Recently in eScience Category

Reality Check on Real-Time Data

The United States Geological Survey (USGS) runs many real-time data streams including water stage data. While the USGS clearly thinks this is worth doing, they provide a succinct reminder to users that, like everything in life, real-time data are not perfect. More importantly, they don't consider this a cause for panic - a cause for later analysis and data revision, certainly - but not panic when initial and public data may be inaccurate. After all, they're measuring events in the real world and not a controlled laboratory setting.

See the FAQ entry for "I frequently kayak the Potomac River and the real-time stage data reported by USGS seem to be too high (or too low). Are the USGS data inaccurate?" their answer.

"During the May 5th meeting of the National Science Board, National Science Foundation (NSF) officials announced a change in the implementation of the existing policy on sharing research data. In particular, on or around October, 2010, NSF is planning to require that all proposals include a data management plan in the form of a two-page supplementary document. The research community will be informed of the specifics of the anticipated changes and the agency's expectations for the data management plans."

For more information, see "Scientists Seeking NSF Funding Will Soon Be Required to Submit Data Management Plans"

Illustrata - Natural Sciences

Searchable tables, figures, graphs, charts and other illustrations from the scholarly research and technical literature. Search results – the objects – can be viewed in full, in either (thumbnail or enhanced format) along with the caption, author and source information and additional index terms that can be used for further searching. A link back to the parent record provides a summary view of all the objects associated with that paper.

http://www.lib.umn.edu/get/illustrata

From ITNews:

"The team will use the grid to analyse the results of experiments on proteins using data collected by scientists at the Hauptman-Woodward Medical Research Institute in Buffalo, New York. The researchers estimate that this analysis would take conventional computer systems 162 years to complete. Dr Jurisica anticipates that the analysis could be finished in one to two years..."

Sequence of genome of Fusarium graminearum

From the University of Minnesota News Service http://www1.umn.edu/umnnews/news_details.php?release=070906_3489&page=NS

"Scientists led by a team from the University of Minnesota have sequenced the genome of the fungal
pathogen that causes the deadly grain disease Fusarium Head Blight (FHB). Their findings [were] published in Science (Cuomo et al, "The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization," vol. 317, 7 September 2007, 1400-1402).

The disease can have devastating effects on wheat and barley crops, because it creates toxins that can sicken humans and livestock who consume infected grain. It is one of the most significant plant pathogens worldwide...Fungicides are costly and not always effective.

The FHB pathogen has about 13,000 genes. However, "(because of the sequencing breakthrough), now we can look at the genes in detail, in terms of their ability to allow the pathogen to cause disease and produce toxin," said H. Corby Kistler, an adjunct professor of plant pathology at the U of M and a research geneticist for the U.S.
Department of Agriculture's Agricultural Research Service.

According to Kistler, sequencing the genome will help researchers determine how the disease operates at a genetic level and eventually, how to prevent it. The research could also help fight other plant diseases."

The research was a multinational effort, with the participation of university researchers in Germany, Spain, Netherlands, Austria, UK, Canada, France, and the Ukraine, along with U.S.-based groups (Broad Institute of MIT and Harvard, Purdue, Michigan State, Cornell, Pacific Northwest National Laboratory, St. Louis University, Universities of Arizona and Tennessee, and the USDA). Further analyses of gene products also will prove to be data-intensive.

More e-science at the University of Minnesota

Cedar Creek Natural History Area http://www.cedarcreek.umn.edu/ is an NSF-sponsored Long-Term Ecological Research (LTER) site. There are 4 major themes to this research:

*Theme 1:* What are the impacts of major perturbations -- especially climatic variation, N deposition, land use history, changes in fire frequency, elevated CO2, exotic species, and changes in trophic structure --on species composition, diversity and ecosystem functioning?
*Theme 2:* What processes, interactions and positive and negative feedbacks control species abundances, community assembly, and community composition, diversity and dynamics in Cedar Creek grasslands and savanna?
*Theme 3:* How do composition and biodiversity directly and indirectly impact ecosystem functioning?
*Theme 4:* What general principles allow integration across scales ranging from ecophysiological and population processes to ecosystem functioning; from single trophic levels to whole foodwebs; from single plots to landscapes; and from snapshots in time to long time series?

