WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing
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{"title"=>"WImpiBLAST: Web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing", "type"=>"journal", "authors"=>[{"first_name"=>"Parichit", "last_name"=>"Sharma", "scopus_author_id"=>"56241626200"}, {"first_name"=>"Shrikant S.", "last_name"=>"Mantri", "scopus_author_id"=>"35741161200"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "sgr"=>"84903625401", "doi"=>"10.1371/journal.pone.0101144", "scopus"=>"2-s2.0-84903625401", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24979410", "pui"=>"373435056"}, "id"=>"13557bea-0c6c-33a7-8070-7f865998d185", "abstract"=>"The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.", "link"=>"http://www.mendeley.com/research/wimpiblast-web-interface-mpiblast-help-biologists-perform-largescale-annotation-using-high-performan", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>9, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>3, "Chemistry"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>3}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Brazil"=>1, "Denmark"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1575126"], "description"=>"<p>Snapshot of Job reporting module.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools"], "article_id"=>1089184, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g006", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshot_of_Job_reporting_module_/1089184", "title"=>"Snapshot of Job reporting module.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575124"], "description"=>"<p>Snapshot of mpiBLAST specific section of create script module.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "mpiblast"], "article_id"=>1089182, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshot_of_mpiBLAST_specific_section_of_create_script_module_/1089182", "title"=>"Snapshot of mpiBLAST specific section of create script module.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575135"], "description"=>"<p>mpiBLAST achieved the highest speedup in case of sequence 6 where it outperforms NCBI BLAST+ by roughly 38 times but on average mpiBLAST performed 16 times faster than NCBI BLAST+ for aggregate run times of all queries. (<i>No. of aligned Sequences = 1; No. of sequences = 12; Type: Nucleotide; Average base pair length: 2389; Query sequences file: ss1_Table_4_and_5_Sequences.fasta</i> (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101144#pone.0101144.s006\" target=\"_blank\">Text S4</a>)<i>; Search database: In-house large nucleotide database (size = 246 GB after formatting)</i>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "computed", "sequenceserver", "smp", "server", "wimpiblast", "HPC"], "article_id"=>1089193, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t004", "stats"=>{"downloads"=>2, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Turnaround_time_computed_using_Sequenceserver_on_SMP_server_and_WImpiBLAST_on_HPC_cluster_/1089193", "title"=>"Turnaround time computed using Sequenceserver on SMP server and WImpiBLAST on HPC cluster.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575120"], "description"=>"<p>WImpiBLAST three-tier architecture defining non overlapping boundaries between fundamental layers of HPC resources, system software and web layer for efficient bug tracking, layer specific statistical logging and record keeping.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "three-tier", "non", "overlapping", "boundaries", "layers", "HPC", "logging"], "article_id"=>1089178, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g001", "stats"=>{"downloads"=>1, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_WImpiBLAST_three_tier_architecture_defining_non_overlapping_boundaries_between_fundamental_layers_of_HPC_resources_system_software_and_web_layer_for_efficient_bug_tracking_layer_specific_statistical_logging_and_record_keeping_/1089178", "title"=>"WImpiBLAST three-tier architecture defining non overlapping boundaries between fundamental layers of HPC resources, system software and web layer for efficient bug tracking, layer specific statistical logging and record keeping.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575133"], "description"=>"<p>The readings show that on the same number of cores i.e. 48, mpiBLAST outperforms NCBI BLAST+ by roughly 1.76 times. The maximum speedup was observed when using all 448 cores on the HPC cluster where mpiBLAST is 23.03 times faster than NCBI BLAST+. (<i>Number of sequences in fasta file = 43758; Type: Nucleotide; No. of aligned Sequences = 1; NCBI BLAST+ executed on SMP server and mpiBLAST executed on HPC cluster; Query sequences file: ss2_Table_6_Sequences.fasta</i> (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101144#pone.0101144.s006\" target=\"_blank\">Text S4</a>)<i>; Search Database: NR protein database (downloaded from NCBI)</i>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "computed", "ncbi", "smp", "server", "mpiblast", "HPC"], "article_id"=>1089191, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t006", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Turnaround_time_computed_using_NCBI_BLAST_on_SMP_server_and_mpiBLAST_on_the_HPC_cluster_/1089191", "title"=>"Turnaround time computed using NCBI BLAST+ on SMP server and mpiBLAST on the HPC cluster.