculation of correlation matrices from any tabular matrix of continuous or discrete values, whereupon the software is designed to rapidly visualise the often very large graphs that result in 2D or 3D space. Following graph construction, an extensive range of measurement algorithms, routines for graph transformation, and options for the visualisation of node and edge attributes are available, for graph exploration and analysis. Combined, these provide a powerful solution for the interpretation of high-dimensional data from many sources, or data already in the form of a network or equivalent adjacency matrix. Several use cases of Graphia are described, to showcase its wide range of applications in the analysis biological data. Graphia runs on all major desktop operating systems, is extensible through the deployment of plugins and is freely available to download from https://graphia.app/.

There is a dearth of appropriate tools for young learners with mixed visual abilities to engage with computational learning. Addressing this gap, Torino is a physical programming language for teaching computational learning to children ages 7–11 regardless of level of vision. To create code, children connect physical instruction pods and tune their parameter dials to create music, audio stories, or poetry. Currently, the uptake of novel educational technologies to support inclusive education of children with disabilities continues to be limited at scale. We consider how the Torino Learning Environment supports non-specialist teachers to teach computational learning to children with mixed visual abilities in a UK-wide evaluation with 75 children and 30 teachers over a period of three months. We demonstrate how children can successfully learn with a novel physical programming language. We articulate how key design constructs such as persistent program overview and liveness supported non-specialist teachers to co-produce learning for children of different ages, visual and cognitive abilities. We conclude with reflective guidance on evaluating inclusive educational technologies at scale.CCS CONCEPTSHuman-centered computing → Accessibility → Empirical studies in accessibility

We present Project Zanzibar: a flexible mat that can locate, uniquely identify and communicate with tangible objects placed on its surface, as well as sense a user's touch and hover hand gestures. We describe the underlying technical contributions: efficient and localised Near Field Communication (NFC) over a large surface area; object tracking combining NFC signal strength and capacitive footprint detection, and manufacturing techniques for a rollable device form-factor that enables portability, while providing a sizable interaction area when unrolled. In addition, we detail design patterns for tangibles of varying complexity and interactive capabilities, including the ability to sense orientation on the mat, harvest power, provide additional input and output, stack, or extend sensing outside the bounds of the mat. Capabilities and interaction modalities are illustrated with self-generated applications. Finally, we report on the experience of professional game developers building novel physical/digital experiences using the platform.

This paper argues that comics are a powerful and valuable medium for representing research through design. We review different formats for representing design including the academic paper, the photo-essay and the annotated portfolio. We argue that the comic book form can be better suited to representing various aspects of the design process including interaction, form and aesthetics. We illustrate our argument with examples taken from a comic book about the design of Paper Street View, an interactive system, which allows users to navigate Google Street View with a paper map and brass marker. We argue that comics are well suited to capturing the dynamic process of making, the dialogue and different viewpoints that contribute to interdisciplinary work as well as the interactive and aesthetic elements of a final design.

We present findings from a year-long engagement with a street and its community. The work explores how the production and use of data is bound up with place, both in terms of physical and social geography. We detail three strands of the project. First, we consider how residents have sought to curate existing data about the street in the form of an archive with physical and digital components. Second, we report endeavours to capture data about the street's environment, especially of vehicle traffic. Third, we draw on the possibilities afforded by technologies for polling opinion. We reflect on how these engagements have: materialised distinctive relations between the community and their data; surfaced flows and contours of data, and spatial, temporal and social boundaries; and enacted a multiplicity of 'small worlds'. We consider how such a conceptualisation of data-in-place is relevant to the design of technology.

Today thousands of artists, designers, and craftspeople turn to digital fabrication tools to invent and manufacture new forms. They use vector-graphics software to sketch models, laser-cutters to customize parts, and 3D printers to generate prototypes. However, how our experiences of expressivity, skill and value shift with these developments remains under-explored. This paper describes our early engagements with emerging fabrication technologies in the domain of ceramics, one of our oldest and most enduring artistic mediums. In particular, we detail a collaboration with Helen Martino that resulted in the Sound Bowl, a vessel designed to record an audio message through surface undulations, much like a vinyl record. As an example of design as inquiry, we developed the bowl to explore the integration of digital fabrication in ceramics production. In the process, we found new and intriguing tensions in the entanglement of code and clay: contrasting temporal frames, blurred traces of breakage, and coinciding human senses. We discuss implications of these observations on the nature and organization of embodied interaction.