"We are pursuing these four themes in five inter-related types of long-term studies that form the heart of the Cedar Creek LTER. Each is guided by our research philosophy and each addresses several themes. LTER funding supports this core long-term work and the research infrastructure of Cedar Creek (computer network, analytical chemistry laboratory, herbarium and insect collections, data management and software development, and shared research equipment)."

The Long Term Ecological Research (LTER) Network is a collaborative effort involving more than 1800 scientists and students investigating ecological processes over long time periods and broad geographical scales. The Network promotes synthesis and comparative research across sites and ecosystems and among other related national and international research programs. The 26 sites that constitute the Network represent diverse ecosystems and research emphases. http://www.lternet.edu/

UMN has 11 principal investigators working on the LTER at Cedar Creek, mostly faculty from Ecology, Evolution, and Behavior, with one from Plant Biology and two from Forest Resources. There are a couple dozen additional UMN faculty involved (see http://www.cedarcreek.umn.edu/people/currentstaff.php)

HarvestChoice http://www.harvestchoice.org/ Funded by the Gates Foundation. (Phil Pardey, et al.)

"Over the coming three years, HarvestChoice and its growing number of partners will deliver a series of databases, tools, analyses, findings, and syntheses designed to improve strategic investment and policy decisions. The overriding objective is to accelerate and enhance the performance of those crops and cropping systems most likely to bring significant benefits to the world's poor and undernourished."

There are a several collaborative NSF plant/crop genome mapping research projects involving the University of Minnesota.

Nevin Young (Plant Pathology/Plant Biology) has an NSF grant to sequence the model legume Medicago Truncatula http://www.medicago.org/genome/ Project goals include: Genome Sequencing: Complete, high quality genome sequence for all eight chromosomes of Medicago.

Informatics: An integrated database of clone, map, assembly, and sequence information combined with coordinated, automated annotation of the Medicago genome sequence.
Project Organization: This NSF project is coordinated with partners in the EU who receive funding from the 6th Framework Programme, BBSRC in the UK and ANR in France. EU partners
come from the UK, France, Germany, Netherlands, and Belgium

Ronald Philips (CFANS) has an NSF grant to work on mapping the corn genome http://corn.ccgb.umn.edu/

Goals include:
* To produce an efficient means to map genes of corn, our major cereal crop.
* To implement a system analogous to one used in the mapping of human genes, where special Chinese hamster cell lines containing portions of the human genome are used. We will use oat lines containing portions of the corn genome.
* To complete the series of the 10 different oat-corn chromosome addition lines and, for each chromosome, produce a series of approximately 100 radiation hybrid lines.
* Arrays of DNA samples ultimately will be available to researchers for mapping any gene or DNA fragment to a small region of a given chromosome.

Electronic laboratory notebooks

Declan Butler discusses the development, applications, and advantages of e-notebooks in his article, "A New Leaf" (Nature, vol.436, 7 July 2005, 20-21). An editorial in Nature, dated approximately two years later, further emphasizes the benefits of e-notebooks, but notes that "academic acceptance of e-notebooks will not improve unless universities promote their use and recognize that e-notebooks can help them fulfill their responsibilities as the owners of most grant-funded data...Institutions therefore need to show leadership in this area, and funding agencies should provide additional infrastructure support earmarked for the development and upkeep of electronic notebook systems" (vol.447, 3 May 2007, 1-2).

Pharmaceutical companies routinely use e-notebooks to document their proprietary research; the U. S. Food and Drug Administration accepts e-notebook records during a drug's evaluation and approval processes.

The University of Minnesota provides some guidelines about the 'use of electronic records' in "Guidelines for Maintaining Laboratory Notebooks" (http://www.research.umn.edu/techcomm/licensingcenter/documents/labnotes.pdf); however, the document emphasizes record-keeping in a paper format.

