Data Platforms and Cities

This section offers a series of joint reflections on (open) data platform from a variety of cases, from cycling, traffic and mapping to activism, environment and data brokering. Data platforms play a key role in contemporary urban governance. Linked to open data initiatives, such platforms are often proposed as both mechanisms for enhancing the accountability of administrations and performing as sites for 'bottom-up' digital invention. Such promises of smooth flows of data, however, rarely materialise unproblematically. The development of data platforms is always situated in legal and administrative cultures, databases are often built according to the standards of existing digital ecologies, access always involves processes of social negotiation, and interfaces (such as sensors) may become objects of public contestation. The following contributions explore the contested and mutable character of open data platforms as part of heterogeneous publics and trace the pathways of data through different knowledge, skills, public and private configurations. They also reflect on the value of STS approaches to highlight issues and tensions as well as to shape design and governance

Internet Predictions

More than a dozen leading experts give their opinions on where the Internet is headed and where it will be in the next decade in terms of technology, policy, and applications. They cover topics ranging from the Internet of Things to climate change to the digital storage of the future. A summary of the articles is available in the Web extras section

The identification of knowledge gaps in the technologies of cyber-physical systems with recommendations for closing these gaps

The paper reports some training, education, and operational findings from an EU Horizon 2020 project that included the production of technology road‐maps for the domain of cyber‐physical systems (CPS). The project reviewed Deliverables from 72 CPS projects, all within Framework Programme 7 and Horizon 2020, including 18 from the ARTEMIS and ECSEL subprograms. This analysis led to the production of a “Knowledge Map” containing 75 technologies identified within the 72 projects as nodes in this map, connected by interoperability links. Filtering this map for each node, in turn, has led, in combination with other parts of the project, to some 48 recommendations for future focus and funding of developments in these technologies to assist in the rapid adoption of CPS in all domains. While the focus has been limited to European Union research and innovation, it is believed that the recommendations are transferable to other regions of the world

2012 Activity Report of the Regional Research Programme on Hadrontherapy for the ETOILE Center

2012 is the penultimate year of financial support by the CPER 2007-2013 for ETOILE's research program, sustained by the PRRH at the University Claude Bernard. As with each edition we make the annual review of the research in this group, so active for over 12 years now. Over the difficulties in the decision-making process for the implementation of the ETOILE Center, towards which all our efforts are focussed, some "themes" (work packages) were strengthened, others have progressed, or have been dropped. This is the case of the eighth theme (technological developments), centered around the technology for rotative beam distribution heads (gantries) and, after being synchronized with the developments of ULICE's WP6, remained so by ceasing its activities, coinciding also with the retirement of its historic leader at IPNL, Marcel Bajard. Topic number 5 ("In silico simulations") has suffered the departure of its leader, Benjamin Ribba, although the work has still been provided by Branka Bernard, a former postdoctoral fellow in Lyon Sud, and now back home in Croatia, still in contract with UCBL for the ULICE project. Aside from these two issues (and the fact that the theme "Medico-economical simulations" is now directly linked to the first one ("Medical Project"), the rest of the teams are growing, as evidenced by the publication statistics at the beginning of this report. This is obviously due to the financial support of our always faithful regional institutions, but also to the synergy that the previous years, the European projects, the arrival of the PRIMES LabEx, and the national France Hadron infrastructure have managed to impulse. The Rhone-Alpes hadron team, which naturally includes the researchers of LPC at Clermont, should also see its influence result in a strong presence in France Hadron's regional node, which is being organized. The future of this regional research is not yet fully guaranteed, especially in the still uncertain context of ETOILE, but the tracks are beginning to emerge to allow past and present efforts translate into a long future that we all want to see established. Each of the researchers in PRRH is aware that 2013 will be (and already is) the year of great challenge : for ETOILE, for the PRRH, for hadron therapy in France, for French hadrontherapy in Europe (after the opening and beginning of treatments in the German [HIT Heidelberg, Marburg], Italian [CNAO, Pavia] and Austrian [MedAustron, Wien Neuerstadt]) centers. Let us meet again in early 2014 for a comprehensive review of the past and a perspective for the future ..

