Parsons, A., Anderson, D., Backer, D., Bankay, R., Chapman, D., Chen, H ...

UC Berkeley SETI Catalysis Parsons, A., Anderson, D., Backer, D., Bankay, R., Chapman, D., Chen, H., Cobb, J., Douglas, K., Korpela, E., Lebofsky, M., Nagpal, V., Werthimer, D., Wright, M. Home: University of Washington
Area: Biology
Goal: Determine the 3-dimensional shapes of proteins in research
that may ultimately lead to finding cures for some major human
diseases. By running Rosetta@home you will help us speed up and
extend our research in ways we couldn't possibly attempt without
your help. You will also be helping our efforts at designing
new proteins to fight diseases such as HIV, Malaria, Cancer, and
Alzheimer's. Home: The Swiss Tropical Institute
Area: Epidemiology
Goal: Simulation models of the transmission dynamics and health
effects of malaria are an important tool for malaria control. They
can be used to determine optimal strategies for delivering mosquito
nets, chemotherapy, or new vaccines which are currently under
development and testing. Such modeling is extremely computer
intensive, requiring simulations of large human populations with a
diverse set of parameters related to biological and social factors that
influence the distribution of the disease. Home: Mathematical Institute of Leiden University, Kennislink
Area: Mathematics
Goal: Search for abc-triples: positive integers a,b,c such that
a+b=c, a<b<c, a,b,c have no common divisors and c > rad(abc),
where rad(n) is the product of the distinct prime factors of n. The
ABC conjecture says that there are only finitely many a,b,c such
that log(c)/log(rad(abc)) > h for any real h > 1. The ABC
conjecture is currently one of the greatest open problems in
mathematics. If it is proven to be true, a lot of other open problems
can be answered directly from it.
A A B B C C @home @home Home: Univ. of Wisconsin - Milwaukee,
Albert Einstein Institute
Area: Astrophysics
Goal: Search for spinning neutron stars (also
called pulsars) using data from the LIGO and
GEO gravitational wave detectors.
Einstein@Home is a World Year of Physics
2005 project supported by the American
Physical Society (APS) and by a number of
international organizations.
Home: Oxford University
Area: Earth sciences
Goal: To investigate the approximations that have to be made in
state-of-the-art climate models. By running the model thousands of
times we hope to find out how the model responds to slight tweaks
to these approximations - slight enough to not make the
approximations any less realistic. This will allow us to improve our
understanding of how sensitive our models are to small changes and
also to things like changes in carbon dioxide and the sulphur cycle.
This will allow us to explore how climate may change in the next
century under a wide range of different scenarios. Home: Scripps Research Institute
Area: Biology
Goal: Protein structure prediction starts from a sequence
of amino acids and attempts to predict the folded,
functioning, form of the protein. Predicting the structure
of an unknown protein is a critical problem in enabling
structure-based drug design to treat new and existing
diseases. Berkeley Open Infrastructure for Network Computing (BOINC) is a non-commercial
middleware system for volunteer computing, originally developed to support the SETI@home
project, but intended to be useful for other applications in areas as diverse as mathematics,
medicine, molecular biology, climatology, and astrophysics. The intent of BOINC is to make it
possible for researchers to tap into the enormous processing power of personal computers
around the world. BOINC has been developed by a team based at the Space Sciences Laboratory at the University
of California, Berkeley led by David Anterson, who also leads SETI@home. As a "quasi-
supercomputing" platform, BOINC has over 435,000 active computers (hosts) worldwide
processing on average 521 TFLOPs as of March 12, 2007. BOINC is funded by the National
Science Foundation through awards SCI/0221529, SCI/0438443, and SCI/0506411. The software is free/open source software, released under the GNU Lesser General Public