Universities, as well as businesses, continue to develop e-notebook software. A selected list follows, with brief descriptions.

ELN (Electronic Laboratory Notebook) from the EMSL Collaboratory, Pacific Northwest National Laboratory (http://collaboratory.emsl.pnl.gov/software/eln). The software, available for download at the EMSL site, is "a shared web-based version of the traditional paper laboratory notebook. Each notebook page shows data and time-stamped entries that include static information such as text and images, as well as dynamic information ranging from animated GIF images and video clips to rotatable 3-D protein structures and X-Y graphs of spectra that support zoom and other capabilities."

The NeuroSys Project from Montana State University (http://neurosys.cns.montana.edu), "provides a set of easy to use tools for data sharing by the scientific community. Neurosys enables users to construct and store a coherent description of their data, according to the hierarchical organizational scheme that makes the most sense for their specific set of applications; allows users to design and construct their own custom GUI screens for data entry, data query and retrieval, combined with automated links to external analytical software tools; automatically creates a controlled vocabulary, and supports the extension and/or migration of that vocabulary to whatever standard might be chosen at a later date..."

The Smart Tea Project (http://www.smarttea.org), based at the University of Southampton and part of the Combechem eScience Research Initiative. Its "first phase will support the complete life cycle of chemists' interactions with the lab; the next phase will integrate the lab aether with the larger network of chemistry on the grid for shared information services." A related project is the "myTea Project" (http://mytea.org.uk), which focuses on "improving capture of experiments for bioinformatics practitioners."

CERF (Collaborative Electronic Research Framework) - The Electronic Lab Notebook for Biology and Multidisciplinary Life Sciences (http://www.rescentris.com/products.html) developed by Rescentris, Ltd. It is an "enterprise scientific information system designed specifically for managing and sharing information in life sciences research organizations. CERF combines a full-featured electronic lab notebook with scientific content management, and extensible knowledge and data integration framework, and a science-driven informatics platform....The CERF server provides a central management of data storage, system functions, projects, organization of experiments, content, annotations, and rich metadata."

Biometerology and Micrometerology

http://www.biometeorology.umn.edu/Biomet_welcome.php
Heat and mass transfer between the biosphere and atmosphere can have important consequences for the climate system. We use biometeorological techniques to better understand the processes and feedback mechanisms that control heat and mass transfer near the Earth's surface from ecosystem to regional scales. Measurement technologies have been developed that allow rapid and continuous measurement of atmospheric properties, such as turbulence and trace gases, providing an opportunity to answer important questions related to the cycles of energy, water, carbon, and many other scalars.

There is access to real-time data, plus archived data (in cooperation with USDA-Agricultural Research Service).

Interagency Information Cooperative

http://iic.gis.umn.edu/index.html

The Interagency Information Cooperative (IIC) was created from the Sustainable Forest Resources Act of 1995 (M.S. Chapter 89A.09). The overall mission of the IIC is to enhance the access and use of forest resources data in Minnesota. The following public organizations have representatives on the IIC: Minnesota Association of County Land Commissioners, United States Forest Service, Land Management Information Center, University of Minnesota, and Department of Natural Resources. The IIC Memorandum of Understanding was created in 1997, and goes into greater depth on the purposes, membership, and duties of the IIC.

Focus here is more on harmonization of data through metadata rather than computationally intensive work. However, it is boundary-spanning in that it is attempting to harmonize biological, geospatial, social science and other kinds of data.

EaGLe

The Environmental Protection Agency (EPA), through its Science To Achieve Results (STAR) competitive grants research program, has established five regional Estuarine & Great Lakes (EaGLe) research centers at major academic research institutions with strong expertise in coastal environmental science. Additionally, NASA is supporting associated remote sensing research at three of these institutions. The researchers at these five regional centers are developing the next generation of environmental indicators to assess the biological health of the Great Lakes coast and estuaries and wetlands along the Atlantic, Pacific and Gulf coasts. Indicators evaluated and developed by the EaGLe centers will be used by the states in their long-term monitoring programs to establish the integrity and sustainability of the nation's coastal ecosystems.

