Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
Identifieur interne : 000221 ( Main/Exploration ); précédent : 000220; suivant : 000222Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
Auteurs : Anjani Ragothaman [États-Unis] ; Sairam Chowdary Boddu [États-Unis] ; Nayong Kim [États-Unis] ; Wei Feinstein [États-Unis] ; Michal Brylinski [États-Unis] ; Shantenu Jha [États-Unis] ; Joohyun Kim [États-Unis]Source :
- BioMed Research International [ 2314-6133 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Proteins.
- methods : Computational Biology.
- Algorithms, Amino Acid Sequence, Genome, Internet, Molecular Sequence Annotation, Protein Conformation, Software, User-Computer Interface.
Abstract
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.
Url:
DOI: 10.1155/2014/348725
PubMed: 24995285
PubMed Central: 4066679
Affiliations:
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08901, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>RADICAL, ECE, Rutgers University, New Brunswick, NJ 08901</wicri:regionArea><placeName><region type="state">New Jersey</region><settlement type="city">New Brunswick (New Jersey)</settlement></placeName><orgName type="university">Université Rutgers</orgName></affiliation></author><author><name sortKey="Boddu, Sairam Chowdary" sort="Boddu, Sairam Chowdary" uniqKey="Boddu S" first="Sairam Chowdary" last="Boddu">Sairam Chowdary Boddu</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Kim, Nayong" sort="Kim, Nayong" uniqKey="Kim N" first="Nayong" last="Kim">Nayong Kim</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Feinstein, Wei" sort="Feinstein, Wei" uniqKey="Feinstein W" first="Wei" last="Feinstein">Wei Feinstein</name><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Brylinski, Michal" sort="Brylinski, Michal" uniqKey="Brylinski M" first="Michal" last="Brylinski">Michal Brylinski</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author><author><name sortKey="Jha, Shantenu" sort="Jha, Shantenu" uniqKey="Jha S" first="Shantenu" last="Jha">Shantenu Jha</name><affiliation wicri:level="4"><nlm:aff id="I1">RADICAL, ECE, Rutgers University, New Brunswick, NJ 08901, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>RADICAL, ECE, Rutgers University, New Brunswick, NJ 08901</wicri:regionArea><placeName><region type="state">New Jersey</region><settlement type="city">New Brunswick (New Jersey)</settlement></placeName><orgName type="university">Université Rutgers</orgName></affiliation></author><author><name sortKey="Kim, Joohyun" sort="Kim, Joohyun" uniqKey="Kim J" first="Joohyun" last="Kim">Joohyun Kim</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author></analytic><series><title level="j">BioMed Research International</title><idno type="ISSN">2314-6133</idno><idno type="eISSN">2314-6141</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Computational Biology (methods)</term><term>Genome</term><term>Internet</term><term>Molecular Sequence Annotation</term><term>Protein Conformation</term><term>Proteins (chemistry)</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Proteins</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Sequence</term><term>Genome</term><term>Internet</term><term>Molecular Sequence Annotation</term><term>Protein Conformation</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>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.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chen, R" uniqKey="Chen R">R Chen</name></author><author><name sortKey="Snyder, M" uniqKey="Snyder M">M Snyder</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Feng, X" uniqKey="Feng X">X Feng</name></author><author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name></author><author><name sortKey="Luo, Q" uniqKey="Luo Q">Q Luo</name></author><author><name sortKey="Liu, B F" uniqKey="Liu B">B-F Liu</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schuster, Sc" uniqKey="Schuster S">SC Schuster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Furey, Ts" uniqKey="Furey T">TS Furey</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chen, R" uniqKey="Chen R">R 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last="Brylinski">Michal Brylinski</name><name sortKey="Feinstein, Wei" sort="Feinstein, Wei" uniqKey="Feinstein W" first="Wei" last="Feinstein">Wei Feinstein</name><name sortKey="Jha, Shantenu" sort="Jha, Shantenu" uniqKey="Jha S" first="Shantenu" last="Jha">Shantenu Jha</name><name sortKey="Kim, Joohyun" sort="Kim, Joohyun" uniqKey="Kim J" first="Joohyun" last="Kim">Joohyun Kim</name><name sortKey="Kim, Nayong" sort="Kim, Nayong" uniqKey="Kim N" first="Nayong" last="Kim">Nayong Kim</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Ticri/CIDE
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|texte= Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
}}
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