scholarly journals Developing science gateways for drug discovery in a grid environment

2015 ◽  
Author(s):  
Horacio Pérez-Sánchez ◽  
Vahid Rezaei Tabar ◽  
Vitaliy Mezhuyev ◽  
Duhu Man ◽  
Jorge Jpg Peña-García ◽  
...  
Keyword(s):  
Distributed Computing ◽  
Large Scale ◽  
Screening Program ◽  
Life Sciences ◽  
In Silico Screening ◽  
Grid Environment ◽  
Access Protocol ◽  
Pipeline Pilot ◽  
Science Gateways ◽  
Large Databases

Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life-sciences with a convenient tool for high-throughput virtual screening (HTVS) on distributed computing resources. To this end, we recently integrated the biophysics-based drug screening program FlexScreen into a service applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation, based on Pipeline Pilot and Simple Object Access Protocol (SOAP) provides an easy-to-use graphical user interface to construct complex workflows which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

scholarly journals Developing science gateways for drug discovery in a grid environment

2015 ◽  
Author(s):  
Horacio Pérez-Sánchez ◽  
Vahid Rezaei Tabar ◽  
Vitaliy Mezhuyev ◽  
Duhu Man ◽  
Jorge Jpg Peña-García ◽  
...  
Keyword(s):  
Distributed Computing ◽  
Large Scale ◽  
Screening Program ◽  
Life Sciences ◽  
In Silico Screening ◽  
Grid Environment ◽  
Access Protocol ◽  
Pipeline Pilot ◽  
Science Gateways ◽  
Large Databases

Methods for in-silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life-sciences with a convenient tool for high-throughput virtual screening (HTVS) on distributed computing resources. To this end, we recently integrated the biophysics-based drug screening program FlexScreen into a service applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation, based on Pipeline Pilot and Simple Object Access Protocol (SOAP) provides an easy-to-use graphical user interface to construct complex workflows which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

scholarly journals Use of Antiplatelet Agents Decreases the Positive Predictive Value of Fecal Immunochemical Tests for Colorectal Cancer but Does Not Affect Their Sensitivity

2021 ◽  
Vol 11 (6) ◽  
pp. 497
Author(s):  
Yoonsuk Jung ◽  
Eui Im ◽  
Jinhee Lee ◽  
Hyeah Lee ◽  
Changmo Moon
Keyword(s):  
Colorectal Cancer ◽  
Large Scale ◽  
Screening Program ◽  
Antiplatelet Agents ◽  
Population Based ◽  
Small Sample ◽  
Antithrombotic Agents ◽  
Predictive Values ◽  
Prescription Rates ◽  
Small Sample Sizes

Previous studies have evaluated the effects of antithrombotic agents on the performance of fecal immunochemical tests (FITs) for the detection of colorectal cancer (CRC), but the results were inconsistent and based on small sample sizes. We studied this topic using a large-scale population-based database. Using the Korean National Cancer Screening Program Database, we compared the performance of FITs for CRC detection between users and non-users of antiplatelet agents and warfarin. Non-users were matched according to age and sex. Among 5,426,469 eligible participants, 768,733 used antiplatelet agents (mono/dual/triple therapy, n = 701,683/63,211/3839), and 19,569 used warfarin, while 4,638,167 were non-users. Among antiplatelet agents, aspirin, clopidogrel, and cilostazol ranked first, second, and third, respectively, in terms of prescription rates. Users of antiplatelet agents (3.62% vs. 4.45%; relative risk (RR): 0.83; 95% confidence interval (CI): 0.78–0.88), aspirin (3.66% vs. 4.13%; RR: 0.90; 95% CI: 0.83–0.97), and clopidogrel (3.48% vs. 4.88%; RR: 0.72; 95% CI: 0.61–0.86) had lower positive predictive values (PPVs) for CRC detection than non-users. However, there were no significant differences in PPV between cilostazol vs. non-users and warfarin users vs. non-users. For PPV, the RR (users vs. non-users) for antiplatelet monotherapy was 0.86, while the RRs for dual and triple antiplatelet therapies (excluding cilostazol) were 0.67 and 0.22, respectively. For all antithrombotic agents, the sensitivity for CRC detection was not different between users and non-users. Use of antiplatelet agents, except cilostazol, may increase the false positives without improving the sensitivity of FITs for CRC detection.

Research and Design of the Distributed Mass Small File Storage System Based on WCF

2013 ◽  
Vol 765-767 ◽  
pp. 1087-1091
Author(s):  
Hong Lin ◽  
Shou Gang Chen ◽  
Bao Hui Wang
Keyword(s):  
Fault Tolerance ◽  
Distributed Computing ◽  
Data Storage ◽  
Large Scale ◽  
Storage System ◽  
Hardware Platform ◽  
File Storage ◽  
Computing Framework ◽  
Research And Design ◽  
Small File

Recently, with the development of Internet and the coming of new application modes, data storage has some new characters and new requirements. In this paper, a Distributed Computing Framework Mass Small File storage System (For short:Dnet FS) based on Windows Communication Foundation in .Net platform is presented, which is lightweight, good-expansibility, running in cheap hardware platform, supporting Large-scale concurrent access, and having certain fault-tolerance. The framework of this system is analyzed and the performance of this system is tested and compared. All of these prove this system meet requirements.

