LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory
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{"title"=>"LabTrove: A Lightweight, Web Based, Laboratory \"Blog\" as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory", "type"=>"journal", "authors"=>[{"first_name"=>"Andrew J.", "last_name"=>"Milsted", "scopus_author_id"=>"14023302300"}, {"first_name"=>"Jennifer R.", "last_name"=>"Hale", "scopus_author_id"=>"41161247000"}, {"first_name"=>"Jeremy G.", "last_name"=>"Frey", "scopus_author_id"=>"7202811746"}, {"first_name"=>"Cameron", "last_name"=>"Neylon", "scopus_author_id"=>"9738760800"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84880735266", "sgr"=>"84880735266", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0067460", "pmid"=>"23935832", "isbn"=>"1932-6203 (Electronic)", "pui"=>"369424151"}, "id"=>"efdf733c-50a7-3670-b873-cda3e8522b8b", "abstract"=>"BACKGROUND: The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.\\n\\nCONCLUSIONS/SIGNIFICANCE: LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.", "link"=>"http://www.mendeley.com/research/labtrove-lightweight-web-based-laboratory-blog-route-towards-marked-up-record-work-bioscience-resear", "reader_count"=>36, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>8, "Lecturer"=>1, "Professor"=>2, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Librarian"=>1, "Researcher"=>4, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>8, "Lecturer"=>1, "Professor"=>2, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>7, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Materials Science"=>1, "Medicine and Dentistry"=>3, "Agricultural and Biological Sciences"=>3, "Physics and Astronomy"=>1, "Chemistry"=>6, "Computer Science"=>13}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>7}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>6}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Computer Science"=>{"Computer Science"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "United Kingdom"=>3, "Germany"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1127602"], "description"=>"<p>Each item on the TimeLine is a hyperlink to the LabTrove entry.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "labtrove"], "article_id"=>752448, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g008", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_a_LabTrove_TimeLine_/752448", "title"=>"Example of a LabTrove TimeLine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127582"], "description"=>"<p>The LabTrove system archives all versions of the post and they are accessible from the final version of the post. All the URLs resolve to a open science laboratory notebook and should be visible. (A) The first version of a post describing an analysis procedure (<a href=\"http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revision=11928\" target=\"_blank\">http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revision=11928</a> Accessed 6 March 2013). (B) The record of revisions, showing the first five revisions of the post (<a href=\"http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revisions\" target=\"_blank\">http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revisions</a>, Accessed 6 March 2013). (C) The final version of the post including further analysis and images (<a href=\"http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revision=11938\" target=\"_blank\">http://biolab.isis.rl.ac.uk/camerons_labblog/11928/Some_analysis_of_reflection_data_from_Crisp_Experiment.html?revision=11938</a>, Accessed 6 March 2013). Copies of these web pages are provided as part of the supplementary material as well as the links to the Labtrove instance at ISIS.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "illustrates", "posts", "recorded", "mistakes"], "article_id"=>752428, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g001", "stats"=>{"downloads"=>2, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_This_sequence_illustrates_how_posts_develop_as_a_process_is_recorded_or_minor_mistakes_are_corrected_/752428", "title"=>"This sequence illustrates how posts develop as a process is recorded or minor mistakes are corrected.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127596"], "description"=>"<p>(A) A template post for a data collection type experiment in which a sample is measured with specific instrument parameters. The template includes placeholders for links to other posts in the ‘Sample’ column - [[Material:Solution]] – and in the ‘Data’ column. Note that the data itself would be created after the current template was used, so the post identifier data would be inserted during a subsequent edit. (B) The rendered template showing drop-down menus for selecting sample posts and text boxes for entering values. (C) A template for an experimental laboratory procedure involving a range of input samples and a single output product. (D) The rendered template being populated.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "illustrating"], "article_id"=>752442, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g006", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extracts_illustrating_the_design_and_use_of_templates_/752442", "title"=>"Extracts illustrating the design and use of templates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127591"], "description"=>"<p>Strictly, scheme (A) is more correct, as every individual process or reaction receives its own post and therefore has its own URI. This approach has the advantage of creating a discrete endpoint for every relationship between inputs, processes, and outputs. However, this scheme has the potential to create an unsustainable burden on the user and to render the records difficult to read as a laboratory notebook. In scheme (B), which we usually adopt, objects (in this case, samples and data) have their own posts but repeated processes are collected together and the relationship between specific inputs and outputs is recorded implicitly in a table. Posts that use this approach are more human-readable, but if necessary specific values can still be extracted programmatically into structured data.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "illustrating", "schemes", "determining", "objects"], "article_id"=>752437, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g004", "stats"=>{"downloads"=>9, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagram_illustrating_the_alternative_schemes_for_determining_which_research_objects_merit_their_own_posts_/752437", "title"=>"Diagram illustrating the alternative schemes for determining which research objects merit their own posts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127604", "https://ndownloader.figshare.com/files/1127605", "https://ndownloader.figshare.com/files/1127606", "https://ndownloader.figshare.com/files/1127607", "https://ndownloader.figshare.com/files/1127608", "https://ndownloader.figshare.com/files/1127617", "https://ndownloader.figshare.com/files/1127618"], "description"=>"<div><p>Background</p><p>The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research.</p><p>Methodology/Principal Findings</p><p>We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system.