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Ramy K Aziz,
Scott Devoid, Terrence Disz,
Robert A Edwards,
Christopher S Henry,
Gary J Olsen,
Robert Olson,
Ross Overbeek,
Bruce Parrello,
Gordon D Pusch,
Rick L Stevens,
Veronika Vonstein,
Fangfang Xia
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ABSTRACT: The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users.
PLoS ONE 01/2012; 7(10):e48053. · 4.09 Impact Factor
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ABSTRACT: Many enzymes and other proteins are difficult subjects for bioinformatic analysis because they exhibit variant catalytic, structural, regulatory, and fusion mode features within a protein family whose sequences are not highly conserved. However, such features reflect dynamic and interesting scenarios of evolutionary importance. The value of experimental data obtained from individual organisms is instantly magnified to the extent that given features of the experimental organism can be projected upon related organisms. But how can one decide how far along the similarity scale it is reasonable to go before such inferences become doubtful? How can a credible picture of evolutionary events be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT)? We present a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how these goals can be accomplished through the use of cohesion group analysis. With this approach, the full collection of homologs is sorted into groups by a method that eliminates bias caused by an uneven representation of sequences from organisms whose phylogenetic spacing is not optimal. Each sufficiently populated cohesion group is phylogenetically coherent and defined by an overall congruence with a distinct section of the 16S rRNA gene tree. Exceptions that occasionally are found implicate a clearly defined LGT scenario whereby the recipient lineage is apparent and the donor lineage of the gene transferred is localized to those organisms that define the cohesion group. Systematic procedures to manage and organize otherwise overwhelming amounts of data are demonstrated.
Microbiology and molecular biology reviews: MMBR 04/2008; 72(1):13-53, table of contents. · 12.59 Impact Factor
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Ramy K Aziz,
Daniela Bartels,
Aaron A Best,
Matthew DeJongh, Terrence Disz,
Robert A Edwards,
Kevin Formsma,
Svetlana Gerdes,
Elizabeth M Glass,
Michael Kubal, [......],
Daniel Paarmann,
Tobias Paczian,
Bruce Parrello,
Gordon D Pusch,
Claudia Reich,
Rick Stevens,
Olga Vassieva,
Veronika Vonstein,
Andreas Wilke,
Olga Zagnitko
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ABSTRACT: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.
We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service.
By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
BMC Genomics 02/2008; 9:75. · 4.07 Impact Factor
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Ramy Aziz,
Daniela Bartels,
Aaron Best,
Matthew DeJongh, Terrence Disz,
Robert Edwards,
Kevin Formsma,
Svetlana Gerdes,
Elizabeth Glass,
Michael Kubal, [......],
Daniel Paarmann,
Tobias Paczian,
Bruce Parrello,
Gordon Pusch,
Claudia Reich,
Rick Stevens,
Olga Vassieva,
Veronika Vonstein,
Andreas Wilke,
Olga Zagnitko
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ABSTRACT: Abstract
Background
The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them.
Description
We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment.
The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service.
Conclusion
By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.
BMC Genomics. 01/2008;
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ABSTRACT: Despite its being a leading cause of nosocomal and community-acquired infections, surprisingly little is known about Staphylococcus aureus stress responses. In the current study, Affymetrix S. aureus GeneChips were used to define transcriptome changes in response to cold shock, heat shock, stringent, and SOS response-inducing conditions. Additionally, the RNA turnover properties of each response were measured. Each stress response induced distinct biological processes, subsets of virulence factors, and antibiotic determinants. The results were validated by real-time PCR and stress-mediated changes in antimicrobial agent susceptibility. Collectively, many S. aureus stress-responsive functions are conserved across bacteria, whereas others are unique to the organism. Sets of small stable RNA molecules with no open reading frames were also components of each response. Induction of the stringent, cold shock, and heat shock responses dramatically stabilized most mRNA species. Correlations between mRNA turnover properties and transcript titers suggest that S. aureus stress response-dependent alterations in transcript abundances can, in part, be attributed to alterations in RNA stability. This phenomenon was not observed within SOS-responsive cells.
Journal of Bacteriology 11/2006; 188(19):6739-56. · 3.83 Impact Factor
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ABSTRACT: Bacterial pathogens regulate virulence factor expression at both the level of transcription initiation and mRNA processing/turnover. Within Staphylococcus aureus, virulence factor transcript synthesis is regulated by a number of two-component regulatory systems, the DNA binding protein SarA, and the SarA family of homologues. However, little is known about the factors that modulate mRNA stability or influence transcript degradation within the organism. As our entree to characterizing these processes, S. aureus GeneChips were used to simultaneously determine the mRNA half-lives of all transcripts produced during log-phase growth. It was found that the majority of log-phase transcripts (90%) have a short half-life (<5 min), whereas others are more stable, suggesting that cis- and/or trans-acting factors influence S. aureus mRNA stability. In support of this, it was found that two virulence factor transcripts, cna and spa, were stabilized in a sarA-dependent manner. These results were validated by complementation and real-time PCR and suggest that SarA may regulate target gene expression in a previously unrecognized manner by posttranscriptionally modulating mRNA turnover. Additionally, it was found that S. aureus produces a set of stable RNA molecules with no predicted open reading frame. Based on the importance of the S. aureus agr RNA molecule, RNAIII, and small stable RNA molecules within other pathogens, it is possible that these RNA molecules influence biological processes within the organism.