Great Lakes Environmental Indicators (GLEI) Project, a subset of EaGLe, is led by the Natural Resources Research Institute at the University of Minnesota Duluth (UMD). Other cooperators include the following: the University of Minnesota Twin Cities; Minnesota Sea Grant; the University of Wisconsin Green Bay; the University of Wisconsin Madison; Cornell University, New York; John Carroll University, Ohio; the University of Michigan; the University of Windsor, Ontario; and the US EPA Mid-Continent Ecology Division, Duluth, Minnesota, and Grosse Ile, Michigan. STAR grant R828675.

GLEI is developing and testing a suite of indicators across the range of habitats that make up the Great Lakes coastal margins. The following indicator types will be tested for their efficacy and technical soundness within three subcategories: 1) the basin as a whole: climate measures, land uses, and landscape characteristics; 2) estuaries, bays and coastal margin waters: water quality, contaminant levels, and the relative abundances of amphibian, bird, diatom, fish, macroinvertebrate and plant species and communities, and 3) the land margins: measures of bird community structure. Each of these indicator types has linkages with habitat condition measures and other stressors.

Data is not currently available and is stored on EPA servers. For details, see http://eagle.nrri.umn.edu/pub_data.htm

Physical Sciences/Engineering Projects

Here are five multi-institutional and/or multi-disciplinary projects:

(1) The MAST Laboratory

"The Multi-Axial Subassemblage Testing (MAST) Laboratory is one node of the Network for Earthquake Engineering Simulation (NEES). The MAST Laboratory was developed as a collaboration between the Departments of Civil Engineering, Electrical and Computer Engineering, and Computer Science and Engineering, University of Minnesota. NEES is a national, networked simulation resource that includes geographically-distributed, shared-use, next-generation experimental research equipment sites built and operated to advance earthquake engineering research and education through collaborative experimentation. Other NEES nodes include SUNY-Buffalo, University of California-Davis, UCLA, Oregon State University and the University of Texas."
Information excerpted from http://nees.umn.edu.

(2) The NCED at St. Anthony Falls Laboratory

"The National Center for Earth-Surface Dynamics is a Science and Technology Center of the National Science Foundation. The NCED's purpose is to catalyze development of an integrated, predictive science of the processes shaping the surface of the Earth in order to transform management of ecosystems, resources, and land use. The principal investigators are at Fond du Lac Tribal and Community College, the Johns Hopkins University, the Science Museum of Minnesota, University of California-Berkeley, University of Colorado-Boulder, University of Illinois at Urbana-Champaign, Louisiana State University, University of Texas-Austin, the St. Anthony Falls Laboratory, and the University of Minnesota."
Information excerpted from http://www.safl.umn.edu

(3) The Center for Compact and Efficient Fluid Power

"Headquartered at the University of Minnesota, the Center's vision is to create new fluid power technology that is compact and efficient. This will lead to significant fuel savings as the new technologies are implemented in existing and new applications. Improved compactness will enable fluid power to perform tasks that are not presently possible, spawning whole new industries. Besides the U of MN, other core universities are the University of Illinois at Urbana-Champaign, Georgia Institute of Technology, Purdue University, and Vanderbilt University. Outreach universities and organizations are the Milwaukee School of Engineering, North Carolina Agricultural & Technical State University, the National Fluid Power Association, Science Museum of Minnesota, and Project Lead the Way."
Information excerpted from http://www.ccefp.org

(4) Program for Human Factors Interdisciplinary Research in Simulation and Transportation (HumanFIRST program)

"The program exists to enhance the safety and mobility of road and transit-based transportation through a focus on human-centered technology. A core staff of cognitive psychologists is linked to a broader multidisciplinary network of researchers."
Information excerpted from http://www.humanfirst.umn.edu

