Workshop on Scientific Instruments
and Sensors on the Grid
Title: A Generalized Service-Oriented
Architecture for Remote Control of Scientific Imaging Instruments
Authors: Tomas Molina, George Yang, Abel Lin, Steven
Peltier and Mark Ellisman. Tomas Molina National Center for Microscopy
and Imaging Research, University of California at San Diego 9500 Gilman
Drive, BSB 1000 La Jolla, CA 92093-0608.
Abstract. Scientific imaging instruments are used in
a variety of disciplines to gather vital data for research and study.
Specifically, in the biomedical field various types of biological imaging
instruments, such as electron microscopes and light microscopes, are
used everyday to acquire 2D and 3D datasets for further understanding
of biological structures. Remote operation or “tele-operation”
of instruments has become a popular solution for research scientists
to acquire and share data across research domains separated by geographical
barriers. A generalized software architecture solution is presented
in this paper to use emerging software technologies to develop a reusable
framework to easily integrate instruments for remote-operation in a
safe and secure fashion. Web services have emerged as a popular technology
to provide software applications with a framework to achieve interoperability
and integration with other applications.
This generalized software architecture was developed to take advantage
of web service middleware technology and to provide a solution for easily
plugging in scientific imaging instruments for tele-operation. The architecture
has also incorporated Grid technology to achieve a more scalable and
robust solution for handling the enormous data sets produced from these
instruments. Finally a set of client libraries is presented to demonstrate
a useful API for developers to quickly develop a graphical user interface
to communicate and acquire data from these instruments.
Title: The Common Instrument Middleware
Architecture: Overview of Goals and Implementation
Authors: Tharaka Devadithya, Kenneth Chiu, Donald McMullen
and Kia Huffman.
Indiana University and SUNY Binghamton.
Abstract. Instruments and sensors and their accompanying
actuators are essential to the conduct of scientific research. In many
cases they provide observations in
electronic format and can be connected to computer networks with varying
degrees of remote interactivity. These devices vary in their architectures
and type of data they capture and may generate data at various rates.
In this paper we present an overview of the design goals and initial
implementation of the Common Instrument Middleware Architecture (CIMA),
a framework for making instruments and sensors network accessible in
a standards-based, uniform way, and for for interacting remotely with
instruments and the data they produce. Some of the issues CIMA addresses
include: flexibility in network transport, efficient and high throughput
data transport, the availability (or lack of ) computational, storage
and networking resources at the instrument or sensor platform, evolution
of instrument design, and reuse of data acquisition and processing
Title: The GRIDCC Project
Authors: David Colling and Andrew Stephen McGough.
Department of Computing, Imperial College London, London, SW7 2BZ, UK.
Abstract. The GRIDCC project is integrating into the
Grid remote interaction with instruments, along with distributed control
and real time interaction. The GRIDCC middleware is being designed with
use cases from a very diverse set of applications and so the GRIDCC
architecture provides access to the instruments in as generic a way
as possible. The middleware will be validated on a representative subset
of these applications. GRIDCC is also developing an adaptable user interface
and a mechanism for performing complex workflows in order to increase
both the usability and the usefulness of the system. Wherever possible
the GRIDCC middleware builds on top of other middleware stacks allowing
the effort to be concentrated on the more novel elements of the project.
The GRIDCC project is a collaboration between 10 organizations in 4
different countries and is funded by the European Union.
Title: Reprocessing D0 data with SAMGrid
Authors: Frederic Villeneuve-Seguier Imperial College
High Energy Physics Department, The Blackett Laboratory, Prince Consort
Road, LONDON SW7 2BW UK.
Abstract. The Dzero experiment studies proton-antiproton
collisions at the Tevatron collider based at Fermilab. Processing, managing
and distributing the large amount of real data coming from the detector
as well as generating sufficient Monte Carlo data are some of the challenges
faced by the Dzero collaboration. SAMGrid combines the SAM data handling
system with the necessary job and information management allowing us
to use the distributed computing resources in the various worldwilde
computing centres. This is one of the first large scale grid applications
in High Energy Physics. After succesful Monte Carlo production and a
limited data reprocessing in the winter of 2003/04, the next milestone
will be the reprocessing of the full current RunII data set. This consists
of ~500 TB of data, encompassing one billion events and has started
in april 2005. Already more than 650 million events have been reprocessed
Title: Sensor Networks and Grid Middleware for Laboratory
Authors: Jamie Michael Robinson, Jeremy G Frey, Andy
J Stanford-Clark, Andrew D Reynolds and Bharat V Bedi, School of Chemistry,
University of Southampton, SOUTHAMPTON, SO17 2HJ, England.