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575134"], "description"=>"<p>It was observed that if a number of aligned sequences is large then mpiBLAST outperforms NCBI BLAST+ by roughly 51 times for sequence 6 (849 bp in length) and by roughly 1000 times for sequence 2 (4857 base pairs in length). (<i>No. of aligned Sequences = 100000; No. of sequences = 2; Type: Nucleotide; Average base pair length: 2853; Query sequences file: ss1_Table_4_and_5_Sequences.fasta</i> (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101144#pone.0101144.s006\" target=\"_blank\">Text S4</a>)<i>; Search database: In-house large nucleotide database (size = 246 GB after formatting)</i>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "computed", "ncbi", "smp", "server", "mpiblast", "HPC"], "article_id"=>1089192, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t005", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Turnaround_time_computed_using_NCBI_BLAST_on_SMP_server_and_mpiBLAST_on_the_HPC_cluster_/1089192", "title"=>"Turnaround time computed using NCBI BLAST+ on SMP server and mpiBLAST on the HPC cluster.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575132"], "description"=>"<p>The readings show that on the same SMP server and a similar number of cores i.e. 48, mpiBLAST outperform NCBI BLAST+ by roughly 1.2 times. (<i>Number of sequences in fasta file = 1000; Type: Nucleotide; No. of aligned Sequences = 1; Both NCBI BLAST+ and mpiBLAST executed on SMP server; Query sequences file: ss3_Table_7_Sequences.fasta</i> (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101144#pone.0101144.s006\" target=\"_blank\">Text S4</a>); <i>Search Database: NR protein database (downloaded from NCBI)</i>).</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "computed", "ncbi", "mpiblast", "smp"], "article_id"=>1089190, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t007", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Turnaround_time_computed_using_NCBI_BLAST_and_mpiBLAST_on_SMP_server_/1089190", "title"=>"Turnaround time computed using NCBI BLAST+ and mpiBLAST on SMP server.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575129"], "description"=>"<p>Feature oriented comparison of WImpiBLAST interface with other BLAST search supporting web interfaces.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "oriented", "wimpiblast", "interface", "supporting"], "article_id"=>1089187, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t003", "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Feature_oriented_comparison_of_WImpiBLAST_interface_with_other_BLAST_search_supporting_web_interfaces_/1089187", "title"=>"Feature oriented comparison of WImpiBLAST interface with other BLAST search supporting web interfaces.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575149", "https://ndownloader.figshare.com/files/1575150", "https://ndownloader.figshare.com/files/1575151", "https://ndownloader.figshare.com/files/1575152", "https://ndownloader.figshare.com/files/1575153", "https://ndownloader.figshare.com/files/1575155"], "description"=>"<div><p>The function of a newly sequenced gene can be discovered by determining its sequence homology with known proteins. BLAST is the most extensively used sequence analysis program for sequence similarity search in large databases of sequences. With the advent of next generation sequencing technologies it has now become possible to study genes and their expression at a genome-wide scale through RNA-seq and metagenome sequencing experiments. Functional annotation of all the genes is done by sequence similarity search against multiple protein databases. This annotation task is computationally very intensive and can take days to obtain complete results. The program mpiBLAST, an open-source parallelization of BLAST that achieves superlinear speedup, can be used to accelerate large-scale annotation by using supercomputers and high performance computing (HPC) clusters. Although many parallel bioinformatics applications using the Message Passing Interface (MPI) are available in the public domain, researchers are reluctant to use them due to lack of expertise in the Linux command line and relevant programming experience. With these limitations, it becomes difficult for biologists to use mpiBLAST for accelerating annotation. No web interface is available in the open-source domain for mpiBLAST. We have developed WImpiBLAST, a user-friendly open-source web interface for parallel BLAST searches. It is implemented in Struts 1.3 using a Java backbone and runs atop the open-source Apache Tomcat Server. WImpiBLAST supports script creation and job submission features and also provides a robust job management interface for system administrators. It combines script creation and modification features with job monitoring and management through the Torque resource manager on a Linux-based HPC cluster. Use case information highlights the acceleration of annotation analysis achieved by using WImpiBLAST. Here, we describe the WImpiBLAST web interface features and architecture, explain design decisions, describe workflows and provide a detailed analysis.