(5) The CSDy Center

"The Control Science and Dynamical Systems Center's mission is to encourage stimulating interdisciplinary research in control science and dynamical system theory within the University of Minnesota's Institute of Technology. Researchers have a broad interest in numerical computation, robust control, nonlinear control, linear and nonlinear dynamical systems, and image processing. Faculty are drawn from the Departments of: Aerospace Engineering and Mechanics; Chemical Engineering and Materials Science; Computer Science and Engineering; Electrical Engineering and Computer Engineering; Mechanical Engineering; Genetics, Cell Biology and Development; Economics; and Political Science."
Information excerpted from http://www.csdy.umn.edu

VLAB -- Four UofM Depts plus 8 other Institutions

"The Virtual Laboratory for Earth and Planetary Materials, VLab, funded by the National Science Foundation and hosted by the Supercomputing Institute for Digital Simulations and Advanced Computation at the University of Minnesota, is an interdisciplinary consortium dedicated to the development and promotion of the theory of planetary materials. Focuses on computational determination of geophysically important materials..."

Participants:
* University of Minnesota (Chemical Eng./Materials Science, Geology, Computer Science, Chemistry, DTC)
* State University of New York-Stony Brook (Physics)
* Florida State University (CSIT)
* Louisiana State University (CS)
* Indiana University (IT)
* University of California-Santa Barbara (GEOL)
* DEMOCRITOS Modeling Center (Italy)
* Daresbury Laboratory (UK) (e-Science)
* University College London (UK) (ES, Physics)

E-Science Projects at the University of Minnesota

MINOS - The NuMI/MINOS project is a collaboration of some thirty-two institutions and almost two hundred members. The overarching goal of NuMI/MINOS is to observe muon neutrino oscillations and, if all goes as planned, make the most sensitive measurement of the corresponding oscillation parameters to date. To this end, NuMI/MINOS will employ a neutrino beam and two particle detectors.

BNL E952: The NuMass Experiment
A Collaboration from
Brookhaven National Laboratory, Boston University,
CERN, Cornell, Heidelberg University,University of Illinois,
KVI, University of Minnesota, New York University, Yale University
The g-2 Storage Ring is a unique facility for precision measurements that test the standard model. This proposal to improve the muon neutrino mass limit by a factor of 20 (from 170 keV down to 8 keV) will be the largest factor improvement made in any neutrino species mass within the last 25 years.

CLEO - The CLEO collaboration consists of roughly 125 physicists from 20 institutions. The University of Minnesota has been a part of the collaboration since 1988. Our group members have held many positions of leadership within the collaboration, including Spokesperson, Analysis Coordinator and Software Coordinator. Ten Minnesota graduate students have earned Ph.D.'s on CLEO.
Analysis of CLEO II and CLEO III data collected at the Upsilon(4S) resonance is approaching completion. CLEO results on B-meson decays continue to be competitive with those of the spectacularly successful B-factories at SLAC and KEK, largely because the experience of the collaboration and the detailed understanding of the response of the CLEO detectors allow measurements of CKM parameters and other quantities with small and well-understood systematic uncertainties.

Storm Belt Probe project - The RBSP EFW collaboration includes physicists from Minnesota, U.C. Berkeley, University of Colorado, University of Alberta, the Air Force Research Laboratory and theorists from Dartmouth.

The HST Treasury Program on Eta Carinae - In December 2001, the first three Hubble Space Telescope "Treasury Programs" were approved. Two criteria for a Treasury Program are:
1. The data must be broadly valuable for astronomy and astrophysics in general, and;
2. Similar observations will become impossible a few years from now when the HST is no longer available.
Here we report on the Eta Carinae program, which satisfies the first criterion well and is a near-perfect example for the second. This is the most intensive spectroscopy ever attempted with the HST, and similar data will almost certainly be unattainable for at least 15 years after 2004 -- by which time Eta Car will have changed. Our program also includes an imaging component. Information about the participants (a multi-institutional team) can be found at http://etacar.umn.edu/treasury/team/

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