</p><p>Conclusions/Significance</p><p>LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.</p></div>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "marked", "bioscience"], "article_id"=>752450, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy Frey", "Cameron Neylon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0067460.s001", "https://dx.doi.org/10.1371/journal.pone.0067460.s002", "https://dx.doi.org/10.1371/journal.pone.0067460.s003", "https://dx.doi.org/10.1371/journal.pone.0067460.s004", "https://dx.doi.org/10.1371/journal.pone.0067460.s005", "https://dx.doi.org/10.1371/journal.pone.0067460.s006", "https://dx.doi.org/10.1371/journal.pone.0067460.s007"], "stats"=>{"downloads"=>17, "page_views"=>59, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LabTrove_A_Lightweight_Web_Based_Laboratory_8220_Blog_8221_as_a_Route_towards_a_Marked_Up_Record_of_Work_in_a_Bioscience_Research_Laboratory_/752450", "title"=>"LabTrove: A Lightweight, Web Based, Laboratory “Blog” as a Route towards a Marked Up Record of Work in a Bioscience Research Laboratory", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127585"], "description"=>"<p>The top two posts represent samples whereas the bottom post is a procedure. This view is accessible at <a href=\"http://biolab.isis.rl.ac.uk/camerons_labblog/month/1280617200\" target=\"_blank\">http://biolab.isis.rl.ac.uk/camerons_labblog/month/1280617200</a>, Accessed 6 March 2013.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "recorded", "presented"], "article_id"=>752431, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extract_from_a_laboratory_notebook_recorded_as_a_blog_presented_in_a_standard_format_and_showing_three_individual_posts_/752431", "title"=>"Extract from a laboratory notebook recorded as a blog, presented in a standard format, and showing three individual posts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127594"], "description"=>"<p>Similar posts, e.g. those that refer to a single type of material can be readily aggregated and parsed based on local knowledge of the structure. This information can then be tabulated or used to populate a relational database. It is also possible to extract parameters, such as the sequence of an oligonucleotide, do external analysis, and pass this information back into the post. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460#pone-0067460-t001\" target=\"_blank\">Table 1</a> for an example of structured data obtained from posts that contain tables and the details of the methodology.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "unstructured", "structured", "labtrove"], "article_id"=>752440, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g005", "stats"=>{"downloads"=>4, "page_views"=>43, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extraction_of_unstructured_and_partially_structured_data_from_LabTrove_posts_/752440", "title"=>"Extraction of unstructured and partially structured data from LabTrove posts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127603"], "description"=>"<p>All posts with the metadata key “DNA” and the metadata value “oligonucleotide” were extracted from the LabTrove blog at <a href=\"http://biolab.isis.rl.ac.uk/camerons_labblog\" target=\"_blank\">http://biolab.isis.rl.ac.uk/camerons_labblog</a>. Despite inconsistency in the description of the oligonucleotides it is possible to obtain structured data from posts that could be used to populate other tables or a relational database as desired. The tables in each post were parsed and data extracted from them, based only on the structure from the table. The extracted data were then converted to a tabular form in html and reformatted into this table. Five rows were removed representing posts where oligonucleotides were described only in free text form. Two columns, one with no entries, and one headed Property with ‘Data’ in every row, resulting from the top row of tables, are not shown for clarity. The columns have been re-ordered. The code that generated the tabular data as well as the data it generated is provided in the Supplementary Information.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "structured", "labtrove"], "article_id"=>752449, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.t001", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Extraction_of_structured_data_from_partially_structured_LabTrove_posts_/752449", "title"=>"Extraction of structured data from partially structured LabTrove posts.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127588"], "description"=>"<p>(A) The editing view for creating text content, with a toolbar for markup, which includes an icon for linking to another post. (B) Clicking the link icon pops up a window from which an existing post can be selected to incorporate a link into the current post. (C) Data files can be added only after a post has been submitted. A popup window enables the selection and naming of the appropriate files, which are then attached to the post. (D) Thumbnails of the files can also be added into the text of the post.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "adding", "editing"], "article_id"=>752434, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tools_used_when_adding_and_editing_posts_/752434", "title"=>"Tools used when adding and editing posts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1127601"], "description"=>"<p>The full set of posts from a single e-Notebook was obtained as an XML document and parsed <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460#pone.0067460-Neylon2\" target=\"_blank\">[30]</a> into Geph (<a href=\"http://gephi.org/\" target=\"_blank\">http://gephi.org/</a>) graph format <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067460#pone.0067460-Hirst1\" target=\"_blank\">[31]</a>. A subset of posts from a specific time frame, during which a number of protein purifications were being carried out, was selected and automatically grouped by sub-network modularity. The modularity analysis successfully differentiates the posts in three separate but parallel experiments carried out at the same time. The inset shows the same graph colour-coded by post type: pink nodes are procedures, yellow nodes are physical samples, and the red node is a dataset.</p>", "links"=>[], "tags"=>["Computer applications", "Web-based applications", "Computer modeling", "Information technology", "databases", "Ontology and logics", "Research assessment", "Research validity", "reproducibility", "Publication practices", "Research integrity", "Publication ethics", "Science education", "posts"], "article_id"=>752447, "categories"=>["Information And Computing Sciences", "Science Policy"], "users"=>["Andrew J. Milsted", "Jennifer R. Hale", "Jeremy G. Frey", "Cameron Neylon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0067460.g007", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualization_of_posts_as_a_network_of_resources_/752447", "title"=>"Visualization of posts as a network of resources.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-07-23 08:01:47"}

PMC Usage Stats | Further Information

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Relative Metric

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