Interactive Visual Analysis of Networked Systems: Workflows for Two Industrial Domains

We report on a first study of interactive visual analysis of networked systems. Working with ABB Corporate Research and Ericsson Research, we have created workflows which demonstrate the potential of visualization in the domains of industrial automation and telecommunications. By a workflow in this context, we mean a sequence of visualizations and the actions for generating them. Visualizations can be any images that represent properties of the data sets analyzed, and actions typically either change the selection of data visualized or change the visualization by choice of technique or change of parameters

Calendar.help: Designing a Workflow-Based Scheduling Agent with Humans in the Loop

Although information workers may complain about meetings, they are an essential part of their work life. Consequently, busy people spend a significant amount of time scheduling meetings. We present Calendar.help, a system that provides fast, efficient scheduling through structured workflows. Users interact with the system via email, delegating their scheduling needs to the system as if it were a human personal assistant. Common scheduling scenarios are broken down using well-defined workflows and completed as a series of microtasks that are automated when possible and executed by a human otherwise. Unusual scenarios fall back to a trained human assistant who executes them as unstructured macrotasks. We describe the iterative approach we used to develop Calendar.help, and share the lessons learned from scheduling thousands of meetings during a year of real-world deployments. Our findings provide insight into how complex information tasks can be broken down into repeatable components that can be executed efficiently to improve productivity.Comment: 10 page

Evolution towards Smart Optical Networking: Where Artificial Intelligence (AI) meets the World of Photonics

Smart optical networks are the next evolution of programmable networking and programmable automation of optical networks, with human-in-the-loop network control and management. The paper discusses this evolution and the role of Artificial Intelligence (AI)

AiiDA: Automated Interactive Infrastructure and Database for Computational Science

Computational science has seen in the last decades a spectacular rise in the scope, breadth, and depth of its efforts. Notwithstanding this prevalence and impact, it is often still performed using the renaissance model of individual artisans gathered in a workshop, under the guidance of an established practitioner. Great benefits could follow instead from adopting concepts and tools coming from computer science to manage, preserve, and share these computational efforts. We illustrate here our paradigm sustaining such vision, based around the four pillars of Automation, Data, Environment, and Sharing. We then discuss its implementation in the open-source AiiDA platform (http://www.aiida.net), that has been tuned first to the demands of computational materials science. AiiDA's design is based on directed acyclic graphs to track the provenance of data and calculations, and ensure preservation and searchability. Remote computational resources are managed transparently, and automation is coupled with data storage to ensure reproducibility. Last, complex sequences of calculations can be encoded into scientific workflows. We believe that AiiDA's design and its sharing capabilities will encourage the creation of social ecosystems to disseminate codes, data, and scientific workflows.Comment: 30 pages, 7 figure

JISC Final Report: IncReASe (Increasing Repository Content through Automation and Services)

The IncReASe (Increasing Repository Content through Automation and Services) was an eighteen month project (subsequently extended to twenty months) to enhance White Rose Research Online (WRRO)1. WRRO is a shared repository of research outputs (primarily publications) from the Universities of Leeds, Sheffield and York; it runs on the EPrints open source repository platform. The repository was created in 2004 and had steady growth but, in common with many other similar repositories, had difficulty in achieving a “critical mass” of content and in becoming truly embedded within researchers’ workflows. The main aim of the IncReASe project was to assess ingestion routes into WRRO with a view to lowering barriers to deposit. We reviewed the feasibility of bulk import of pre-existing metadata and/or full-text research outputs, hoping this activity would have a positive knock-on effect on repository growth and embedding. Prior to the project, we had identified researchers’ reluctance to duplicate effort in metadata creation as a significant barrier to WRRO uptake; we investigated how WRRO might share data with internal and external IT systems. This work included a review of how WRRO, as an institutional based repository, might interact with the subject repository of the Economic and Social Research Council (ESRC). The project addressed four main areas: (i) researcher behaviour: we investigated researcher awareness, motivation and workflow through a survey of archiving activity on the university web sites, a questionnaire and discussions with researchers (ii) bulk import: we imported data from local systems, including York’s submission data for the 2008 Research Assessment Exercise (RAE), and developed an import plug-in for use with the arXiv2 repository (iii) interoperability: we looked at how WRRO might interact with university and departmental publication databases and ESRC’s repository. (iv) metadata: we assessed metadata issues raised by importing publication data from a variety of sources. A number of outputs from the project have been made available from the IncReASe project web site http://eprints.whiterose.ac.uk/increase/. The project highlighted the low levels of researcher awareness of WRRO - and of broader open access issues, including research funders’ deposit requirements. We designed some new publicity materials to start to address this. Departmental publication databases provided a useful jumping off point for advocacy and liaison; this activity was helpful in promoting awareness of WRRO. Bulk import proved time consuming – both in terms of adjusting EPrints plug-ins to incorporate different datasets and in the staff time required to improve publication metadata. A number of deposit scenarios were developed in the context of our work with ESRC; we concentrated on investigating how a local deposit of a research paper and attendant metadata in WRRO might be used to populate ESRC’s repository. This work improved our understanding of researcher workflows and of the SWORD protocol as a potential (if partial) solution to the single deposit, multiple destination model we wish to develop; we think the prospect of institutional repository / ESRC data sharing is now a step closer. IncReASe experienced some staff recruitment difficulties. It was also necessary to adapt the project to the changing IT landscape at the three partner institutions – in particular, the introduction of a centralised publication management system at the University of Leeds. Although these factors had some impact on deliverables, the aims and objectives of the project were largely achieved

Nanoscale integration of single cell biologics discovery processes using optofluidic manipulation and monitoring.

The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high-paced workflows necessary to support modern large molecule drug discovery. A high-level aspiration is a true integration of "lab-on-a-chip" methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light-induced electrokinetics with micro- and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single-cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low-throughput bioprocess workflows in biopharma and life science research