{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,25]],"date-time":"2024-09-25T10:58:33Z","timestamp":1727261913791},"reference-count":8,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2014,2,13]],"date-time":"2014-02-13T00:00:00Z","timestamp":1392249600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"Summary:<\/ns4:bold> wigExplorer<\/ns4:italic> is a BioJS component whose main purpose is to provide a platform for visualisation of wig-formatted data. Wig files are extensively used by genome browsers such as the UCSC Genome Browser. wigExplorer <\/ns4:italic>follows the BioJS standard specification, requiring a simple configuration and installation. wigExplorer<\/ns4:italic> provides an easy way to navigate the visible region of the canvas and allows interaction with other components via predefined events.<\/ns4:p>Availability: <\/ns4:bold>http:\/\/github.com\/biojs\/biojs; <\/ns4:ext-link>http:\/\/dx.doi.org\/10.5281\/zenodo.7721<\/ns4:ext-link><\/ns4:p>","DOI":"10.12688\/f1000research.3-53.v1","type":"journal-article","created":{"date-parts":[[2014,2,13]],"date-time":"2014-02-13T08:39:05Z","timestamp":1392280745000},"page":"53","update-policy":"http:\/\/dx.doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["wigExplorer, a BioJS component to visualise wig data"],"prefix":"10.12688","volume":"3","author":[{"given":"Anil S.","family":"Thanki","sequence":"first","affiliation":[]},{"given":"Rafael C.","family":"Jimenez","sequence":"additional","affiliation":[]},{"given":"Gemy G.","family":"Kaithakottil","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-4417-1018","authenticated-orcid":false,"given":"Manuel","family":"Corpas","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5589-7754","authenticated-orcid":false,"given":"Robert P.","family":"Davey","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2014,2,13]]},"reference":[{"key":"ref-1","doi-asserted-by":"publisher","first-page":"996-1006","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC.","volume":"12","author":"W Kent","year":"2002","journal-title":"Genome Res."},{"key":"ref-2","doi-asserted-by":"publisher","DOI":"10.1002\/0471250953.bi0909s28","article-title":"Using the Generic Genome Browser (GBrowse).","author":"M Donlin","year":"2009","journal-title":"Curr Protoc Bioinformatics."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"1630-1638","DOI":"10.1101\/gr.094607.109","article-title":"JBrowse: A next-generation genome browser.","volume":"19","author":"M Skinner","year":"2009","journal-title":"Genome Res."},{"key":"ref-4","doi-asserted-by":"publisher","first-page":"1103-1104","DOI":"10.1093\/bioinformatics\/btt100","article-title":"BioJS: an open source JavaScript framework for biological data visualization.","volume":"29","author":"J G\u00f3mez","year":"2013","journal-title":"Bioinformatics."},{"year":"2013","key":"ref-5","article-title":"BioJS: registry"},{"year":"2012","key":"ref-6","article-title":"D3.js data-driven documents"},{"article-title":"TGAC Browser: visualisation solutions for big data in the genomic era","year":"2013","author":"A Thanki","key":"ref-7"},{"key":"ref-8","doi-asserted-by":"publisher","DOI":"10.5281\/zenodo.7721","article-title":"wigExplorer, a BioJS component to visualise wig data.","author":"A Thanki","year":"2014","journal-title":"Zenodo."}],"updated-by":[{"updated":{"date-parts":[[2014,5,30]],"date-time":"2014-05-30T00:00:00Z","timestamp":1401408000000},"DOI":"10.12688\/f1000research.3-53.v2","type":"new_version","label":"New version"},{"updated":{"date-parts":[[2016,8,9]],"date-time":"2016-08-09T00:00:00Z","timestamp":1470700800000},"DOI":"10.12688\/f1000research.3-53.v3","type":"new_version","label":"New version"}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/3-53\/v1\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/3-53\/v1\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/3-53\/v1\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,3]],"date-time":"2018-12-03T11:58:52Z","timestamp":1543838332000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/3-53\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,2,13]]},"references-count":8,"URL":"http:\/\/dx.doi.org\/10.12688\/f1000research.3-53.v1","relation":{"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.3732.r3699","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.3732.r3697","asserted-by":"subject"}]},"ISSN":["2046-1402"],"issn-type":[{"type":"electronic","value":"2046-1402"}],"subject":[],"published":{"date-parts":[[2014,2,13]]},"assertion":[{"value":"Not Approved, Approved with reservations","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.3732.r3699, Robert Buels, JBrowse, University of California, Berkeley, CA, USA, 25 Feb 2014, version 1, 1 approved with reservations, 1 not approved","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#referee-response-3699","order":0,"name":"referee-response-3699","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Anil Thanki<\/b>; \nPosted: 26 Feb 2014<\/i>; Hi Robert,I thank you for your useful comments, and I fully understand your concerns about the code and the performance of the tool. I have already started working on fixes regarding your comments, and happy to say that the first two of your three comments have already been fixed. I am now working on the third point and hope to have a solution as soon as possible. Once i do have one I will submit a revised version of the new code and manuscript.Thanks a lot again,Anil","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#referee-comment-719","order":1,"name":"referee-comment-719","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Anil Thanki<\/b>; \nPosted: 28 May 2014<\/i>; Dear Robert We would like to thank you for taking the time to review the manuscript. Please find below our responses to your comments. \n1) wigExplorer<\/i> does not provide any useful error messages when it fails to fetch, or fails to parse, the file specified in its `dataSet` option. This can be a major issue for prospective users (i.e. installers) of the software.Answer: After considering this comment we have added more informative error messages, depending on the errors that can occur while running the component, e.g. \u201cUnknown format detected\u201d, \u201cNo data for selected reference\u201d, \u201cFile not found\u201d, etc. This will help make any installation problems clearer to users during installation.2) Also, when I installed it and ran it via the included TestwigExplorer2.html, the "top controls ... designed to scroll sideways" described in the manuscript were not shown. To rule out any problems with the way I installed it (caused by missing stylesheets or the like), I inspected the browser's (Google Chrome 32) document object model (DOM) using its built-in development tools, and verified that the controls were not even being placed in the DOM by the code itself. I didn't debug any further.Answer: Outside of the BioJS registry environment, the component\u2019s CSS behaviour changes, which resulted in disappearing controls. We have reformatted the CSS for this component and this is now fixed.3) Most importantly, and I think this is a showstopper: wigExplorer does not actually support the Wiggle format as set forth by UCSC at http:\/\/genome.ucsc.edu\/goldenPath\/help\/wiggle.html. It supports a limited tab-separated value format, which bears some resemblance to BedGraph format, but is not BedGraph either. So: it is named for a standard data format that it does not support, and the data format that it actually supports is not a standard format.Answer: We thanks Robert t raise this concern and we have rewritten the code and now the component fully supports the standard fixedStep and variableStep wig file format (as set out by UCSC) with span information and multiple references in one file if available.","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#referee-comment-841","order":2,"name":"referee-comment-841","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.3732.r3697, Phil Lord, School of Computing Science, University of Newcastle, Newcastle, UK, 07 Mar 2014, version 1, 1 approved with reservations, 1 not approved","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#referee-response-3697","order":3,"name":"referee-response-3697","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Anil Thanki<\/b>; \nPosted: 23 May 2014<\/i>; We would like to thank Phil for taking the time to review the manuscript. Please find below our responses to your comments1) The link to the software on Zenodo in the Software Availability section (Zenodo: wigExplorer, a BioJS component to visualise wig data, doi:10.5281\/zenodo.77218) seems a bit pointless as the download bundle requires a large number of dependencies which are not included and for which paths have been hardcoded to local machine locations. The authors should also include either a tag or a commit hash so that the version of the software in the download bundle can be identified in GitHub.Answer: We have uploaded a new version of the code to Zenodo with dependencies provided (http:\/\/dx.doi.org\/10.5281\/zenodo.8516). This new version is also included in BioJS Release 1.0 https:\/\/github.com\/biojs\/biojs\/releases\/tag\/v1.02) It does make me rather doubt the validity of the statement: "Like any other BioJS component, \nwigExplorer <\/i>requires little technical knowledge for its utilisation." Answer: We understand that there are a number of required dependencies for this component, and not including these in the component\u2019s distribution made it harder to install and utilise. As above, we have included these dependencies as well as sample datasets, so simply unzipping the distribution is sufficient to install and start using the component.3) The article is, essentially, an advert with relatively little technical content. This is appropriate; there is little point including, for example, precise instructions for the use of wigExplorer as this article will be checkpointed and the code will become out of date. I would however have liked a bit more information on the expected performance of the software: for instance, how big a chromosome can it visualize? How manipulable is the visualisation?Answer: \nF1000Research<\/i> requires a working copy of the code when article get published (for archival purposes) so, we have uploaded current version of code to zenodo (https:\/\/zenodo.org\/record\/8516#.U334LlhdV0s) so this copy of code will be same though main code can be updated. So this article will always point to the version of the code that it describes, which is stored in zenodo. And on the performance issue, in this case size of the file matters rather than size of genomic region. Because size of data depends on depth of the genomic information, though we tried to make an effort to make it clear in manuscript. In first paragraph of wigExplorer component section, \u201cWig files contains minimalistic information of genomic data, \nwigExplorer <\/i>can handle large genomic region like a chromosome (tested with a single file containing 12 chromosome with average length of 60 Mb), but it depends on depth of data rather than length of genomic region.\u201d4) The writing in the article is okay, but there are a few parts, which could do with improvement. For example, in the first paragraph of the Introduction section, the statement "biological web applications are usually implemented with no standard reutilisation guidelines in mind, hence BioJS was developed" I am not at all sure what "reutilisation guidelines" means with respect to code base. Do the authors just mean a defined and documented API? In which case, they should probably say this. Answer: Here by using the word "reutilisation guidelines\u201d, we mean that BioJS components can be easily implemented and can interact with each other with standard API. We have added a statement explaining this in the last line of the first paragraph of introduction that \u201cBioJS code contains standard guidelines that how to use components and how API can be implemented to interact with other components.\u201d5) There are also a couple of places, which could do with simplification. In the second paragraph of the Introduction section:" To our knowledge, this is the first modular component to visualise wig data that complies with BioJS standards." This statement could be seen as a caveat, and I think the authors could risk saying "This is the only BioJS component to show wig data". Also in the second paragraph of the Application section the statement "We are aware that third party browsers are also using \nwigExplorer<\/i>." could perhaps be simplified to "Third party browsers are also using \nwigExplorer<\/i>". I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Answer: We have reformatted the first statement to \u201cCurrently, this is the only BioJS component to show wig data\u201d and we have changed the second statement as reviewer suggested, \u201cThird party browsers are also using \nwigExplorer\u201d<\/i>","URL":"https:\/\/f1000research.com\/articles\/3-53\/v1#referee-comment-832","order":4,"name":"referee-comment-832","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"AT, GK, MC and RD were supported by the UK Biotechnology and Biological Sciences Research Council (BBSRC) National Capability Grant (BB\/J010375\/1) at TGAC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}
