Metagenome Annotation Using a Distributed Grid of Undergraduate Students
Publication Date
November 25, 2008
Journal
PLOS Biology
Authors
Pascal Hingamp, Céline Brochier, Emmanuel Talla, Daniel Gautheret, et al
Volume
6
Issue
11
Pages
e296
DOI
http://doi.org/10.1371/journal.pbio.0060296
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.0060296
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19067492
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586363
Europe PMC
http://europepmc.org/abstract/MED/19067492
Web of Science
000261187900007
Scopus
56849121330
Mendeley
http://www.mendeley.com/research/metagenome-annotation-using-distributed-grid-undergraduate-students
Events
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CiteULike | Further Information

Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/452440", "https://ndownloader.figshare.com/files/452579", "https://ndownloader.figshare.com/files/452592", "https://ndownloader.figshare.com/files/452674"], "description"=>"Metagenome Annotation Using a Distributed Grid of Undergraduate Students", "links"=>[], "tags"=>["metagenome", "annotation", "distributed", "grid", "students"], "article_id"=>149117, "categories"=>["Biological Sciences", "Science Policy", "Genetics"], "users"=>["Pascal Hingamp", "Céline Brochier", "Emmanuel Talla", "Daniel Gautheret", "Denis Thieffry", "Carl Herrmann"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.0060296.sg001", "https://dx.doi.org/10.1371/journal.pbio.0060296.sg002", "https://dx.doi.org/10.1371/journal.pbio.0060296.sd001", "https://dx.doi.org/10.1371/journal.pbio.0060296.sd002"], "stats"=>{"downloads"=>15, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Metagenome_Annotation_Using_a_Distributed_Grid_of_Undergraduate_Students/149117", "title"=>"Metagenome Annotation Using a Distributed Grid of Undergraduate Students", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-11-25 02:31:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/914803"], "description"=>"<p>Starting with a short DNA metagenomic sequencing read, students predict both functional and phylogenetic classifications using classical bioinformatics analyses.</p>", "links"=>[], "tags"=>["Computational biology", "genetics and genomics", "science policy"], "article_id"=>585254, "categories"=>["Biological Sciences", "Science Policy", "Genetics"], "users"=>["Pascal Hingamp", "Céline Brochier", "Emmanuel Talla", "Daniel Gautheret", "Denis Thieffry", "Carl Herrmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0060296.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotation_Work_Flow_/585254", "title"=>"Annotation Work Flow", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-25 01:27:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/914884"], "description"=>"<p>Initial student annotations are reviewed the first time by instructors. Students take advantage of this review to improve their analyses and produce a final annotation, which is reviewed a second time; each review is accompanied by a quantitative evaluation. This process is repeated for <i>n</i> sequences (here <i>n</i> = 3).</p>", "links"=>[], "tags"=>["annotation"], "article_id"=>585340, "categories"=>["Biological Sciences", "Science Policy", "Genetics"], "users"=>["Pascal Hingamp", "Céline Brochier", "Emmanuel Talla", "Daniel Gautheret", "Denis Thieffry", "Carl Herrmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0060296.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_Stage_Sequence_Annotation_Cycle_/585340", "title"=>"Two-Stage Sequence Annotation Cycle", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-25 01:29:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/914972"], "description"=>"<p>The five DNA fragments, assigned to a student, illustrate each possible annotation stage: ongoing initial “Annotations 1,” awaiting initial “Evaluation 1,” ongoing final “Annotations 2,” awaiting final “Evaluation 2,” and sequence annotations “Finished.” Quantitative evaluations are represented as blue horizontal bars, and an example of qualitative evaluations is shown in red in the “Comments” field associated with each sequence record. The popup menu in the center shows GOS sampling locations, from which sequences can be added to the cart.</p>", "links"=>[], "tags"=>["Computational biology", "genetics and genomics", "science policy"], "article_id"=>585428, "categories"=>["Biological Sciences", "Science Policy", "Genetics"], "users"=>["Pascal Hingamp", "Céline Brochier", "Emmanuel Talla", "Daniel Gautheret", "Denis Thieffry", "Carl Herrmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0060296.g003", "stats"=>{"downloads"=>2, "page_views"=>37, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Annotathon_Sequence_Cart_/585428", "title"=>"Annotathon Sequence Cart", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-25 01:30:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/915059"], "description"=>"<p>(A) Taxonomic domain-level classifications, determined either by students using phylogenetic tree reconstructions (Annotathon, 182 sequences classified) or by an automatic BLAST-based scheme (GOS, 5,058,757 sequences classified [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060296#pbio-0060296-b004\" target=\"_blank\">4</a>]). (B) Distribution of sequences across bacteria taxa. Proportions are determined either by students using phylogenetic tree reconstructions (Annotathon, 182 sequences classified) or by 16S-based estimates (GOS, 4,125 sequences classified [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060296#pbio-0060296-b003\" target=\"_blank\">3</a>]). (C) Gene products functional classifications. Proportions are determined either by students (Annotathon, 685 sequences classified) or by automatic TIGR (The Institute for Genomic Research) role assignment (GOS, 760,659 sequences classified [<a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060296#pbio-0060296-b002\" target=\"_blank\">2</a>]). Only categories from each partition that could be matched are shown.</p>", "links"=>[], "tags"=>["Computational biology", "genetics and genomics", "science policy"], "article_id"=>585511, "categories"=>["Biological Sciences", "Science Policy", "Genetics"], "users"=>["Pascal Hingamp", "Céline Brochier", "Emmanuel Talla", "Daniel Gautheret", "Denis Thieffry", "Carl Herrmann"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.0060296.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_Student_Annotathon_Versus_Literature_GOS_Annotations_/585511", "title"=>"Comparison of Student (Annotathon) Versus Literature (GOS) Annotations", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-11-25 01:31:51"}

PMC Usage Stats | Further Information

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Relative Metric

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