Journal of Bacteriology 04/2006; 188(7):2593-603. · 3.83 Impact Factor
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ABSTRACT: UbiWorld is a concept being developedbytheFutures Laboratory group at Argonne National Laboratory that ties together the notion of ubiquitous computing (Ubicomp) with that of using virtual reality for rapid prototyping. The goal is to develop an environment where one can exploreUbicomp-typeconcepts without having to build real Ubicomp hardware. The basic notion is to extend object models in a virtual world by using distributed wide area heterogeneous computing technology to provide complex networking and processing capabilities to virtual reality objects. 1 Introduction In the Futures Laboratory [1] in the Mathematics and Computer Science (MCS) Division at Argonne National Laboratory (ANL), our research agenda is driven partly by discussions of advanced computing scenarios. We find that by suspending disbelief momentarily and by engaging in serious discussion of such topics as off-planet infrastructure, green nomadic computing, and molecular nanotechnology,we are able to project bey...
07/2000;
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ABSTRACT: With the growing presence of multimedia-enabled systems, we will see an integration of collaborative computing concepts into future scientific and technical workplaces. Desktop teleconferencing is common today,while more complex teleconferencing technology that relies on the availability of multipoint-enabled tools is starting to become available on PCs. A critical problem when using these collaborative tools is archiving multistream, multipoint meetings and making the content available to others. Ideally, one would like the ability to capture, record, play back, index, annotate, and distribute multimedia stream data as easily as we currently handle text or still-image data. The Argonne Voyager project is exploring and developing media server technology needed to provide such a flexible, virtual multipoint recording/playback capability. In this article we describe the motivating requirements, architecture, implementation, operation, performance, and related work. 1 Introduction As mul...
06/1997;
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ABSTRACT: The Argonne Voyager Multimedia Server is being developed in the Futures Lab of the Mathematics and Computer Science Division at Argonne National Laboratory. As a network-based service for recording and playing multimedia streams, it is important that the Voyager system be capable of sustaining certain minimal levels of performance in order for it to be a viable system. In this article, we examine the performance characteristics of the server. As we examine the architecture of the system, we try to determine where bottlenecks lie, show actual vs potential performance, and recommend areas for improvement through custom architectures and system tuning. 1 Introduction The Argonne Computing and Communications Infrastructure Futures Laboratory (Futures Lab) [1] was created to explore, develop, and prototype nextgeneration computing and communications infrastructure systems. An important goal of the Futures Lab project is to understand how to incorporate advanced display and media server sy...
03/1997;
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[show abstract]
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ABSTRACT: UbiWorld is a concept being developed by the Futures Laboratory group at Argonne National Laboratory that ties together the notion of ubiquitous computing (Ubicomp) with that of using virtual reality for rapid prototyping. The goal is to develop an environment where one can explore Ubicomp-type concepts without having to build real Ubicomp hardware. The basic notion is to extend object models in a virtual world by using distributed wide area heterogeneous computing technology to provide complex networking and processing capabilities to virtual reality objects. 1 Introduction In the Futures Laboratory [1] in the Mathematics and Computer Science (MCS) Division at Argonne National Laboratory (ANL), our research agenda is driven partly by discussions of advanced computing scenarios. We find that by suspending disbelief momentarily and by engaging in serious discussion of such topics as off-planet infrastructure, green nomadic computing, and molecular nanotechnology, we are able to proje...
02/1997;
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ABSTRACT: : When performing communications mapping experiments for massively parallel processors, it is important to be able to visualize the mappings and resulting communications. In a molecular dynamics model, visualization of the atom to atom interaction and the processor mappings provides insight into the effectiveness of the communications algorithms. The basic quantities available for visualization in a model of this type are the number of molecules per unit volume, the mass, and velocity of each molecule. The computational information available for visualization is the atom to atom interaction within each time step, the atom to processor mapping, and the energy rescaling events. We use the CAVE (CAVE Automatic Virtual Environment) to provide interactive, immersive visualization experiences. 1 Introduction Molecular dynamic simulations are increasingly being used to perform simulations of materials and in the modeling of drug compounds. The validation of these simulations is done by comp...
07/1995;
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Ewing Lusk,
Ralph Butler, Terrence Disz,
Robert Olson,
Ross Overbeek,
Rick Stevens,
David H. D. Warren,
Alan Calderwood,
Péter Szeredi,
Seif Haridi,
Per Brand,
Mats Carlsson,
Andrzej Ciepielewski,
Bogumil Hausman
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ABSTRACT: Aurora is a prototype or-parallel implementation of the full Prolog language for shared-memory multiprocessors, developed
as part of an informal research collaboration known as the “Gigalips Project”. It currently runs on Sequent and Encore machines.
It has been constructed by adapting Sicstus Prolog, a fast, portable, sequential Prolog system. The techniques for constructing
a portable multiprocessor version follow those pioneered in a predecessor system, ANL-WAM. The SRI model was adopted as the
means to extend the Sicstus Prolog engine for or-parallel operation. We describe the design and main implementation features
of the current Aurora system, and present some experimental results. For a range of benchmarks, Aurora on a 20-processor Sequent
Symmetry is 4 to 7 times faster than Quintus Prolog on a Sun 3/75. Good performance is also reported on some large-scale Prolog
applications.
New Generation Computing 04/1990; 7(2):243-271. · 0.94 Impact Factor
