The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The diversity of northwest coast shell middens : late pre-contact settlement-subsistence patterns on Valdes Island, British Columbia

This study explores the nature of late pre-contact settlement-subsistence activity (1400/1000 - 200 B.P.) on Valdes Island, a large southern Gulf Island in the Gulf of Georgia region of the Northwest Coast. Settlement-subsistence patterns on Valdes Island demonstrate an economic orientation toward exploiting critical resource locations in the marine environment, specifically sandy intertidal environments and tidal streams, where populations aggregated to collect predictable, localized and abundant coastal resources, particularly shellfish and Pacific herring. The diversity of shell middens (or shell matrix sites (cf. Claasen 1998)) on Valdes Island agree with patterns of logistical mobility indicative of a "collector strategy" (cf. Binford 1980). The majority of small-sized, shallow shell matrix sites on Valdes Island represent limited-activity sites, such as shellfish resource-processing locations and task-specific field camps, where specific, highly localized resources in the coastal environment were collected. Large, deep, highly-stratified shell matrix sites on Valdes Island - several of which are identified as ethnographic Central Coast Salish Halkomelem winter villages - represent long-term residential bases located to maximize access multiple, overlapping coastal resource zones in proximity to the tidal streams and sandy foreshore environments of the southwest coast. This settlement study identifies an important strategy Central Coast Salish populations used to engage the highly variable, locally diverse nature of subsistence resources in the Gulf of Georgia was to strategically position settlement locations at dense, biologically-diverse marine micro-environments. This settlement strategy enabled these complex hunter-gatherer populations to generate economic surplus for subsistence, exchange and feasting, and provided the economic base for competition among elites.Arts, Faculty ofAnthropology, Department ofGraduat

Human settlement, coastal landforms and later Holocene sea level change in southwestern British Columbia, Canada

Funding: Washington State University; BC ParksWashington State UniversityGrier, Colin et al. (2010, March 26). Human settlement, coastal landforms and later Holocene sea level change in southwestern British Columbia, Canada. Poster presented at the Washington State University Academic Showcase, Pullman, WA

Houses and households in the Gulf of Georgia: archaeological investigations of Shingle Point (DgRv 2), Valdes Island, British Columbia

Report to: Archaeology Branch, Victoria, B.C.; Lyacksun First Nation; Social Science and Humanities Research Council of Canada, Ottawa. [Replacements of incompletely scanned tables on pages 189-192 of Part 2 were inserted into the PDF file, February 8, 2012.]Arts, Faculty ofAnthropology and Sociology, Department ofUnreviewedFacult

Ancient Mariculture in the Salish Sea: Documenting the Past for the Future

In the Salish Sea, as elsewhere, the recognition and re-establishment of traditional mariculture practices are linked to issues of food security, health, economic development, governance, and community engagement in heritage. The Clam Garden Network is a collaborative team of First Nations knowledge holders, archaeologists, and ecologists who focus on traditional marine resource management systems throughout the Northwest Coast. In several locations in the Salish Sea, we have 1) documented the location of ancient mariculture features (clam gardens and cleared beaches) and associated terrestrial archaeological sites; 2) conducted ecological surveys and experiments that suggest clam abundance, growth and survival are higher in extant clam gardens beaches than in other beaches; 3) collected zooarchaeological samples to assess ecological changes in ancient clam gardens; 4) recorded local knowledge about the social and ecological aspects of traditional mariculture; and 5) dated the construction of ancient mariculture features. Inter-disciplinary and inter-community efforts are an effective way to document traditional resource management systems, as well as situating them within current socio-political and ecological contexts

Images of Earth and Space II

This videotape tours the Solar System and outer space using scientific visualizations from Goddard Space Flight Center, Jet Propulsion Laboratory, and the HPCC Earth and Space Sciences Project. At the Sun, simulations investigate processes that create magnetic field and release energetic particles. Earth science begins with the Pacific Ocean, studying the 1997-98 El Nino and Cyclone Susan. Crossing the globe, visualizations trace North Americas East Coast and ocean currents in the North Atlantic Ocean. The lights of the worlds cities then show human impact. Next, two models probe nearby-space phenomena, fluid behavior in microgravity conditions and an asteroid collision. A jaunt to Mars explores the mountains and trenches of its dry, rocky exterior. The video concludes at a binary neutron star system, where two city-sized objects with the Suns mass merge in a titanic explosion. Educational levels: Undergraduate lower division, Undergraduate upper division, Graduate or professional

HARMONI: a single-field wide-band integral-field spectrograph for the European ELT

Trabajo presentado en SPIE Astronomical Telescopes, celebrado en San Diego (California), del 15 de junio al 2 de julio de 2010We describe the results of a Phase A study for a single field, wide band, near-infrared integral field spectrograph for the European Extremely Large Telescope (E-ELT). HARMONI, the High Angular Resolution Monolithic Optical & Nearinfrared Integral field spectrograph, provides the E-ELT’s core spectroscopic requirement. It is a work-horse instrument, with four different spatial scales, ranging from seeing to diffraction-limited, and spectral resolving powers of 4000, 10000 & 20000 covering the 0.47 to 2.45 μm wavelength range. It is optimally suited to carry out a wide range of observing programs, focusing on detailed, spatially resolved studies of extended objects to unravel their morphology, kinematics and chemical composition, whilst also enabling ultra-sensitive observations of point sources. We present a synopsis of the key science cases motivating the instrument, the top level specifications, a description of the opto-mechanical concept, operation and calibration plan, and image quality and throughput budgets. Issues of expected performance, complementarity and synergies, as well as simulated observations are presented elsewhere in these proceeding