License. It is also used for commercial usages, as there are some private companies that are
beginning to use the platform to assist in their own research The goal of SETI@home is to detect intelligent life outside Earth. SETI@home
searches for possible evidence of radio transmissions from extraterrestrial intelligence
using data from the Arecibo radio telescope. The software searches for four signals:
Spikes in power spectra, gaussian rises and falls in transmission power, possibly
representing the telescope beam's main lobe passing over a radio source, Triplets
three power spikes in a row, pulsing signals that possibly represent a narrow band
digital-style transmission There are so many variations on how a signal would arrive at Earth that signals are
processed to ensure that each possible way it could arrive might be checked. For
instance, another planet is very unlikely to be at the same distance from Earth all the
time. The distances across the universe between different galaxies is ever changing, so
a variety of speeds must be accommodated - the reason being that a signal will look
very different if the broadcasting location is moving towards us or away from us. This
is the Doppler effect, the same effect that is observed if an ambulance is going past us
at speed - the whole pitch of the siren's sound changes as it goes into the distance. So
SETI software checks the signal by taking each individual frequency and analyzing it
as if it were not moving relative to the Earth, or moving away or towards its at
different speeds. The process is somewhat like tuning a radio to various channels, and looking at the
signal strength meter. If the strength of the signal goes up, that gets attention. More
technically, it involves a lot of digital signal processing, mostly discrete Fourier
transforms at various chirp rates and durations. The goal of CASPER is to streamline and reduce the current radio astronomy instrumentation
design flow through the development of an open-source, platform-independent design
approach. This incorporates reconfigurable, modular, easily upgradable hardware with standard,
parameterized design libraries that abstract away the underlying details of the system. Existing radio astronomy instrumentation is highly specialized, with custom, complex,
dedicated instruments being built for individual applications. Each instrument takes 3-5 years
to design, construct, and debug, and by the time it is deployed, it has usually been made
obsolete by the Moores Law growth of the electronics industry. This development cycle could
be shortened by taking advantage of commodity hardware and developing signal processing
libraries which are device independent. There is a growing trend in radio astronomy for high-performance real-time DSP applications
such as beam forming, spatial correlation, and wideband, fine-resolution spectroscopy. The
next generation of radio telescopes (eg: Allen Telescope Array (ATA), the Combined Array
for Research in Millimeter-wave Astronomy (CARMA), the next generation Epoch of
Reionization (EoR) array, and the Square Kilometer Array (SKA)), are being designed and
built using large numbers of small antennas. Home: University of California, Berkeley
Area: Cosmology
Goal: We are developing the Precision Array to Probe the Epoch of Reionization.
Ideas were in gestation 2001-2003. In 2003/2004 Don Backer and Rich Bradley
began collaboration with goal to rapidly prototype and field hardware to probe the
sky in the 100-200 MHz band. A simple, non-phase tracking, full-sky coverage,
2-element interferometer on a 150m baseline was deployed at the NRAO Green
Bank site in the summer of 2004 using a software correlator. As of this update, an
8-element array (pictured above) is operational in Green Bank, and plans are
brewing for a deployment of a second array in Western Australia during 2007
May/June Home: University of California, Berkeley
Area: Astrophysics (Pulsars)
Wide bandwidth signal processors for pulsar and other science at a number of large telescopes
around the globe are now based on computing in cpu clusters rather than custom hardware.
