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1. Developing a Computational Chemistry Framework for the Exascale Era

Author

Richard, RM, Bertoni, C, Boschen, JS, Keipert, K, Pritchard, B, Valeev, EF, Harrison, RJ, De Jong, WA, and Windus, TL

Subjects
Networking and Information Technology R&D, Numerical And Computational Mathematics, Computation Theory And Mathematics, Distributed Computing, Fluids & Plasmas, Numerical and Computational Mathematics, Computation Theory and Mathematics
Abstract

Within computational chemistry, the NWChem package has arguably been the de facto standard for running high-accuracy numerical simulations on the most powerful supercomputers. In order to better address the challenges presented by emerging exascale architectures, the decision has been made to rewrite NWChem. Design of the resulting package, NWChemEx, has been driven by exascale computing; however, significant additional design considerations have arisen from the team's involvement with the Molecular Sciences Software Institute (MolSSI). MolSSI is a National Science Foundation initiative focused on establishing coding and data standards for the computational chemistry community. As a result, NWChemEx is built upon a general computational chemistry framework called the simulation development environment (SDE) that is designed with a focus on extensibility and interoperability. The present manuscript describes the modular approach of the SDE and how it has been used to implement the self-consistent field algorithm within NWChemEx.

Published
2019

8. Ensembl 2008

Author

Flicek, P, Aken, BL, Beal, K, Ballester, B, Caccamo, M, Chen, Y, Clarke, L, Coates, G, Cunningham, F, Cutts, T, Down, T, Dyer, SC, Eyre, T, Fitzgerald, S, Fernandez-Banet, J, Gräf, S, Haider, S, Hammond, M, Holland, R, Howe, KL, Howe, K, Johnson, N, Jenkinson, A, Kähäri, A, Keefe, D, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Megy, K, Meidl, P, Overduin, B, Parker, A, Pritchard, B, Prlic, A, Rice, S, Rios, D, Schuster, M, Sealy, I, Slater, G, Smedley, D, Spudich, G, Trevanion, S, Vilella, AJ, Vogel, J, White, S, Wood, M, Birney, E, Cox, T, Curwen, V, Durbin, R, Fernandez-Suarez, XM, Herrero, J, Hubbard, TJP, Kasprzyk, A, Proctor, G, Smith, J, Ureta-Vidal, A, and Searle, S

Subjects
Internet, Mice, User-Computer Interface, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Computer Graphics, Animals, Humans, Genomics, Regulatory Elements, Transcriptional, Software
Abstract

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Published
2020
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9. A position statement on screening and management of prediabetes in adults in primary care in Australia.

Author

Bell, K, Shaw, JE, Maple-Brown, L, Ferris, W, Gray, S, Murfet, G, Flavel, R, Maynard, B, Ryrie, H, Pritchard, B, Freeman, R, Gordon, BA, Bell, K, Shaw, JE, Maple-Brown, L, Ferris, W, Gray, S, Murfet, G, Flavel, R, Maynard, B, Ryrie, H, Pritchard, B, Freeman, R, and Gordon, BA

Abstract

Prediabetes has a high prevalence, with early detection essential to facilitate optimal management to prevent the development of conditions such as type 2 diabetes and cardiovascular disease. Prediabetes can include impaired fasting glucose, impaired glucose tolerance and elevated HbA1c. This position statement outlines the approaches to screening and management of prediabetes in primary care. There is good evidence to implement intensive, structured lifestyle interventions for individuals with impaired glucose tolerance. The evidence for those with impaired fasting glucose or elevated HbA1c is less clear, but individuals should still be provided with generalised healthy lifestyle strategies. A multidisciplinary approach is recommended to implement healthy lifestyle changes through education, nutrition and physical activity. Individuals should aim to lose weight (5-10% of body mass) using realistic and sustainable dietary approaches supported by an accredited practising dietitian, where possible. Physical activity and exercise should be used to facilitate weight maintenance and reduce blood glucose. Moderate-vigorous intensity aerobic exercise and resistance training should be prescribed by an accredited exercise physiologist, where possible. When indicated, pharmacotherapy, metabolic surgery and psychosocial care should be considered, in order to enhance the outcomes associated with lifestyle change. Individuals with prediabetes should generally be evaluated annually for their diabetes status.

Published
2020

11. AN EXPERIMENTAL APPROACH TO THE CHALLENGES OF MISSION PLANNING FOR COLLABORATIVE MARITIME AUTONOMOUS SYSTEMS.

Author

Turnock, S. R., Hoang, T. S., Downes, J., Lam, J., and Pritchard, B.

