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CERN openlab Whitepaper on Future IT Challenges in Scientific Research
This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates
Towards Exascale Scientific Metadata Management
Advances in technology and computing hardware are enabling scientists from
all areas of science to produce massive amounts of data using large-scale
simulations or observational facilities. In this era of data deluge, effective
coordination between the data production and the analysis phases hinges on the
availability of metadata that describe the scientific datasets. Existing
workflow engines have been capturing a limited form of metadata to provide
provenance information about the identity and lineage of the data. However,
much of the data produced by simulations, experiments, and analyses still need
to be annotated manually in an ad hoc manner by domain scientists. Systematic
and transparent acquisition of rich metadata becomes a crucial prerequisite to
sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and
domain-agnostic metadata management infrastructure that can meet the demands of
extreme-scale science is notable by its absence.
To address this gap in scientific data management research and practice, we
present our vision for an integrated approach that (1) automatically captures
and manipulates information-rich metadata while the data is being produced or
analyzed and (2) stores metadata within each dataset to permeate
metadata-oblivious processes and to query metadata through established and
standardized data access interfaces. We motivate the need for the proposed
integrated approach using applications from plasma physics, climate modeling
and neuroscience, and then discuss research challenges and possible solutions
Virtual Astronomy, Information Technology, and the New Scientific Methodology
All sciences, including astronomy, are now entering the era of information abundance. The exponentially increasing volume and complexity of modern data sets promises to transform the scientific practice, but also poses a number of common technological challenges. The Virtual Observatory concept is the astronomical community's response to these challenges: it aims to harness the progress in information technology in the service of astronomy, and at the same time provide a valuable testbed for information technology and applied computer science. Challenges broadly fall into two categories: data handling (or "data farming"), including issues such as archives, intelligent storage, databases, interoperability, fast networks, etc., and data mining, data understanding, and knowledge discovery, which include issues such as automated clustering and classification, multivariate correlation searches, pattern recognition, visualization in highly hyperdimensional parameter spaces, etc., as well as various applications of machine learning in these contexts. Such techniques are forming a methodological foundation for science with massive and complex data sets in general, and are likely to have a much broather impact on the modern society, commerce, information economy, security, etc. There is a powerful emerging synergy between the
computationally enabled science and the science-driven computing, which will drive the progress in science, scholarship, and many other venues in the 21st century
The Dawn of Open Access to Phylogenetic Data
The scientific enterprise depends critically on the preservation of and open
access to published data. This basic tenet applies acutely to phylogenies
(estimates of evolutionary relationships among species). Increasingly,
phylogenies are estimated from increasingly large, genome-scale datasets using
increasingly complex statistical methods that require increasing levels of
expertise and computational investment. Moreover, the resulting phylogenetic
data provide an explicit historical perspective that critically informs
research in a vast and growing number of scientific disciplines. One such use
is the study of changes in rates of lineage diversification (speciation -
extinction) through time. As part of a meta-analysis in this area, we sought to
collect phylogenetic data (comprising nucleotide sequence alignment and tree
files) from 217 studies published in 46 journals over a 13-year period. We
document our attempts to procure those data (from online archives and by direct
request to corresponding authors), and report results of analyses (using
Bayesian logistic regression) to assess the impact of various factors on the
success of our efforts. Overall, complete phylogenetic data for ~60% of these
studies are effectively lost to science. Our study indicates that phylogenetic
data are more likely to be deposited in online archives and/or shared upon
request when: (1) the publishing journal has a strong data-sharing policy; (2)
the publishing journal has a higher impact factor, and; (3) the data are
requested from faculty rather than students. Although the situation appears
dire, our analyses suggest that it is far from hopeless: recent initiatives by
the scientific community -- including policy changes by journals and funding
agencies -- are improving the state of affairs
Information access tasks and evaluation for personal lifelogs
Emerging personal lifelog (PL) collections contain permanent digital records of information associated with individualsâ daily lives. This can include materials such as emails received and sent, web content and other documents with which they have interacted, photographs, videos and music experienced passively or created, logs of phone calls and text messages, and also personal and contextual data such as location (e.g. via GPS sensors), persons and objects present (e.g. via Bluetooth) and physiological state (e.g. via biometric sensors). PLs can be collected by individuals over very extended periods, potentially running to many years. Such archives have many potential applications including helping individuals recover partial forgotten information, sharing experiences with friends or family, telling the story of oneâs life, clinical applications for the memory impaired, and fundamental psychological investigations of memory. The Centre for Digital Video Processing (CDVP) at Dublin City University is currently engaged in the collection and exploration of applications of large PLs. We are collecting rich archives of daily life including textual and visual materials, and contextual context data. An important part of this work is to consider how the effectiveness of our ideas can be measured in terms of metrics and experimental design. While these studies have considerable similarity with traditional evaluation activities in areas such as information retrieval and summarization, the characteristics of PLs mean that new challenges and questions emerge. We are currently exploring the issues through a series of pilot studies and questionnaires. Our initial results indicate that there are many research questions to be explored and that the relationships between personal memory, context and content for these tasks is complex and fascinating
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