This approach is driven by a number of features: (1) The processing algorithms are in software
where they are easily accessible to change by the general user community for particular
scienti¯c applications. (2) The algorithmic software can be ported to clusters with ever more
powerful cpus. (3) The data can be represented by many bits to provide accuracy of power
measurements for time-variable signals. A major challenge in this approach has been input of the digitized data into the cluster. The
generic architecture involves a set of cpus acting as \data servers" with commercial digital I/O
boards running at speeds up to 1 Gbs. The data servers pass data along with minor processing
to a high speed switch that feeds data segments to the main cluster of \slave cpus", which run
specialized algorithms. Modern data servers with appropriate mother board design can (just)
robustly handle a 1 Gbs input and subsequent 1 Gbs output. Cluster-based processors are now employed at Jodrell Bank (COBRA); Nancay (LBP); Parkes
(CPSR); Green Bank Telescope (CGSR,GASP) and Arecibo (ASP). Each of these can handle
realtime signal processing of bandwidths ranging from 64 to 128 MHz depending on unit and
observing parameters. The principal application for all of these processors is the removal of
dispersion in pulsar signals via Fourier ¯ltering and subsequent detection and synchronous
averaging modulo the apparent pulse period. Dispersion removal requires forward and reverse
FFTs of lengths that often exceed the L2 cache; FFTW library is employed for optimum
performance. Home: SETI Institute, University of California, Berkeley
Area: Astrophysics, SETI
Goal: The new instrument, appropriately called the Allen Telescope Array, known formerly
as the One Hectare Telescope, or 1hT, is a joint effort by the SETI Institute and the University
of California, Berkeley. Because of its novel construction - an array of inexpensive antennas -
it can be simultaneously used for both SETI and cutting-edge radio astronomy research. It is
being built at the existing Hat Creek Observatory, run by the Radio Astronomy Lab at
Berkeley, and located in the Cascades just north of Lassen Peak (California).
Most SETI experiments of the past have relied on existing radio telescopes. While this
allows such searches to be conducted on quite large instruments (for example, the mammoth
305 m Arecibo dish, in Puerto Rico), the amount of telescope time available for the search is
necessarily restricted. Project Phoenix for example took control of the Arecibo telescope for
approximately three weeks in the spring and a similar block of time in the fall. Since our
observations take place only at night (the sun can seriously degrade the type of narrow-band
signals that SETI looks for when observing close to the ecliptic, as required by Arecibo's
limited sky coverage), this really amounts to a total of three weeks of full-time observing
annually. The Allen Telescope Array will offer SETI scientists access to the telescope 24 hours
per day, seven days a week and permit the search of many different target stars
simultaneously. As a result, the Allen Telescope Array will speed up SETI targeted searching
by a factor of at least 100. Home: NASA Jet Propulsion Laboratory
Area: BioAstronomy
GoalThe NASA Mars Volcanic Emission and Life (MARVEL) mission proposes to globally
survey the Martian atmospheres photochemistry in a search for signs of microbial metabolic
activity or active volcanism. The survey will be conducted using high-resolution sub-
millimeter spectroscopy in a solar occultation geometry. This mission could potentially put
very stringent limits on near-surface microbial
activity on Mars and would be a significant step forward in the investigation of life on Mars.
The CASPER-built MARVEL spectrometer has been prototyped on an iBOB board, but it is
being respun, using BWRCs INSECTA toolflow, as a radiation-tolerant ASIC-based unit for
deployment on the MARVEL orbiter. The spectrometer is currently slated to feature a 1GHz
bandwidth and 4096 spectral channels with power consumption less than 5 Watts. The NASA Mars Volcanic Emission and Life (MARVEL) mission proposes to globally survey
the Martian atmospheres photochemistry in a search for signs of microbial metabolic activity
or active volcanism. The survey will be conducted using high-resolution sub-millimeter
spectroscopy in a solar occultation geometry. This mission could potentially put very stringent
limits on near-surface microbial activity on Mars and would be a significant step forward in
the investigation of life on Mars. The CASPER-built MARVEL spectrometer has been
prototyped on an iBOB board, but it is being respun, using BWRCs INSECTA toolflow, as a
radiation-tolerant ASIC-based unit for deployment on the MARVEL orbiter. The
spectrometer is currently slated to feature a 1 GHz bandwidth and 4096 spectral channels with