We present findings from a study of Tokens of Search, a system comprising physical RFID "tokens" that point to web content, and a wooden tray fixed to a small screen, which can be used to access that content. Three families lived with the system for a month, as an exploration of how tokens might be used as resources for practical action. Our findings highlight existing web practices and their individual and collective nuances; tokens were employed in the creation of short-term collections and long-lasting mementos, their physicality giving bookmarking a visibility that could be used to attract attention, serve as reminders, and make observable progress through tasks. However, while all families saw the potential for shared use, only one used it this way in earnest. We reflect on design choices that were expected to encourage collaboration, and the need to support key users such as parents when establishing joint practices.

We describe the design, implementation and deployment of Photobox, a domestic technology that prints four or five randomly selected photos from the owner's Flickr collection at random intervals each month. We deployed Photobox in three homes for fourteen months, to explore how the slow pace at which it operates could support experiences of anticipation and re-visitation of the past. Findings reveal changes in attitude toward the device, from frustration to eventual acceptance. Participants drew on the photos to reflect on past life events and reactions indicated a renewed interest for their Flickr collection. Photobox also provoked reflection on technology in and around the home. These findings suggest several opportunities, such as designing for anticipation, better supporting reflection on the past, and, more generally, expanding the slow technology research program within the HCI community.

Drawing on interviews with 12 software engineers, we investigate the relationship between developers and the tools they use to build code through the lens of craft. We analyze different conceptualizations of craft in accounts of software development, including craft as a process of building, craft as materiality, and craft as a community of practice. By working through these different facets of craft, we investigate tensions of perceiving coding work as, on the one hand, highly rational, and on the other, deeply personal and embodied. In working through these tensions of code as abstract and concrete, cerebral and intuitive, we note implications for craft, both as a theory relevant to computer human interaction, and for paradigms of education in computer science.

It has been argued that technologies for 'memory' should be designed to support creativity and meaning building, rather than the passive capture of cues for remembering [25]. We report findings from a study inspired by this insight, in which older people made personal digital timelines using a new tool called Project Greenwich. We explore how the constraints of the timeline metaphor offer a framework for authoring, and examine how timelines can be used to underpin meaning building in relation to personal content. We highlight the importance of making, this being a vehicle for connecting with others in the present, and a potential means of emphasizing those elements of the past felt to be most salient when looking back.

Web-based technologies are often built to capitalize on the flexibility and fluidity that is supported by the internet, with the value of 'access anywhere' underpinning a blurring of boundaries across home and work. Yet the home is well known in HCI to have a unique set of qualities that can use-fully be drawn upon when designing to support domestic life. In this paper we ask what it means to design domestic web-connected technologies, placing the aesthetic and material properties intrinsic to the home and home life at the centre of our design exploration. We present three concepts that were selected and prototyped from a broader process of research-through-design: Tokens of Search provides tangible handles to web resources; Hole in Space connects the home intimately to a remote place; and Manhattan enables the tangible exploration of events in the community, putting the home at the centre. Discussions in the paper consider not only how aesthetics is articulated in the material and digital properties of the artefacts, but also how a consideration of the properties of the home can create a potentially new design space to explore.

In recent years the Web has evolved substantially, transforming from a place where we primarily find information to a place where we also leave, share and keep it. This presents a fresh set of challenges for the management of personal information, which include how to underpin greater awareness and more control over digital belongings and other personally meaningful content that is hosted online. In the study reported here, we follow up on research that suggests a sense of ownership and control can be reinforced by federating online content as a virtual, single store; we do this by conducting interviews with 14 individuals about their Web-based content. Participants were asked to give the researchers a tour of online content that is personally meaningful to them; to perform a search for themselves in order to uncover additional content; and to respond to a series of design envisionments. We examine whether there is any value in an integrated personal archive that would automatically update and serve firstly, as a source of information regarding the content within it (e.g. where it is stored, who has the rights to it), and secondly, as a resource for crafting personal artefacts such as scrapbooks, CVs and gifts for others. Our analysis leads us to reject the concept of a single archive. Instead, we present a framework of five different types of online content, each of which has separate implications for personal information management.