Bioinformatics for the human microbiome project

Microbes inhabit virtually all sites of the human body, yet we know very little about the role they play in our health. In recent years, there has been increasing interest in studying human-associated microbial communities, particularly since microbial dysbioses have now been implicated in a number of human diseases [1]–[3]. Dysbiosis, the disruption of the normal microbial community structure, however, is impossible to define without first establishing what “normal microbial community structure” means within the healthy human microbiome. Recent advances in sequencing technologies have made it feasible to perform large-scale studies of microbial communities, providing the tools necessary to begin to address this question [4], [5]. This led to the implementation of the Human Microbiome Project (HMP) in 2007, an initiative funded by the National Institutes of Health Roadmap for Biomedical Research and constructed as a large, genome-scale community research project [6]. Any such project must plan for data analysis, computational methods development, and the public availability of tools and data; here, we provide an overview of the corresponding bioinformatics organization, history, and results from the HMP (Figure 1).National Institutes of Health (U.S.) (NIH U54HG004969)National Institutes of Health (U.S.) (grant R01HG004885)National Institutes of Health (U.S.) (grant R01HG005975)National Institutes of Health (U.S.) (grant R01HG005969

GEORAC: an RNA-seq Atlas Constructor for the Gene Expression Omnibus

The meteoric rise of next-generation sequencing technologies over the past 15 years has resulted in a voluminous amount of data generated by modern biological and clinical studies. RNA sequencing, colloquially referred to as RNA-Seq, is a next-generation approach capable of surveying and quantifying whole organism transcriptomes. RNA-Seq methods are valued over microarray assays for their ability to avoid cross-hybridization signal noise, to quantify gene or transcript expression without assay-specific upper limits, to natively provide single-nucleotide genomic resolution, and to allow for de novo transcriptome assemblies. Many thousands of RNA-Seq studies have been published over the past seven years, and a significant area of bioinformatics research has focused on the creation of atlases that aggregate RNA-Seq results. These atlases are crucially useful for surveying trends in gene expression across published studies, for inspecting potentially contentious claims made by novel or prior work, and for synthesizing future research directions. The Expression Atlas currently serves as the canonical example for an RNA-Seq atlas and presents results from over 3,000 studies across numerous model research organisms. An issue with the Expression Atlas is that it forcibly applies a uniform secondary re-analysis pipeline to each RNA-Seq study incorporated within its database; this approach presents a conceptual challenge to studies whose results have been generated and published using established, well-tested workflows. Thus, there exists a critical need to provide for construction of RNA-Seq atlases that precisely reflect original results presented within the literature, and the primary objective of this dissertation is to provide a workflow that allows for transparent, reproducible construction of RNA-Seq atlases from study meta- and expression data housed within the National Center for Biomedical Information’s Gene Expression Omnibus (GEO). The challenge of this goal is exacerbated by the highly flexible design of GEO, which allows researchers to define novel metadata attributes and values at will and to submit expression results in virtually any format. Following an introductory background into modern genomics and RNA-Seq, the second chapter of this work presents GEOMP, a metadata parser and relational database constructor for the Gene Expression Omnibus. The subsequent third chapter describes GEOMP2, an in-place augmentation of GEOMP that provides further atomization and loading of sample-specific characteristics tags; this chapter significantly presents results from a pilot study surveying bioinformatics methods reproducibility across the zebrafish, mouse, and human research communities using metadata parsed and output by GEOMP2. Chapter four details GEORGET, a pipeline designed to rehabilitate, translate, and load expression data pulled from GEO into the relational database store constructed by GEOMP2. Chapter five concludes with discussion of future directions needed to expand and improve upon the current GEORAC workflow and the associated methods reproducibility study

Social impact of artificial intelligence in Europe

La Inteligencia Artificial (IA) puede ser una herramienta de gran ayuda para el crecimiento y desarrollo de la sociedad. Para conseguir un enfoque más cercano y una evolución más eficaz de esta tecnología, la Comision Europea ha creado la red AI DIH, la cual centra su visión en el soporte de las pymes y sector público para implementar la IA en las diferentes regiones de Europa, ayudando a reducir la brecha entre las grandes corporaciones especializadas. En este documento se contextualiza la funcionalidad de la red DIH y cómo está actuando de cara a la IA, para introducir el análisis de los diferentes centros colaborativos enfocados a la IA. El resultado es una propuesta de técnicas, modelos y parámetros que pueden implementarse en esta red de centros, con el apoyo de Living Labs, para incrementar la efectividad y mejorar el producto/servicio final.Artificial intelligence (AI) can be a very useful tool for the growth and development of society. To achieve a closer approach and a more effective evolution of this technology, the European Commission has created the AI DIH network, which focuses its vision on supporting SMEs and the public sector to implement AI in the different regions of Europe, helping to close the gap between large specialized corporations. This document contextualizes the functionality of the DIH network and how it is acting in the face of AI, to introduce the analysis of the different collaborative centers focused on AI. The result is a proposal of techniques, models and parameters that can be implemented in this network of centers, supported by Living Labs, to increase effectiveness and improve the final product/service