Subjects
MANAGEMENT controls, COMMUNICATION planning, AUTONOMOUS vehicles
Abstract

It is expected that a key part of a future with increasing use of maritime autonomous systems, will require collaborative and integrated approaches to working. How such approaches can be developed and tested was the focus of the Integrated Mission Management Systems 2019 project. The immediate objective was to experimentally demonstrate the ability of a single mission management system to control a fleet of heterogeneous, multi-domain autonomous vehicles whereby their collaborative mission could be planned, verified, and delivered. To challenge the various spatial-temporal-energetic- communication-environmental constraints when operating such a fleet, real-world demonstration trials were carried out in Plymouth Sound deployed from the Thales Maritime Autonomy Centre at Turnchapel Wharf. The trials were focussed on providing essential information into how such collaborations can be best executed, alongside invaluable lessons as to how existing vehicles need to enhance their interoperability and in particular, robustness of communications and mission plans. [ABSTRACT FROM AUTHOR]

Published
2022
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19. Ensembl 2009

Author

Hubbard, T. J. P., Aken, B. L., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S., and Flicek, P.

Published
2009

20. Ensembl 2008

Author

Flicek, P., Aken, B. L., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S. C., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Gräf, S., Haider, S., Hammond, M., Holland, R., Howe, K. L., Howe, K., Johnson, N., Jenkinson, A., Kähäri, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A. J., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J. P., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A., and Searle, S.

Published
2008

23. Ensembl 2011

Author

Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, H. S., Rios, D., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, Y. A., Trevanion, S., Vandrovcova, J., Vilella, A. J., White, S., Wilder, S. P., Zadissa, A., Zamora, J., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Vogel, J., and Searle, S. M. J.

Subjects
0303 health sciences, Genetic Variation, Molecular Sequence Annotation, Articles, Genomics, Regulatory Sequences, Nucleic Acid, Rats, Mice, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Genetics, Animals, Humans, Software, Zebrafish, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary, functional and regulatory annotation. The most advanced resources are provided for key species including human, mouse, rat and zebrafish reflecting the popularity and importance of these species in biomedical research. As of Ensembl release 59 (August 2010), 56 species are supported of which 5 have been added in the past year. Since our previous report, we have substantially improved the presentation and integration of both data of disease relevance and the regulatory state of different cell types.

Published
2010
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24. Ensembl 2008

Author

Flicek, P., Aken, B., Beal, K., Ballester, Benoit, Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, S., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Gräf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Johnson, N., Jenkinson, A., Kähäri, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, X. M., Herrero, J., Hubbard, J., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A., Searle, S., Graf, S., Kahari, A., Technologies avancées pour le génôme et la clinique (TAGC), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Expert and Training Centre for Breast Cancer Screening, Radboud University Medical Center [Nijmegen], Techniques de l'Informatique et de la Microélectronique pour l'Architecture des systèmes intégrés (TIMA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Institut de physique du globe de Strasbourg (IPGS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Louis Pasteur - Strasbourg I-Centre National de la Recherche Scientifique (CNRS), Dep. of Energy, Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Techniques of Informatics and Microelectronics for integrated systems Architecture (TIMA), and Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)

Subjects
Internet, 0303 health sciences, 030302 biochemistry & molecular biology, Articles, Genomics, Mice, User-Computer Interface, 03 medical and health sciences, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Computer Graphics, Genetics, Animals, Humans, Regulatory Elements, Transcriptional, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software, 030304 developmental biology
Abstract

International audience; The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein–DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Published
2007
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27. Ensembl 2012

Author

Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kahari, A. K., Keefe, D., Keenan, S., Kinsella, R., Komorowska, M., Koscielny, G., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Muffato, M., Overduin, B., Pignatelli, M., Pritchard, B., Riat, H. S., Ritchie, G. R. S., Ruffier, M., Schuster, M., Sobral, D., Tang, Y. A., Taylor, K., Trevanion, S., Vandrovcova, J., White, S., Wilson, M., Wilder, S. P., Aken, B. L., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X. M., Harrow, J., Herrero, J., Hubbard, T. J. P., Parker, A., Proctor, G., Spudich, G., Vogel, J., Yates, A., Zadissa, A., and Searle, S. M. J.

