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The DIR Participants

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Instructions

Please start with your name as a heading (copy the format below), tell us your current role and affiliation; give a little work/research and life history if you wish and then say what your interests in data are. Finish with a URL to your home page and your signature. Please copy the format of the following entry, so that your name gets added to the contents list.

Contents

Malcolm Atkinson

Malcolm is a professor in the School of Informatics, University of Edinburgh, Director of the e-Science Institute, e-Science Envoy and a member of Edinburgh Data-Intensive Research. He is leading the organisation of this DIR workshop and hopes to lead a follow on year-long research theme on an aspect of DIR. He has been involved in data issues since the late 60s, with work on computer-aided design data, horse-racing data, whisky bottling data, medical data and biological data. He has worked on databases, database languages and persistent languages. More information can be found here and here. I hope that during the workshop I will develop a better understanding of how to select a key subtopic for the theme and recruit kindred spirits to engage in it.

--MalcolmAtkinson 22:06, 4 March 2010 (UTC)

Jerome Avondo

Dr. Jerome Avondo is a Research Associate in the School of Computing, University of East Anglia, Norwich. He is also jointly based at the John Innes Centre, BBSRC, Norwich. His primary area of research is in the visualisation, quantification and data management of microscopy images. This involves developing algorithms for interactive visualization and quantification of microscopy images through space, time and spectral channels using the graphics processing unit (GPU). To address the data management issues involved with large bio-image data sets a prototype OMERO [1] system is being explored as a site wide (John Innes Centre) back bone to facilitate management and quantification.

Lab website: Enrico Coen's Lab

--JeromeAvondo 11:57, 10 March 2010 (UTC)

Neil Chue Hong

Neil Chue Hong is the Director of OMII-UK which cultivates and supports software for e-Research, and Director of the UK Software Sustainability Institute which works with research communities across the UK to help them develop key research software. OMII-UK has recently sponsored a set of four data-related software projects (DataMINX, DiGS/SRM, Enhancing CIAS and OSCAR-ChEBI) working with the physics, neuroscience, climate policy and biochemistry communities.

His primary area of research is the development of community driven software, however he has had a history of working in the area of data intensive research including optical microscopy reconstruction, mushroom processing, database integration (OGSA-DAI), and integration of social simulation data (NeISS).

He is probably based in Edinburgh, although that data may be open to interpretation.

Websites:

--NeilChueHong 11:00, 15 March 2010 (UTC)

Oscar Corcho

Oscar is Associate Professor at Universidad Politécnica de Madrid (UPM). He belongs to the Ontology Engineering Group at UPM. Previously, he worked as a Marie Curie research fellow at the University of Manchester, and was a research manager at iSOCO.

His research activities are focused on the combination of semantic technologies, ontology engineering and e-Science, mainly focusing providing support for large-scale data integration and ontology-based data integration techniques that go beyond the current rigid ontological frameworks for integration, incorporating geographical and social information, as well as dynamic data sources such as those coming from sensor networks. In these areas, he has participated in a number of EU projects (ADMIRE, SemsorGrid4Env and OntoGrid), and in privately-funded projects like ICPS (International Classification of Patient Safety), funded by the World Health Organisation, and HALO, funded by Vulcan Inc.

--OscarCorcho 11:00, 19 March 2010 (UTC)


David De Roure

David De Roure is a Professor of Computer Science in the School of Electronics and Computer Science at the University of Southampton, UK. Closely involved in the UK e-Science programme, David is National Strategic Director for e-Social Science, Chair of OMII-UK and a Co-Director of e-Research South. His work focuses on creating new research methods in and between multiple disciplines, and his projects draw on Web 2.0, Semantic Web and workflow technologies. From July 2010 he will be based in the Oxford e-Research Centre.

Dave runs the myExperiment social web site for scientists sharing scientific workflows and other research objects, in conjunction with Carole Goble at The University of Manchester. He is currently embarking on an exercise of "eating his own dogfood" (or rather, "drinking his own champagne") by using his own tools to conduct research in the Digging into Data project "SALAMI" - Structural Analysis of Large Amounts of Musical Information.

In September 2009 Dave travelled around the US with Malcolm Atkinson on a fact-finding mission, and is very pleased to welcome some of our new US colleagues to the workshop this week.

Websites:

--David De Roure 11:59, 18 March 2010 (UTC)

Liangxiu Han

Dr. Liangxiu Han is a Research Associate in the School of Informatics, University of Edinburgh. Dr. Han’s primary research interest is in Computer Networks and Large Scale Distributed Computing Systems, ranging from system architecture, network protocols, applications to algorithms on Performance Analysis, Modeling and Evaluation using Data-Driven Analyses and Agent-Based methods. Currently, her work in the ADMIRE project [2] mainly focuses on two aspects: 1) Developing a data intensive application in the Life Sciences using data mining techniques; 2) Investigating a high-performance distributed data mining and integration architecture for facilitating data intensive applications. During the workshop she would like to meet researchers from multi-disciplines (e.g., Life sciences, Environmental Sciences and Social Sciences), who are keen to work together to respond to emerging societal challenges.

