Annette Adler

Integration of biological networks and gene expression data using Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.

Your place or mine? Learning from long-term use of audio-video communication

Workstations and personal computers are increasingly being delivered with the ability to handle multimedia data; more and more of us are linked by high-speed digital networks. With multimedia communication environments becoming more commonplace, what have we learned from earlier experiences with prototype media environments? This paper reports on some of our experiences as developers, researchers and users of flexible, networked, multimedia computer environments, or “media spaces”. It focusses on the lessons we can learn from extended, long-term use of media spaces, with connections that last not hours or days, but months or years. We take as our starting point a set of assumptions which differ from traditional analytical perspectives. In particular, we begin from the position that that real-world baseline is not always an appropriate point of comparison for new media technologies; that a set of complex and intricate communicative behaviours arise over time; and that media spaces connect not only individuals, but the wider social groups of which they form part. We outline a framework based on four perspectives — individual, interactional, communal and societal — from which to view the behaviour of individuals and groups linked by multimedia environments. On the basis of our long-term findings, we argue for a view of media spaces which, first, focuses on a wider interpretation of media space interaction than the traditional view of person-to-person connections, and, second, emphasises emergent communicative practices, rather than looking for the transfer of face-to-face behaviours.

A diary study of work-related reading: design implications for digital reading devices

In this paper we describe a diary study of how people read in the course of their daily working lives. Fifteen people from a wide variety of professions were asked to log their daily document activity for a period of 5 consecutive working days. Using structured interviews, we analysed their reading activities in detail. We examine the range of reading activities that our subjects carried out, and then present findings relating to both common characteristics and variation across the sample. From these findings, we discuss some implications for the design of digital readiig devices.

Design for network communities

Collaboration has long been of considerable interest in the CHI community. This paper proposes and explores the concept of network communities as a crucial part of this discussion. Network communities are a form of technologymediated environment that foster a sense of community among users. We consider several familiar systems and describe the shared characteristics these systems have developed to deal with critical concerns of collaboration. Based on our own experience as designers and users of a variety of network communities. we extend this initial design space along three dimensions: the articulation of a persistent sense of location, the boundary tensions between real and virtual worlds, and the emergence and evolution of community.

Network Communities: Something Old, Something New, Something Borrowed …

Collaboration has long been of considerable interest to both designers and researchers in the CHI and CSCW communities. This paper contributes to this discussion by proposing the concept of network communities as a new genre of collaboration for this discussion. Network communities are robust and persistent communities based on a sense of locality that spans both the virtual and physical worlds of their users. They are a technosocial construct that requires understanding of both the technology and the sociality embodying them. We consider several familiar systems as well as historical antecedents to describe the affordances these systems offer their community of users. Based on our own experience as designers, users and researchers of a variety of network communities, we extend this initial design space along three dimensions: the boundary negotiations between real and virtual worlds, support for social rhythms and the emergence and development of community. Finally we offer implications for designers, researchers and community members based on our findings.

Making a place for seniors on the Net: SeniorNet, senior identity, and the digital divide

The most recent edition of the annual “Falling Through the Net” report from the U.S. Department of Commerce says that people aged 50 and older are among those groups who are least likely to be Internet users [1]. While we might question whether demographic categories are the most useful way to track Internet use, it’s clear that these categories are dominant in conversations about the digital divide. In this paper, we will follow that thread to look at the digital divide for the category of seniors, based on our year-long study of SeniorNet, an organization that supports seniors in learning about technology. By focusing on seniors as a group, we conform to the discourse of the digital divide. At the same time, we want to open up this discourse, to move outside of its conventional story lines and categories. We are both speaking the language of the digital divide and questioning some of its assumptions.

An architecture for biological information extraction and representation

Technological advances in biomedical research are generating a plethora of heterogeneous data at a high rate. There is a critical need for extraction, integration and management tools for information discovery and synthesis from these heterogeneous data. In this paper, we present a general architecture, called ALFA, for information extraction and representation from diverse biological data. The ALFA architecture consists of: (i) a networked, hierarchical object model for representing information from heterogeneous data sources in a standardized, structured format; and (ii) a suite of integrated, interactive software tools for information extraction and representation from diverse biological data sources. As part of our research efforts to explore this space, we have currently prototyped the ALFA object model and a set of interactive software tools for searching, filtering, and extracting information from scientific text. In particular, we describe BioFerret, a meta-search tool for searching and filtering relevant information from the web, and ALFA Text Viewer, an interactive tool for user-guided extraction, disambiguation, and representation of information from scientific text. We further demonstrate the potential of our tools in integrating the extracted information with experimental data and diagrammatic biological models via the common underlying ALFA representation.

CSCW '96 workshop: widening the net: the theory and practice of physical and network communities: Nov.16–17, 1996, Cambridge, MA

This introduction is a summary of the workshop from the perspective of one of the workshop participants. It is followed by a report written by the workshop organizers, giving their perspective, and then the position papers.

Debating the media space design space

Why do Audio Video (AV) communications infrastructures differ so widely in some of their key features? What factors led designers and mearchers to choose radically different se Iutions to the same design problems? This panel brings to gether users, researchm and key designers to expose their rationale and debate some of the issues which are cunently being confronted in the development of such technology.