Subjects
0303 health sciences, Genetic Variation, Molecular Sequence Annotation, Genomics, Articles, Rats, 03 medical and health sciences, Mice, 0302 clinical medicine, Gene Expression Regulation, Databases, Genetic, Genetics, Animals, Humans, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

Published
2011

28. Ensembl 2009

Author

Hubbard, T J P, Aken, B L, Ayling, S, Ballester, Benoit, Beal, K, Bragin, E, Brent, S, Chen, Y, Clapham, P, Clarke, L, Coates, G, Fairley, S, Fitzgerald, S, Fernandez-Banet, J, Gordon, L, Graf, S, Haider, S, Hammond, M, Holland, R, Howe, K, Jenkinson, A, Johnson, N, Kahari, A, Keefe, D, Keenan, S, Kinsella, R, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Megy, K, Meidl, P, Overduin, B, Parker, A, Pritchard, B, Rios, D, Schuster, M, Slater, G, Smedley, D, Spooner, W, Spudich, G, Trevanion, S, Vilella, A, Vogel, J, White, S, Wilder, S, Zadissa, A, Birney, E, Cunningham, F, Curwen, V, Durbin, R, Fernandez-Suarez, X M, Herrero, J, Kasprzyk, A, Proctor, G, Smith, J, Searle, S, Flicek, P, and Spinelli, Lionel

Subjects
[INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

no abstract

Published
2009

29. Ensembl 2008

Author

Flicek, P, Aken, BL, Beal, K, Ballester, B, Caccamo, M, Chen, Y, Clarke, L, Coates, G, Cunningham, F, Cutts, T, Down, T, Dyer, SC, Eyre, T, Fitzgerald, S, Fernandez-Banet, J, Gräf, S, Haider, S, Hammond, M, Holland, R, Howe, KL, Howe, K, Johnson, N, Jenkinson, A, Kähäri, A, Keefe, D, Kokocinski, F, Kulesha, E, Lawson, D, Longden, I, Megy, K, Meidl, P, Overduin, B, Parker, A, Pritchard, B, Prlic, A, Rice, S, Rios, D, Schuster, M, Sealy, I, Slater, G, Smedley, D, Spudich, G, Trevanion, S, Vilella, AJ, Vogel, J, White, S, Wood, M, Birney, E, Cox, T, Curwen, V, Durbin, R, Fernandez-Suarez, XM, Herrero, J, Hubbard, TJP, Kasprzyk, A, Proctor, G, Smith, J, Ureta-Vidal, A, Searle, S, Graf, Stefan [0000-0002-1315-8873], Megy, Karyn [0000-0002-2826-3879], and Apollo - University of Cambridge Repository

Subjects
Internet, Mice, User-Computer Interface, ComputingMethodologies_PATTERNRECOGNITION, Databases, Genetic, Computer Graphics, Animals, Humans, Genomics, Regulatory Elements, Transcriptional, Software
Abstract

The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of genome annotation, databases and other information for chordate and selected model organism and disease vector genomes. As of release 47 (October 2007), Ensembl fully supports 35 species, with preliminary support for six additional species. New species in the past year include platypus and horse. Major additions and improvements to Ensembl since our previous report include extensive support for functional genomics data in the form of a specialized functional genomics database, genome-wide maps of protein-DNA interactions and the Ensembl regulatory build; support for customization of the Ensembl web interface through the addition of user accounts and user groups; and increased support for genome resequencing. We have also introduced new comparative genomics-based data mining options and report on the continued development of our software infrastructure.

Published
2008

30. Canine reproductive ultrasound examination for predicting future sperm quality.

Author

England, GCW, Bright, L, Pritchard, B, Bowen, IM, Souza, MB, Silva, LDM, and Moxon, R

Subjects
DOG reproduction, SEMEN analysis, SPERMATOZOA analysis, DOG breeding, DOPPLER ultrasonography, TESTIS physiology
Abstract