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "interface", "mpiblast", "biologists", "large-scale", "annotation"], "article_id"=>1089201, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101144.s001", "https://dx.doi.org/10.1371/journal.pone.0101144.s002", "https://dx.doi.org/10.1371/journal.pone.0101144.s003", "https://dx.doi.org/10.1371/journal.pone.0101144.s004", "https://dx.doi.org/10.1371/journal.pone.0101144.s005", "https://dx.doi.org/10.1371/journal.pone.0101144.s006"], "stats"=>{"downloads"=>16, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_WImpiBLAST_Web_Interface_for_mpiBLAST_to_Help_Biologists_Perform_Large_Scale_Annotation_Using_High_Performance_Computing_/1089201", "title"=>"WImpiBLAST: Web Interface for mpiBLAST to Help Biologists Perform Large-Scale Annotation Using High Performance Computing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575128"], "description"=>"<p>Snapshot of File Manager module showing user home directory in the file system and options of download/upload/view for files.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "module", "directory", "options"], "article_id"=>1089186, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g007", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshot_of_File_Manager_module_showing_user_home_directory_in_the_file_system_and_options_of_download_upload_view_for_files_/1089186", "title"=>"Snapshot of File Manager module showing user home directory in the file system and options of download/upload/view for files.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575123"], "description"=>"<p>Snapshot of computational resource specific section of script creation module.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "computational"], "article_id"=>1089181, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g003", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshot_of_computational_resource_specific_section_of_script_creation_module_/1089181", "title"=>"Snapshot of computational resource specific section of script creation module.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575122"], "description"=>"<p>Procedural workflow in WImpiBLAST showing the initiation of mpiBLAST job, the input required at each stage and validations between stages to prevent invalid data from entering into successive stages.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "workflow", "wimpiblast", "initiation", "mpiblast", "validations", "stages", "invalid", "entering", "successive"], "article_id"=>1089180, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g002", "stats"=>{"downloads"=>1, "page_views"=>66, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Procedural_workflow_in_WImpiBLAST_showing_the_initiation_of_mpiBLAST_job_the_input_required_at_each_stage_and_validations_between_stages_to_prevent_invalid_data_from_entering_into_successive_stages_/1089180", "title"=>"Procedural workflow in WImpiBLAST showing the initiation of mpiBLAST job, the input required at each stage and validations between stages to prevent invalid data from entering into successive stages.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575131"], "description"=>"<p>Comparative analysis of existing bioinformatics web portals catering for BLAST search.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "bioinformatics", "portals", "catering"], "article_id"=>1089189, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t001", "stats"=>{"downloads"=>4, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_analysis_of_existing_bioinformatics_web_portals_catering_for_BLAST_search_/1089189", "title"=>"Comparative analysis of existing bioinformatics web portals catering for BLAST search.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575130"], "description"=>"<p>Feature oriented comparison of command line open source NCBI BLAST+ and mpiBLAST application.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "oriented", "ncbi", "mpiblast"], "article_id"=>1089188, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.t002", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Feature_oriented_comparison_of_command_line_open_source_NCBI_BLAST_and_mpiBLAST_application_/1089188", "title"=>"Feature oriented comparison of command line open source NCBI BLAST+ and mpiBLAST application.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-30 03:40:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/1575125"], "description"=>"<p>Sample created script.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Gene ontologies", "Gene prediction", "Genome scans", "Sequence assembly tools", "Transcriptome analysis", "Comparative genomics", "genetics", "genomics", "Functional genomics", "Gene function", "molecular biology", "Molecular biology techniques", "Sequencing techniques", "Genome sequencing", "Sequence analysis", "Computer applications", "Web-based applications", "Computer architecture", "Computing methods", "cloud computing", "software engineering", "Software design", "Software tools", "created"], "article_id"=>1089183, "categories"=>["Biological Sciences"], "users"=>["Parichit Sharma", "Shrikant S. Mantri"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101144.g005", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_created_script_/1089183", "title"=>"Sample created script.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-30 03:40:06"}

PMC Usage Stats | Further Information

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