PHENYLKETONURIA, AND GUTHRIE INHIBITION ASSAY SCREENING PROCEDURE

PEDIATRICS ◽  
1963 ◽  
Vol 32 (3) ◽  
pp. 344-346
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Human Genetics ◽  
Screening Program ◽  
Genetic Diseases ◽  
State Department ◽  
The State ◽  
Detection Methods ◽  
Inhibition Assay ◽  
Pilot Studies

Recommendations were made in view of the following facts: (1) the need for further information on the mechanisms involved in the phenotypic expressions of phenylketonuria; (2) the present lack of adequate data on the effectiveness of the Guthrie Inhibition Assay, in terms of number of cases which may be missed, factors making for positive determinations and providing other information on which to evaluate the appropriateness of the large-scale screening program proposed; (3) the undesirability of deploying inordinate resources in the evaluation of the Guthrie Inhibition Assay to the detriment of the needs of other areas of child health including phenylketonuria; (4) the indications that a multi-faceted approach to phenylketonuria would be productive, not only in resolving the problems involving this disorder but also as a model for the investigation of and application to the treatment of other genetic diseases; (5) the possibility that the Guthrie Inhibition Assay could be a useful tool in the early detection, treatment and investigation of phenylketonuria; and (6) the fact that other state health departments are participating in the Guthrie Field Trials, indicating that the California State Department of Public Health should apply its resources to a more intensive study of PKU and detection methods. The consultants made the following recommendations, through resolution, to the California State Department of Public Health. It was resolved that: 1. The State of California not be responsible at this time for initiating or recommending that the Guthrie procedure be accomplished on a state-wide basis in all newborn nurseries (one dissent). 2. The State of California initiate and coordinate the development of pilot studies in selected hospitals and medical centers throughout the State in the investigation of phenylketonuria, utilizing the Guthrie Inhibition Assay or other tests. 3. A scientific committee be appointed immediately as an advisory committee to the State Department of Public Health to develop recommendations for carrying out the suggested investigations. 4. A registry for phenylketonuria and other diseases (as listed in the recommendations by the Subcommittee on Human Genetics) be established within the framework of the State organization.

Clustering error messages produced by distributed computing infrastructure during the processing of high energy physics data

2021 ◽  
Vol 36 (10) ◽  
pp. 2150070
Author(s):  
Maria Grigorieva ◽  
Dmitry Grin
Keyword(s):  
Distributed Computing ◽  
Large Scale ◽  
High Energy Physics ◽  
High Energy ◽  
Machine Learning Algorithms ◽  
Service Failures ◽  
Fault Handling ◽  
Scientific Experiments ◽  
Computing Centers ◽  
Distributed Computing Infrastructures

Large-scale distributed computing infrastructures ensure the operation and maintenance of scientific experiments at the LHC: more than 160 computing centers all over the world execute tens of millions of computing jobs per day. ATLAS — the largest experiment at the LHC — creates an enormous flow of data which has to be recorded and analyzed by a complex heterogeneous and distributed computing environment. Statistically, about 10–12% of computing jobs end with a failure: network faults, service failures, authorization failures, and other error conditions trigger error messages which provide detailed information about the issue, which can be used for diagnosis and proactive fault handling. However, this analysis is complicated by the sheer scale of textual log data, and often exacerbated by the lack of a well-defined structure: human experts have to interpret the detected messages and create parsing rules manually, which is time-consuming and does not allow identifying previously unknown error conditions without further human intervention. This paper is dedicated to the description of a pipeline of methods for the unsupervised clustering of multi-source error messages. The pipeline is data-driven, based on machine learning algorithms, and executed fully automatically, allowing categorizing error messages according to textual patterns and meaning.

UNICORE as Uniform Grid Environment for Life Sciences

2005 ◽  
pp. 364-373 ◽  
Author(s):  
Krzysztof Benedyczak ◽  
Michał Wroński ◽  
Aleksander Nowiński ◽  
Krzysztof S. Nowiński ◽  
Jarosław Wypychowski ◽  
...  
Keyword(s):  
Life Sciences ◽  
Uniform Grid ◽  
Grid Environment

scholarly journals A High Prevalence Rate of a Positive Screen for Cognitive Impairment in Patients With Human Immunodeficiency Virus Attending an Irish Clinic

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Patricia H. McNamara ◽  
Robert Coen ◽  
Janice Redmond ◽  
Colin P. Doherty ◽  
Colm Bergin
Keyword(s):  
Human Immunodeficiency Virus ◽  
Cognitive Impairment ◽  
Large Scale ◽  
Screening Program ◽  
Cross Sectional Study ◽  
Hiv Positive ◽  
Study Cohort ◽  
Cross Sectional ◽  
Positive Screen ◽  
Immunodeficiency Virus

Abstract Background Human immunodeficiency virus (HIV)-associated neurocognitive disorders occurs in 20%–50% of HIV-positive patients. We undertook this study to assess the prevalence of a positive screen for cognitive impairment in the clinic population at our institution and to demonstrate the feasibility of implementing a screening program in routine clinical encounters. Methods This was a cross-sectional study, and patients were recruited prospectively between December 2010 and February 2013. Inclusion criteria were as follows: patients were HIV positive, over the age of 18, capable of giving informed consent, and had sufficient ability to communicate in English. Patients were screened for cognitive impairment using the Brief Neurocognitive Screen. Results A total of 604 patients were recruited, and 51.5% had a positive screen for cognitive impairment. The majority of the study cohort were male (78.8%), mean age was 40.9 (standard deviation, 10.2) years, 70.9% were Irish, the most common mode of transmission was men who have sex with men (49.3%), 83% were on antiretroviral therapy, and 88.7% were virally suppressed. Logistic regression showed that the main factors predictive of a positive screen for cognitive impairment were the endorsement of cognitive symptoms (P = .024), being born in Africa (P < .000001), the use of benzodiazepines (P = .00341), being unemployed (P = .008), and consumption of more than 40 units of alcohol weekly (P = .035). There was a positive screen for depression in 9.1% and a positive screen for anxiety in 24.5%. Conclusions The study highlights the necessity for a structured, prospective, large-scale screening program for cognitive impairment across countries with limited resources and demonstrates the feasibility of easily implementing this with minimal training.

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