Contents The reproductive potential of male animals is commonly evaluated using a breeding soundness examination incorporating B-mode ultrasound examination of the testes and recently Doppler ultrasound examination of the testicular arteries. These techniques may detect testicular normality or pathology, and while some measured parameters are associated with semen quality at the time of ultrasound examination, few studies have investigated the relationship with future semen quality. We hypothesized that B-mode and Doppler ultrasound measurements would correlate with future semen quality. Within two studies, we investigated the relationship between ultrasound measured testicular volume, testicular echogenicity, testicular homogeneity, subjective assessment of the testicular parenchyma, testicular artery resistance index, and pulsatility index with subsequent semen quality. Fifty-five normal fertile dogs of which 29 had stable semen quality and 26 had a subsequent decline in semen quality were examined during a 6-month period commencing 62 days after the ultrasound examination. Statistical analysis showed that no ultrasound parameters were predictive of future total sperm output or percentage live normal sperm. However, mean testicular echogenicity was positively related to future sperm motility ( t = 2.202, p = .039). We conclude that quantitative ultrasound assessment of the appearance of the testicular parenchyma has potential for the evaluation of future semen quality in dogs. [ABSTRACT FROM AUTHOR]

Published
2017
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32. Population-based surveillance for scedosporiosis in Australia: Epidemiology, disease manifestations and emergence of Scedosporium aurantiacum infection.

Author

McGregor A., Cooley L., Cox E., Franklin C., Korman T., Morrissey O., Spelman D., Speed B., Boan P., Dyer J., Gardam D., McLennan D., Murray R., Pryce T., Heath C.H., Slavin M.A., Sorrell T.C., Handke R., Harun A., Phillips M., Nguyen Q., Delhaes L., Ellis D., Meyer W., Chen S.C.A., Collignon P., Benn R., Chambers I., Dennis N., DeWit D., Ferguson J., Gosbell I., Gottlieb T., Halliday C., Holland J., Kesson A., Lawrence R., Marriott D., Newton P., Palasanthrian P., Pickles R., Pritchard B., Tierney L., Tomasotos V., Vaz R., Weeks K., Currie B., Allworth A., Coulter C., Faoagali J., Johnson B., Looke D., McCormack J., Nimmo G., O'Kane G., Playford E.G., Robson J., Rowlands K., Shaw D., McGregor A., Cooley L., Cox E., Franklin C., Korman T., Morrissey O., Spelman D., Speed B., Boan P., Dyer J., Gardam D., McLennan D., Murray R., Pryce T., Heath C.H., Slavin M.A., Sorrell T.C., Handke R., Harun A., Phillips M., Nguyen Q., Delhaes L., Ellis D., Meyer W., Chen S.C.A., Collignon P., Benn R., Chambers I., Dennis N., DeWit D., Ferguson J., Gosbell I., Gottlieb T., Halliday C., Holland J., Kesson A., Lawrence R., Marriott D., Newton P., Palasanthrian P., Pickles R., Pritchard B., Tierney L., Tomasotos V., Vaz R., Weeks K., Currie B., Allworth A., Coulter C., Faoagali J., Johnson B., Looke D., McCormack J., Nimmo G., O'Kane G., Playford E.G., Robson J., Rowlands K., and Shaw D.

Abstract

Australia-wide population-based surveillance for scedosporiosis identified 180 cases, with 118 (65.6%) cases of colonization and 62 (34.4%) cases of infection. Predisposing factors for isolation of Scedosporium spp. included chronic lung disease in 37.8% and malignancy in 21.7% of cases. Predictors of invasive disease (n = 62) included haematological stem cell transplantation (n = 7), leukaemia (n = 16) and diabetes mellitus (n = 8). Of 183 phenotypically-speciated isolates, 75 (41%) were Scedosporium prolificans (risk factors: haematologic cancer (n = 17), neutropaenia (n = 14)) and 108 (59%) had Scedosporium apiospermum/Pseudallescheria boydii phenotype [risk factor: diabetes (n = 15)]. Scedosporium prolificans (p 0.01) and leukaemia (p 0.03) independently predicted death. Epidemiological and antifungal susceptibility profiles of Scedosporium aurantiacum (prevalence >=15.8%) and S. apiospermum were similar. No patient with S aurantiacum infection (n = 6) died. This is the first description of clinical features associated with S. aurantiacum. © 2009 The Authors Journal compilation © 2009 European Society of Clinical Microbiology and Infectious Diseases.

Published
2012

34. Introduction

Author

Pritchard, B, Hearn, A, HEARN, A, Pritchard, B, Hearn, A, and HEARN, A

Published
2005

46. Whole genome comparison ofAspergillus flavusandA. oryzae

Author

Payne, G. A., primary, Nierman, W. C., additional, Wortman, J. R., additional, Pritchard, B. L., additional, Brown, D., additional, Dean, R. A., additional, Bhatnagar, D, additional, Cleveland, T. E., additional, Machida, Masayuki, additional, and Yu, J., additional

Published
2006
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