DIYbio (Do It Yourself Biology) aims to 'open source', tinker and experiment with biology outside of professional settings. In this paper, we present the origins, practices, and challenges of DIYbio initiatives around the world. Our findings depict DIYbio as operating across intersections ('seams') between a range of stakeholders, materials and concerns. To map out the role of Human Computer Interaction (HCI) across these seams, we present design exercises (functional prototypes) that explore three areas for future work: internal collaboration tools within the DIYbio and professional community; mechanisms for external communication with stakeholders from the general public; and bio-electronic assemblies of organic and digital materials. In doing so, we hope to critically re-envision the role of HCI at the emerging intersection of biology, computation and DIY.

We describe the design and implementation of Photobox, a device intended to be used over many years, which occasionally prints a randomly selected photo from the owner's Flickr collection inside of a wooden chest. We describe and reflect on how engaging in the design of this slow technology [5] led to some unexpected challenges and provoked us to re-think approaches to making technologies that are intended to be used over long time scales and which might act infrequently. We also reflect on how living with the device during the implementation phase led to unexpected insights. We conclude with implications for research and practice in the slow technology design space.

We present findings from the deployment of a mobile application, Take and Give, which allows users to place image files in a virtual folder or 'Pocket' on a mobile phone. This content can be viewed by a set of 'Buddies', who can, if they wish, attempt to take ownership of a file for themselves, following which they can keep it, delete it, or place it in the Pocket of someone else. There is only one version of each file, creating a twist on traditional sharing technologies. We report findings from a three week trial of the application in an office space, and describe how Take and Give provided a means of self-presentation and supported a sense of awareness, mutual attentiveness and connectedness. Our findings suggest that the taking of unique content can be an engaging form of sharing and can facilitate awareness and connectedness between people.

As more technologies enter the home, householders are burdened with the task of digital housekeeping-managing and sharing digital resources like bandwidth. In response to this, we created and evaluated a domestic tool for bandwidth management called Home Watcher. Our field trial showed that when resource contention amongst different household members is made visible, people's understanding of bandwidth changes and household politics are revealed. In this paper, we describe the consequences of showing real time resource usage in a home, and how this varies depending on the social make up of the household.

In this paper, we report, first of all, the discovery of a particular kind of emerging social practice involving the exchange of multimedia content on mobiles that we label 'trafficking'. Second, the iteration of a design solution to extend these practices to include the trafficking of broadcast TV content 'segments'. Third, the implications this had for basic assumptions in the interaction design afforded by the two primary OS's in the mobile handset domain. And, fourth, the legal and business inhibitors-enablers that affected not only this research but which are likely to affect all attempts to stretch the capacity of mobile devices and mobile interaction design to afford new ways of 'trafficking' multimedia content.

In this paper we describe a field trial designed to investigate the potential of remote, situated messaging within the home. Five households used our "HomeNote" device for approximately a month. The results show a diversity of types of communication which highlight the role of messaging both to a household and to a place. It also shows the ways in which these kinds of messages enable subtle ways of requesting action, expressing affection, and marking identity in a household -- communication types which have received little attention in the research literature. These in turn point to new concepts for technology which we describe.

Inhabited television combines collaborative virtual environments (CVEs) with broadcast television so that on-line audiences can participate in television shows within shared virtual worlds. We describe a series of experiments with inhabited television, beginning with the NOWninety6 poetry performance, The Mirror, and Heaven & Hell—Live. These early experiments raised fundamental questions for inhabited television concerning the extent to which it is possible to establish fast-paced social interaction within a CVE, and to which it is possible to produce a coherent and engaging broadcast of this action. We then present a fourth more recent experiment, Out of This World, that directly addressed these questions. We describe how the formulation of inhabited television design principles, combined with the use of dedicated production software for scripting and directing a show and for controlling virtual cameras, enabled us to create a fast-moving and more coherent experience.