power consumption less than 5 Watts. Home: Massachussetts Institute of Technology
Area: Astrophysics
Goal: The primary scientific goal of recent work to extend Very Long Baseline
Interferometry (VLBI) into the sub-millimeter regime is an imaging observation of the
event horizon of a black hole [2]. In this context, the sources most likely to be
studied are SgrA and M87. VLBI at 0.8 mm wavelength has the potential to image up to 20
micro-arc second angular resolution. There is also a radiative transfer advantage obtained
due to reduced electron scattering. Therefore we have a strong case to retrofit the Sub
Millimeter Array (SMA) with a phased array processor and VLBI recording interface,
thereby enabling it to participate in such VLBI observations with its full collecting area. Home: Harvard University
Area: Astrophysics
Goal: The primary scientific goal of recent work to extend Very Long
Baseline Interferometry VLBI) into the sub-millimeter regime is an
imaging observation of the event horizon of a black hole [2]. In this
context, the sources most likely to be studied are SgrA and M87. VLBI
at 0.8 mm wavelength has the potential to image up to 20 micro-arc
second angular resolution. There is also a radiative transfer advantage
obtained due to reduced electron scattering. Therefore we have a strong
case to retrofit the Sub Millimeter Array (SMA) with a phased array
processor and VLBI recording interface, thereby enabling it to
participate in such VLBI observations with its full collecting area. Home: Arecibo Observatory
Area: Astrophysics
Goal: Radio observations of the Milky Way are of vital importance for understanding what really occurs within galaxies. The unique sensitivity of Arecibo's 305m
dish is now enhanced 7-fold with ALFA to provide an unprecedented new tool for the investigation of star formation and evolution, the recycling of material
between stars and the interstellar medium (ISM), the large-scale transfer of energy among the different components of the ISM, and the evolution of elemental
abundances over cosmic timescales. These phenomena can be observed with ALFA over the portion of the Galactic sky between declinations of -1.33 and +38.03
degrees, marked below in red.
ALFA's unprecedented combination of sensitivity and mapping speed enables a unique H I sky survey, one that will serve as a standard Galactic astronomy
reference for many years to come. The science case for GALFA - H I studies is rich and diverse. A few areas of special interest are: (1) the formation and lifetimes
of molecular clouds; (2) disk-halo interaction energetics and structures; (3) high-velocity clouds in the Galactic halo; (4) the cold neutral medium in emission and
self-absorption; (5) forbidden-velocity line wings from hidden stellar sources; and (6) turbulent energy injection and cascades in different Galactic environments.
GALFA - H I observations are planned to cover the entire Arecibo sky but will be carried out in a series of smaller projects to enable more rapid scientific yields.
These ``jigsaw puzzle'' pieces will be combined at the end to form a single, seamless survey.
All GALFA - H I observations use the specially-designed GALSPECT backend, covering a 1413 km/s range with 7679 channels, each 0.184 km/s wide. The SERENDIP 5 spectrometer board was designed for applications in SETI, FX
correlators, pulsar, and general radio astronomy. Each spectrometer board processes two polarizations, each polarization with up to 128
MHz bandwidth and 64 million channels. The CompactPCI board utilizes four 200 MHz 8-
bit ADC's for analog input, and 176 digital I/O lines for optional digital input and/or fast
readout. The signal processing is implemented in a Xilinx Virtex-II Field Programmable
Gate Array (FPGA) chip (XC2V4000 or XC2V6000), which can be dynamically
programmed for various applications. A smaller additional Xilinx FPGA (XC2V1000) is
used as a reconfigurable backend processor which can pass data off to an independent
computer. The spectrometer uses a polyphase filter bank (PFB) to implement a bank of steep cut-off
bandpass filters, providing a significant improvement in signal-to-noise and out-of-band-
rejection over the common FFT algorithm. The PFB uses a biplex pipelined architecture
which allows data to be input and output at the full sample rate, and can do two
polarizations simultaneously with no extra cost in hardware or data flow rate. SERENDIP5-based spectrometers are currently in use at Arecibo, Greenbank, and ATNF
for pulsar, epoch of reionization and galactic hydrogen surveys. The upcoming
SERENDIP V SETI sky survey will utilize Arecibo Observatory's seven-beam L-band feed
array and 21 spectrometer boards for a 2.7 billion-channel instrument. The JPL SETI sky
survey plans to use 200 of these boards to cover 20 GHz band with 25 billion channels.
