An Architecture for Scaling NVO Services to TeraGrid

The term "cyberinfrastructure" has been adopted by the US National Science Foundation to mean "advanced computing engines, data archives and digital libraries, observation and sensor systems, and other research and education instrumentation [linked] into a common framework". One of the largest awards in this program is the TeraGrid, a linkage of large supercomputer centers based on the Globus software. Another cyberinfrastructure program is the National Virtual Observatory, a linkage of astronomical data publishers into a service-oriented framework. There are different philosophies behind the TeraGrid and the NVO architecture. This note explains a proposed service-oriented architecture for TeraGrid nodes that is an attempt to bridge these ways of working, and a prototype instantiation at Caltech

IVOA Recommendation: Simple Image Access Specification Version 1.0

This specification defines a protocol for retrieving image data from a variety of astronomical image repositories through a uniform interface. The interface is meant to be reasonably simple to implement by service providers. A query defining a rectangular region on the sky is used to query for candidate images. The service returns a list of candidate images formatted as a VOTable. For each candidate image an access reference URL may be used to retrieve the image. Images may be returned in a variety of formats including FITS and various graphics formats. Referenced images are often computed on the fly, e.g., as cutouts from larger images

IVOA Recommendation: IVOA Registry Interfaces Version 1.0

Registries provide a mechanism with which VO applications can discover and select resources--e.g. data and services--that are relevant for a particular scientific problem. This specification defines the interfaces that support interactions between applications and registries as well as between the registries themselves. It is based on a general, distributed model composed of so-called searchable and publishing registries. The specification has two main components: an interface for searching and an interface for harvesting. All interfaces are defined by a standard Web Service Description Language (WSDL) document; however, harvesting is also supported through the existing Open Archives Initiative Protocol for Metadata Harvesting, defined as an HTTP REST interface. Finally, this specification details the metadata used to describe registries themselves as resources using an extension of the VOResource metadata schema

Digital Data Preservation and Curation: A Collaboration Among Libraries, Publishers, and the Virtual Observatory

Digital Data Preservation and Curation: A Collaboration Among Libraries, Publishers, and the Virtual Observatory. Astronomers are producing and analyzing data at ever more prodigious rates. NASA's Great Observatories, ground-based national observatories, and major survey projects have archive and data distribution systems in place to manage their standard data products, and these are now interlinked through the protocols and metadata standards agreed upon in the Virtual Observatory. However, the digital data associated with peer-reviewed publications is only rarely archived. Most often, astronomers publish graphical representations of their data but not the data themselves. Other astronomers cannot readily inspect the data to either confirm the interpretation presented in a paper or extend the analysis. Highly processed data sets reside on departmental servers and the personal computers of astronomers, and may or may not be available a few years hence. We are investigating ways to preserve and curate the digital data associated with peer-reviewed journals in astronomy. The technology and standards of the VO provide one component of the necessary technology. A variety of underlying systems can be used to physically host a data repository, and indeed this repository need not be centralized. The repository, however, must be managed and data must be documented through high quality, curated metadata. Multiple access portals must be available: the original journal, the host data center, the Virtual Observatory, or any number of topically-oriented data services utilizing VO-standard access mechanisms

Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers

The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic

Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant

Catechol-O-methyltransferase (COMT) is a major enzyme controlling catecholamine levels that plays a central role in cognition, affective mood and pain perception. There are three common COMT haplotypes in the human population reported to have functional effects, divergent in two synonymous and one nonsynonymous position. We demonstrate that one of the haplotypes, carrying the non-synonymous variation known to code for a less stable protein, exhibits increased protein expression in vitro. This increased protein expression, which would compensate for lower protein stability, is solely produced by a synonymous variation (C166T) situated within the haplotype and located in the 5′ region of the RNA transcript. Based on mRNA secondary structure predictions, we suggest that structural destabilization near the start codon caused by the T allele could be related to the observed increase in COMT expression. Our folding simulations of the tertiary mRNA structures demonstrate that destabilization by the T allele lowers the folding transition barrier, thus decreasing the probability of occupying its native state. These data suggest a novel structural mechanism whereby functional synonymous variations near the translation initiation codon affect the translation efficiency via entropy-driven changes in mRNA dynamics and present another example of stable compensatory genetic variations in the human population

2011 Report of NSF Workshop Series on Scientific Software Security Innovation Institute

Over the period of 2010-2011, a series of two workshops were held in response to NSF Dear Colleague Letter NSF 10-050 calling for exploratory workshops to consider requirements for Scientific Software Innovation Institutes (S2I2s). The specific topic of the workshop series was the potential benefits of a security-focused software institute that would serve the entire NSF research and development community. The first workshop was held on August 6th, 2010 in Arlington, VA and represented an initial exploration of the topic. The second workshop was held on October 26th, 2011 in Chicago, IL and its goals were to 1) Extend our understanding of relevant needs of MREFC and large NSF Projects, 2) refine outcome from first workshop with broader community input, and 3) vet concepts for a trusted cyberinfrastructure institute. Towards those goals, the participants other 2011workshop included greater representation from MREFC and large NSF projects, and, for the most part, did not overlap with the participants from the 2010 workshop. A highlight of the second workshop was, at the invitation of the organizers, a presentation by Scott Koranda of the LIGO project on the history of LIGO’s identity management activities and how those could have benefited from a security institute. A key analysis he presented is that, by his estimation, LIGO could have saved 2 senior FTE-years of effort by following suitable expert guidance had it existed. The overarching finding from the workshops is that security is a critical crosscutting issue for the NSF software infrastructure and recommended a security focused activity to address this issue broadly, for example a security software institute (S2I2) under the SI2 program. Additionally, the 2010 workshop participants agreed to 15 key additional findings, which the 2011 workshop confirmed, with some refinement as discussed in this report.NSF Grant # 1043843Ope