Abstract. By combining automatic environment sensing
and experimental data collection with broker based messaging middleware,
a system has been produced for the real-time monitoring of experiments
whilst away from the lab. Changes in the laboratory environment are
encapsulated as simple XML messages, which are published using an MQTT
compliant broker. Clients subscribe to the MQTT stream, and perform
a data transform on the messages; this may be to produce a user display
or to change the format of the message for republishing. For example
an MQTT client written for the Java MIDP platform, can be run on a smart-phone
with a GPRS Internet connection, freeing us from the constraints of
the network. We present an overview of the technologies used, and how
these are helping chemists make the best use of their time.
Title: Sensor Networks on the Great Barrier Reef: Overview
Author: Ian Atkinson, VeRG Lab, School of Information
Technology, James Cook University, Townsville, Queensland, 4811, Australia.
Abstract. The environmental dynamics of marine systems
such as the Great Barrier Reef (GBR) are highly complex. With over 3,200
reefs extended over 280,000 km2, and fluctuations ranging from kilometres
(oceanic mixing) to millimetres (inter-skeletal currents) the understanding
of the GBR presents challenges at many levels. In order to manage anthropogenic
stresses effectively on the GBR, an observational knowledge base of
orders of magnitude greater in size than that presently available is
required. Many parts of the GBR will remain under sampled as a result
of the economically unviable manual sampling methods currently in use.
Clearly the only form of observational system that
has the capacity to meet this requirement is some form of remote sensor
network system. We are therefore in the process of developing a pilot
sensor network to test and research the concept in our environment,
with the long-term goal of a complete GBR observation system. Our basic
environmental sensor platform measures temperature, salinity and light,
and initial site locations are Davies Reef, Magnetic Island and Heron
Island in North Queensland. We hope the gathered data will give us a
better understanding of the relationship between various environmental
parameters, the impact of temperature changes on coral reefs and the
impact of global warming on the GBR system.
As much as possible, we are building the sensor network
to utilise standard network protocols and hardware. The sensors packages
are be IP based, spatially aware and will eventually be able to adapt
to conditions they are monitoring. There are several major challenges
we face in the rollout of a sensor network across the GBR:
• Establishing long range communications to outer reefs (>100
• Local short range/ad hoc sensor networks for reef deployment
• Sensor design, packaging, development and power supply
• Handling large number of independent data streams
• Data curation and management
In addition there are particular problems raised by
deployment of sensors in marine environments. One of the major problems
faced is how to establish a low-power, low-cost data link from remote
reefs to the shore. Fortunately, we can exploit the phenomenon of humidity
ducts to channel low-power microwave transmission over long ranges.
However, this technique is not consistently reliable, varying in bandwidth
and reliability depending on local climatic conditions (humidity, rainfall
etc.). We are developing a multi scale approach to the sensor network
that is network adaptable so as to cope with this unreliability.
While traditional approaches coping with large volumes
of realtime sensor data involve the deployment systems such as object
ring buffers (ORB’s) we have used an orbless approach in order
to reduce complexity and cost. Data in our environment is streamed directly
into the storage resource broker (SRB) data federation system, where
it is remotely quality assured. Because of link reliability issues we
are using a store forward approach.
Title: Monitoring and remote control of scientific
instrumentation through the Grid
Authors: Claudio Vuerli, Giuliano Taffoni, Igor Coretti,
Fabio Pasian and Paolo Santin
Claudio Vuerli, INAF - Osservatorio Astronomico di Trieste, Via Tiepolo
11, I-34131 Trieste (Italy).
Abstract. Grid infrastructures currently in use for
production purposes are strongly computing-oriented, suitable for scientific
communities whose applications require intensive computation on a relatively
small amount of data. Middleware implementations underlying such infrastructures
well support the sharing and distribution of Grid-embedded computational
resources but problems arise when trying to use such Grids to satisfy
the sharing of data-oriented and services-oriented resources. The Grid
middleware model does not allow the embedding of a meta-computing machine.
Some scientific communities are strongly limited in using such Grid
infrastructures for their applications; they have a wider perception
of the Grid and their applications require not only traditional computation
but also access to complex data repositories and services as well as
mixed distributed computations. The astrophysical community certainly
has this perception of the Grid.
This work concentrates on the interoperability aspects between the Grid
and the scientific instrumentation. The new IE (Instrument Element)
Grid Element has been designed, built and tested for this purpose.
