![](/images/graphics-bg.png)
Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
المؤلفون المشاركون
Boddu, Sairam Chowdary
Brylinski, Michal
Ragothaman, Anjani
Kim, Joohyun
Feinstein, Wei
Jha, Shantenu
Kim, Nayong
المصدر
العدد
المجلد 2014، العدد 2014 (31 ديسمبر/كانون الأول 2014)، ص ص. 1-12، 12ص.
الناشر
Hindawi Publishing Corporation
تاريخ النشر
2014-06-05
دولة النشر
مصر
عدد الصفحات
12
التخصصات الرئيسية
الملخص EN
While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function.
However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool.
To leverage its utility, we have developed a pipeline for eThread—a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively.
We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements.
Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements.
We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure.
Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution.
Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes.
The developed pipeline is easily extensible to other types of distributed cyberinfrastructure.
نمط استشهاد جمعية علماء النفس الأمريكية (APA)
Ragothaman, Anjani& Boddu, Sairam Chowdary& Kim, Nayong& Feinstein, Wei& Brylinski, Michal& Jha, Shantenu…[et al.]. 2014. Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics. BioMed Research International،Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-464766
نمط استشهاد الجمعية الأمريكية للغات الحديثة (MLA)
Ragothaman, Anjani…[et al.]. Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics. BioMed Research International No. 2014 (2014), pp.1-12.
https://search.emarefa.net/detail/BIM-464766
نمط استشهاد الجمعية الطبية الأمريكية (AMA)
Ragothaman, Anjani& Boddu, Sairam Chowdary& Kim, Nayong& Feinstein, Wei& Brylinski, Michal& Jha, Shantenu…[et al.]. Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics. BioMed Research International. 2014. Vol. 2014, no. 2014, pp.1-12.
https://search.emarefa.net/detail/BIM-464766
نوع البيانات
مقالات
لغة النص
الإنجليزية
الملاحظات
Includes bibliographical references
رقم السجل
BIM-464766
قاعدة معامل التأثير والاستشهادات المرجعية العربي "ارسيف Arcif"
أضخم قاعدة بيانات عربية للاستشهادات المرجعية للمجلات العلمية المحكمة الصادرة في العالم العربي
![](/images/ebook-kashef.png)
تقوم هذه الخدمة بالتحقق من التشابه أو الانتحال في الأبحاث والمقالات العلمية والأطروحات الجامعية والكتب والأبحاث باللغة العربية، وتحديد درجة التشابه أو أصالة الأعمال البحثية وحماية ملكيتها الفكرية. تعرف اكثر
![](/images/kashef-image.png)