The Data Capacitor (DC), a 535 TB online data cache at IU, is a
key cyberinfrastructure component in an international federation of
crystallography laboratories. Crystallography is the premier
technique for determining the precise three-dimensional structure
of molecules and is instrumental in a broad range of research in
chemistry, biology and medicine. It supports activities ranging from
understanding how a catalyst functions to reduce greenhouse gas
emissions, to developing models of disease processes at the
molecular level and predicting the activity of new pharmaceuticals.
Crystallography produces very large amounts of data and one of the
primary bottlenecks in the productivity of crystallography labs is
management of this data through acquisition, reduction, analysis,
and archiving.
The consortium of crystallography labs has about a dozen members
at national research facilities and universities in North America,
Europe, and Australia. A second critical component of the "glue"
binding the consortium together is software based on the Common
Instrument Middleware Architecture (CIMA) used to acquire data
from instruments across the consortium and store it temporarily on
the DC to await further processing. CIMA, a general approach for
"cyber-enabling" instruments and sensors, is being developed at IU
through a contract with the National Science Foundation as a part
of the NSF Middleware Initiative.
The DC's capacity, network accessibility, and I/O speeds are
important capabilities in the overall system design. As data is
acquired from labs across the consortium, metadata describing the
data's type, origin, and storage locations are generated and stored
so sample data cannot be misplaced or accidentally destroyed and so
that applications can collate and present data from many sources in
near real time.
A third critical piece of the consortium's cyberinfrastructure is a
web portal that allows individual researchers to interact with
instruments and labs remotely, monitor their experiments while in
progress, and manage their data wherever and whenever they want.
The international crystallography consortium uses these elements of
cyberinfrastructure to create an open, flexible environment for
real-time remote access to instruments; massive online and archival
storage capacity; inter-site collaboration and instrument sharing;
and open data sharing, re-use, and problem-solving, augmenting the
discovery capabilities of all members.
For further information see
http://newsinfo.iu.edu/news/page/print/5817.html
http://cimaportal.informatics.indiana.edu:8080/gridsphere
http://www.instrument-middleware.org:8080/cima
Indiana University Cyberinfrastructure News
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Instrument-driven science using the Data Capacitor and the Common Instrument Middleware Architecture
-
Students from the Indiana Academy for Science, Mathematics, and
Humanities visited a virtual kitchen, a mad scientist's lab, and a
village created by their peers, using facilities at the Advanced
Visualization Lab (AVL) on the IUPUI campus. The AVL, part of
University Information Technology Services, is a facility that
includes some of the world's most advanced virtual reality and
visualization technologies.The experience was part of an advanced computer class for
juniors
and seniors enrolled at the Indiana Academy, a residential high
school for gifted and talented students. During the 2007 spring
semester, students from the program received instruction from their
computer science teacher, Susie Sechrest, and expert guidance from
the AVL staff to create a virtual environment of their choice.
For six weeks, the students worked in teams to program their
projects in Virtual Reality Modeling Language (VRML). Using
standard personal computers, in a 2D environment, they could only
imagine what their projects would look like in 3D when they were
imaged in the AVL's Virtual Reality theatre. Sechrest said the Indiana Academy students
have benefited greatly
from their experience. "I could never relay the amount information
that can be absorbed through the use of the 3D glasses, the theatre,
(and) the big computer screen," she said. "This experience will stay
with the students for a lifetime."For more information on the Indiana Academy, visit
http://www.bsu.edu/academy/.
For more information on IU's Advanced Visualization Lab, visit
http://www.avl.iu.edu/. -
Wednesday-Friday,-- HUF 2007, the HPSS Users Forum.
Indiana University is hosting the HPSS Users Forum, October 17-19.
HUF 2007 is the annual gathering for the HPSS community, bringing
together new and existing HPSS users from around the globe to
discuss best practices, new implementations, and future directions
and releases. Attendees will include technologists, researchers,
faculty, postdocs, and industry representatives involved in the
development, implementation, and management of HPSS software. For
more information, see
http://www.indiana.edu/~uits/huf2007/index.html -
There are several job openings available in Indianapolis, focused on
development of applications for multi-core processors.
Technical staff are expected to be computational or computer
scientists with a Ph.D. or M.S. in an appropriate scientific or
engineering discipline, able to work with other scientists/engineers
in creating applications and middleware (tools, libraries, etc.) for
advanced multi-core technologies in targeted disciplines. Experience
developing and optimizing highly scalable parallel code is
essential. Other key skills needed/desired are:
* Initiative, self-motivated, able to work successfully and
achieve objectives without frequent supervision.
* Able to excel in working in situations where not all project
elements are fully or clearly defined.
* Successful in working in distributed collaborative teams.
Demonstrated talents and success in leading teams is valued.
* Strong communication skills, both oral and written.
* Effective in engaging with customers/business partners in
establishing projects and acheiving the project objectives.
Those interested should contact researchtechnologies@iu.edu -
Wednesday, August 29, 12:30-1:30 -- ICTC Room 497 & IMU Walnut Room:
Research Technologies Round Table
Kurt Seiffert, manager of the UITS Research Storage group, will talk
about the Research File System (RFS). Based on OpenAFS, the Research
File System allows researchers to store and access files from a wide
range of platforms, from desktop systems to supercomputers. Recently
RFS was upgraded, to increase both storage capacity and the number
of simultaneous users supported. This talk will discuss these
enhancements, and the the various uses of RFS.
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Sunday, October 14, 2007 -- Boston, MA
Indiana University is offering a TeraGrid-related tutorial, "Using
IU's Big Red PowerPC Cluster and IU Storage Resources via the
TeraGrid" at BiBE 2007 (Bioinformatics and Biomedical Engineering),
The primary purpose of this tutorial is to enable TeraGrid users to
learn about the Big Red system so that they can easily use codes
already ported and optimized for that system (e.g. WRF, NAMD, MILC),
or rapidly migrate other applications to Big Red.
In addition, as massive computations commonly depend on massive data
sets as input, and produce massive data sets as output, it may be
useful to obtain a working knowledge of IU's archival data storage
system, and how to store and access files via gridftp.
Plan to attend to gain hands-on experience with Big Red and IU's
High Performance Storage System, as resources on the TeraGrid.
This tutorial will be given in conjunction with the Workshop on
Progress Toward Petascale Applications in Bioinformatics and
Computational Biology. For more information, see
http://www.cs.gsu.edu/BIBE07/workshops.php -
Outages
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System Date Time Failure
Data Capacitor,
Big Red 07/04 0900-1430 power outage
Planned maintenance
-------------------
System Date Time Action
Libra 08/07 0800-1200 OS Patches
RDC 08/07 0800-1700 OS Patches
Steel 08/07 0600-1000 OS Patches
Data Capacitor 08/07 0800-1700 updates and patches -
If you have questions pertaining to IU's cyberinfrastructure, or you
are encountering some difficulty, there are several ways to obtain
help.
An introduction and overview titled "Indiana University's
CyberInfrastructure: The least you need to know" has been updated
and is available at http://rc.uits.iu.edu/education_and_training/ .
The IU Knowledge Base (http://kb.iu.edu) is an excellent source of
help on how to do things.
If you have problems which the KB does not enable you to solve,
questions about system outages, or if you just have a problem and
you don't know who to contact, send email to
researchtechnologies@iu.edu.