--LiangxiuHan 8:45, 10 March 2010 (UTC)

Jano van Hemert

Jano is a research fellow in the School of Informatics, University of Edinburgh. He is the Research Leader of the UK National e-Scienec Centre and he leads Edinburgh Data-Intensive Research. His group consists of computer scientists that work on interdisciplinary projects that involve data-intensive challenges. We have booked successes on many data-intensive aspects in areas such as developmental biology, brain imaging, seismology, cell biology, proteomics, molecular medicine, breast cancer and astronomy. During this workshop he wants to develop new collaborations with both groups that have adventurous data-intensive challenges and groups that can provide methods for addressing these challenges that are useful and complementary to our own.

--Jvhemert 13:32, 9 March 2010 (UTC)

Ally Hume

Ally Hume is a software architect at EPCC, The University of Edinburgh. He has worked for many years on the OGSA-DAI project [3]. OGSA-DAI is an extensible framework for pipelined data access, processing and integration. Additionally Ally also works on the ADMIRE project [4] investigating the suitability of pipelined data architectures for large scale data integration and data mining.

During the workshop Ally is interested to discuss whether there are other common data patterns that can be supported by the development of framework software in a similar way to how Hadoop has supported the use of the map reduce pattern.

Daniel S. Katz

Dan is TeraGrid GIG Director of Science, and is a Senior Fellow at the Computation Institute, University of Chicago and Argonne National Laboratory. He is interested in all types of applications, how they work with infrastructure, and how they are expressed. He has been part of the eSI theme on Distributed Programming Abstraction. His most data-intensive project has been the Montage project. He wonders if there is a general abstraction for the ideal infrastructure for data-intensive research.

More information is available at: http://www.ci.uchicago.edu/~dsk/

--Daniel S. Katz 12:26, 19 March 2010 (UTC)

Rob Kitchen

Rob is a 3rd year PhD student in the School of Physics, University of Edinburgh. His work is focussed on assessing technical variability that limits the resolution of modern, high-throughput molecular biology experiments measuring gene expression. He has worked extensively with two types of experiments, quantitative polymerase chain reaction (qPCR) and microarray providing, for each, a means with which to quantify and minimise confounding noise in the experiment data; a list of Rob's publications can be found here, on pubmed. Before the end of his degree he will perform similar analyses on state-of-the-art ultra high-throughput sequencing technologies with special consideration to how they compare to older techniques, such as microarrays and qPCR, in terms of the reliability, accuracy, and reproducibility of reported data. During the workshop he is keen to meet researchers working in genetics and related fields to exchange ideas and foster further collaborations.

--Robk 14:59, 9 March 2010 (UTC)

Chee Sun Liew

Chee Sun is a 2nd year PhD student in the School of Informatics, University of Edinburgh. His work is focused on workflows optimisation where data-streaming is used to enable parallel enactment of workflows. He is a member of Edinburgh Data-Intensive Research and involved in the ADMIRE project. During the workshop he is keen to talk researchers working in workflow systems and related fields in exchanging ideas. Besides, he is looking forward to meet scientists from different domains dealing with data-intensive challenges which can be potential use cases for the ADMIRE project and his optimisation work.

--Csliew 17:55, 12 March 2010 (UTC)

David Rodriguez

David is a postdoctoral research associate in the School of Informatics, University of Edinburgh. He is integrated in the Edinburgh Data-Intensive Research group and is also part of the SFC Brain Imaging Centre. He works for the SINAPSE network in several brain imaging related projects involving data sharing for multicentre studies and data privacy. During the workshop he is interested in learning from other groups involved in data-intensive research, and in particular in meeting other people working with brain imaging or other medical data.

--DavidRG 16:30, 9 March 2010 (UTC)

Costantino Thanos

Costantino is a research director at the ISTI - CNR (Italian National Research Council). He has been the scientific coordinator of an EU funded Network of Excellence on Digital Libraies (NoE DELOS). He is involved in the DL.org project, funded by the EC 7th FP. The project addresses the problem of DL interoperability from many different perspectives: content, user, functionality, policy, quality, and architecture. He is also involved in the GRDI2020 project funded by the EC 7th FP. The project aims at producing a roadmap for building global research data infrastructures addressing both technological and organizational/policy aspects. During this Workshop he is keen to meet researchers working on global data interoperability, including quality, context, and provenance issues to exchange ideas and foster further collaborations.

Networked Multimedia Information Systems Lab website: [5]

Graham Kemp

Graham is an Associate Professor in the Department of Computer Science and Engineering at Chalmers University of Technology, Sweden. His main research interests are in bioinformatics and databases, and include protein modelling and docking, and query processing in fedatated database systems (recent work with relational and RDFS). He is co-chair for the Data Integration in the Life Sciences conference, which will be held in Gothenburg in August 2010. He is also active in other projects that are related to the DIR workshop themes: a PhD student in his group is working with radiotherapy dose-volume response data; he is the academic supervisor for current industrial masters projects in biological text mining, and web advertising analytics; he was involved in a recent project developing ontologies and interface standards for communication between vehicle simulator components.