The IE makes possible to monitor and remotely control
any scientific instrumentation. The first implementation of the IE is
focused on the monitoring aspects; astronomers having access to a Grid
infrastructure through a Grid-UI can interface the observing facility
where his/her observing runs are in progress and check the telemetric
data as well as scientific data during their acquisition. Future releases
of the IE will be extended to the remote control so that remote working
sessions using remote astronomical instrumentation shall also be possible.
This work is part of the wider project (including the Query Element)
whose goal is to exploit the Grid technology to build a homogeneous
astronomical working environment where scientific data are acquired,
checked, compared with data coming from other databases, processed and
Title: Elettra Virtual Collaboratory: the evolution of
a Virtual Laboratory Software from a simple web application to the GRIDCC
Authors: Roberto Pugliese, Alessandro Busato, Alessio
Curri, Enrico Mariotti, Daniele Favretto, Valentina Chenda, Fulvio Billh,
Michele Turcinovich, Roberto Borghes, Lawrence Iviani, Fabio Asnicar
and Laura Del Cano., Sincrotrone Trieste S.C.p.A. di interesse nazionale,
Strada Statale 14 - km 163,5 in AREA Science Park, 34012 Basovizza,
Abstract. Elettra Virtual Collaboratory (EVC) is an
example of virtual laboratory, a system which allows a team of researchers
distributed anywhere in the world to perform a complete experiment on
the beamlines and experimental stations of ELETTRA. The creation and
introduction of effective CSCW systems aims at bringing the following
main advantages: provide remote access to expensive and hard-to-duplicate
equipment; increase the effectiveness of the experimental activity,
since more experts can participate to experiments, give useful hints
and solve problems; facilitate multi-institutional consortia collaborations
on large-scale projects.
Experience and know-how acquired during the development
of the first release of EVC was exploited in the FP6 EU founded projects
in which ELETTRA is currently involved. In the BIOXHIT project which
will develop an integrated platform for high-throughput structure determination
ELETTRA is developing the Virtual Collaboratory System a Virtual Organization
(VO) connecting all the European laboratories doing research in the
field of structural genomics.
In the EURO TeV project the design study of the International
Linear Collider ELETTRA is developing the Multipurpose Virtual Laboratory,
the core tool to implement the Global Accelerator Network, a VO connecting
all the international laboratories doing research in the field of Accelerators.
Remote control of an accelerator facility has the potential of revolutionizing
the mode of operation and the degree of exploitation of large experimental
physics facilities. The first prototype of the system allowed in May
2005 the remote control of ELETTRA storage ring from DESY.
The GRIDCC project (Grid Enabled Instrumentation with Distributed Control
and Computation) has the goal of extending the by introducing the handling
of real-time constraints and interactive response into the existing
Grid middleware. GRIDCC will introduce the concept of GRID enabled sensor
which is extremely important for industrial applications.
The paper describes the status ofthe Elettra Virtual Collaboratory
as evolved under the pressure of the above mentioned projects and presents
the development plans for the future.
EVC software has been improved in these years moving from a simple
single facility web application to a multi-facility integration platform
based on webservices. We are currently refactoring EVC in order to migrate
to the GRIDCC MCE middleware. EVC can be considered now another testbed
application of the GRIDCC project.
Most of this work is founded by the EC through the BIOXHIT, EUROTeV
and particularly the RIDCC project (IST-511382) .
Title: Grid-enabling an existing instrument-based national
Authors: Simon Coles, Jeremy Frey, Mike Hursthouse,
Mark Light, Mike Surridge, Ken Meacham, Hugo Mills, Dave DeRoure and
Ed Zaluska, School of Chemistry, University of Southampton, Southampton
SO17 1BJ, United Kingdom.
Abstract. Recent work by the UK National Crystallography
Service (NCS) has integrated the service environment into a Grid environment.
The existing high-throughput crystallography facility is enhanced by
on-line feedback and the ability to monitor and steer diffraction experiments
remotely. Grid-based security mechanisms are used to determine authorisation
attributes and hence to allow user interaction at appropriate stages,
together with access of a database recording the status of the submitted
samples. The user can see the position of their samples, be alerted
to all stages from submission to experiment and then analysis, visualise
raw data as it is generated, be involved in the key decision-making
during the parameterisation and initialization of the experiment and
may then monitor the data collection to ensure its successful completion.
Results data are staged to a secure area and made available for download
(either the raw diffraction data or as a refined structure generated
by NCS staff).