Participatory analytics for transport decision-making

This thesis investigates the design and evaluation of several software platforms that facilitate participatory outcomes in transport decision-making across operational, local and strategic scales. These platforms act as instruments to explore aspects of the research question: "How can urban dashboards be contextualised, designed & evaluated in a way that is sensitive to the changing role of digital democracy, immersive technologies and the increasingly collaborative nature of planning?". The concept of participatory urban dashboards is introduced, followed by process of participatory analytics. This process involves bringing more people on board with both using the dashboard (e.g., together or collaboratively) and allowing a more general audience of citizens or stakeholders to make sense and validate what is displayed. The research is applied to the city of Sydney, Australia. Sydney is a growing, global city with a wide variety of transport infrastructure ambitions and a strong, open-data ecosystem. Sydney’s transport system underpins the case studies of the operational, local and strategic digital artefacts assessed in this research. Participatory analytics outcomes as a result of interacting with these digital prototypes are evaluated. This will, in turn, help direct research and real-life applications and development of these tools. Further, it aims to build on research gap calling for further understanding of context-specific, user-centric design and evaluation of these participatory analytics tools

Model organism databases: essential resources that need the support of both funders and users.

Modern biomedical research depends critically on access to databases that house and disseminate genetic, genomic, molecular, and cell biological knowledge. Even as the explosion of available genome sequences and associated genome-scale data continues apace, the sustainability of professionally maintained biological databases is under threat due to policy changes by major funding agencies. Here, we focus on model organism databases to demonstrate the myriad ways in which biological databases not only act as repositories but actively facilitate advances in research. We present data that show that reducing financial support to model organism databases could prove to be not just scientifically, but also economically, unsound

Canto: an online tool for community literature curation.

MOTIVATION: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species. AVAILABILITY: Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/)

Fission stories: using PomBase to understand Schizosaccharomyces pombe biology

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualization, PomBase also drives innovation in the MOD community