The Allen Telescope Array will soon be using the spectrometer boards in the FX
correlator. We hope others will find these boards or the FPGA-based spectrometer designs
useful. SERENDIP has been in operation
for 19 years, beginning with
SERENDIP I in 1979. The
SERENDIP I instrument consisted
of a 100-channel spectrum
analyzer which was located at UC
Berkeley's Hat Creek
Observatory.
Since that time, SERENDIP has
undergone a series of sequential
improvements. SERENDIP II,
which ran from 1986 to 1988, was
thousands of times more powerful
than its predecessor. The second-
generation instrument was able to
observe 65,000 channels per
second and was primarily located
at the 300-foot NRAO radio
telescope at Green Bank and to a
lesser extent on four other high-
quality telescopes around the
world. SERENDIP III began operations at Arecibo in April 15, 1992. The end of its 4
year survey coincided with the beginning of a major upgrade at Arecibo. The
upgrade is now complete, and SERENDIP IV was installed at Arecibo in June
1997. Home: Cape Town, South Africa
Area: Astrophysics
Goal: South Africa plans to build the Karoo Array Telescope (KAT) very near the proposed site
for the core of the SKA. The KAT will be located in a radio quiet reserve within the Karoo region
of South Africa. Its sparse population and dry climate make it an ideal site for a radio telescope. It
is intended that the site will be proclaimed as a radio quiet reserve. A high-speed fibre-optic link
will connect the KAT to the Centre for High-Performance Computing (CHPC) in Cape Town.
The KAT will be a so-called "demonstrator" of SKA technology, and will also prove South
Africas commitment, capacity and technological readiness to host the SKA. At about 1% to 2% of
the survey capacity of the SKA, the KAT will be a world-class research instrument in its own
right. The KAT is scheduled to be completed by 2009.
A KAT prototype, including the electronics and dish design, will be built at the Hartebeesthoek
Radio Astronomy Observatory by the end of 2007. The KAT team has agreed on technical
collaboration with teams in Australia, the UK, the Netherlands and the USA.The technical
collaboration will result in a reduction in cost and risks for the KAT. A joint science case for the
KAT has been discussed with all these collaborators. Home: Pune, India
Area: Astrophysics
Goal: The Giant Metrewave Radio Telescope (GMRT), located
near Pune in India, is a world class radio astronomy facility in
the frequency range of 150 MHz to 1420 MHz. Consisting of 30
antennas of 45 metre diameter each, it can be used as an
aperture-synthesis array for mapping extended sources, as well
as a phased array to study compact radio sources like pulsars.
This talk will describe the main digital back-ends that make this
possible : the 30 antenna, 256 spectral channel correlator, the
phased array combiner and the different pulsar receivers. In the
next few years, the GMRT is expected to undergo a significant
upgrade that will increase the maximum instantaneous
bandwidth from the present 32 MHz to upto 400 MHz, along
with improvements in the total system noise. This talk will cover
the plans for building the matching digital back-ends and explore
the synergy of these with ongoing international efforts.
One of the most computationally difficult problems in radio astronomy instrumentation is
a real-time imaging system for very large arrays, with computation time scaling as
O(N2). Applications requiring several gigahertz of continuous RF bandwidth over
hundreds of physical antennas require peta-operations per second. Such computational
requirements are far beyond the capabilities of the general purpose computing clusters
which have traditionally been the commodity solution to radio astronomy signal
processing. Because of their iteration-based, inherently non-parallel architectures, CPUs
can only process a bandwidth equal to their clock rate divided by the number of
operations per sample. For computationally intensive applications, this number is low,
even for multi-gigahertz processors.

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