Website: http://www.cse.chalmers.se/~kemp/

--GrahamKemp 21:12, 12 March 2010 (UTC)

Gagarine Yaikhom

Gagarine is currently a postdoctoral Research Associate within the School of Informatics at the University of Edinburgh. He is a member of the Data-Intensive Research group, and his primary research interests are parallel and distributed computing, and structured programming languages. He is currently working in two projects: the Advanced Data-Mining and Integration Research for Europe (ADMIRE), and the Next Generation Embryology (NGEmbryo). In the ADMIRE project, he is involved with the design of the DISPEL (Data-Intensive Systems Process Engineering Language) language, which allows expression and encapsulation of pattern-oriented workflow structures using functions. In the NGEmbryo project, he is designing and implementing a Web 2.0 portal for annotating three-dimensional models of developing embryos. During this workshop he plans to engage with colleagues in similar fields, and participate in the advancement of data-intensive computing research.


Mike Mineter

I support earth systems modelling, at present especially climate modelling, for an initiative called SAGES, the Scottish Alliance for Geoscience, Environment and Society. I'm based in the School of Geosciences, University of Edinburgh. I have developed software for HPC in geography and the geosciences since 1992; during 2004-8 I was a member of the training team based here in NeSC, creating and giving courses primarily for the National Grid Service and EGEE.

I'm expecting the integration of diverse data and models to become increasingly vital in our Earth system research. During the workshop I hope to develop my understanding of how this can happen, and to meet people similarly motivated.

website: [6] --MikeMineter 09:30, 15 March 2010 (UTC)

Andy Heath

Andy is a senior research fellow in the Department of Earth & Ocean Sciences at the University of Liverpool. He has previously developed a variety of data-intensive applications for HPC compute and HPC-based 3D visualisation. He is currently involved in the NERIES (EC 6th FP) project working with large volumes of seismological data. During the workshop he hopes to learn from the experience gained by others working in data-intensive research areas.

website: http://pcwww.liv.ac.uk/~aeh

Alastair Droop

Alastair is a post-doctoral researcher at the University of York, working with both the York Centre for Complex Systems Analysis (YCCSA) and the Cancer Research Unit (CRU). His current project involves the creation and processing of large-scale datasets of human transcriptomic information from publicly-available sources. Alastair is also interested in complexity and data-centric modelling of complex systems.

At this meeting, Alastair hopes to increase his understanding of large transcriptomic data processing, and to meet other researchers in large-scale biological data analysis.

website: http://www-users.york.ac.uk/~apd500/

Jason Swedlow

Jason Swedlow earned a BA in Chemistry from Brandeis University in 1982 and PhD in Biophysics from UCSF in 1994. After a postdoctoral fellowship at UCSF and then Harvard Medical School, Dr Swedlow established his own laboratory in 1998 at the Wellcome Trust Biocentre, University of Dundee, as a Wellcome Trust Career Development Fellow. He was awarded a Wellcome Trust Senior Research Fellowship in 2002 and named Professor of Quantitative Cell Biology in 2007. His lab focuses on studies of mitotic chromosome structure and dynamics and has published numerous leading papers in the field. He is co-founder of the Open Microscopy Environment, a community-led open source software project that develops specifications and tools for biological imaging and participates as Faculty and Co-Director of the Analytical and Quantitative Microscopy Course at MBL.

At the workshop, I hope to identify potential collaborations, and especially discuss potential interactions and solutions for data intensive research. Ultimately, we want to use these tools to drive discovery in cell and developmental biology and improve human health and society.

Lab website: Swedlow Lab at GRE; Open Microscopy Environment


--JasonSwedlow 09:04, 16 March 2010 (UTC)

Beth Plale

Beth is a professor in the School of Informatics and Computing, Indiana University Bloomington and Director of the Data to Insight Center of Pervasive Technology Institute. Beth has a strong research interest in metadata and provenance of digital scientific data particularly for purposes of long term preservation and focuses on "the first mile" where collection is automatic and close to the generation source. Plale is deeply engaged in environmental and atmospheric science research and has substantive experience in developing stable and useable scientific cyberinfrastructure. Website: Data and Search Informatics

I have looked forward to the workshop and would like to see at least one collaborative effort result.

--BethPlale 09:17, 17 March 2010 (UTC)

Simon Dobson

Simon is a professor of computer science at the University of St Andrews, having previously worked (amongst other places) at UCD Dublin, STFC Rutherford Appleton Laboratory, and as CEO of a start-up company. His research interests are in sensor networks, large-scale data manipulation, autonomic control, and programming in the presence of uncertainty. He is particularly interested in adaptive environmental sensing, where the network adapts its behaviour to the phenomena it is sensing. More details are on his web page.

-- 13:55, 18 March 2010 (UTC)

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