[version 2; peer review: 1 approved, 1 approved with reservations, 1 not approved]
AT and RJ developed the code for
We have re-coded some of the code to add an alerting system to inform users of errors. The code now also accepts fixedStep and variableStep wiggle files as defined by UCSC standards (
Numerous web applications exist for visualisation of biological data. Data can be prepared for visualisation using a variety of formats, one of which is the widely used wiggle (wig) file. A wiggle file contains text that defines either a feature or a data track. The wiggle format was developed by the UCSC genome browser
BioJS is an open source JavaScript library of components for the visualisation of biological data on the web. Here we present
The top controls are designed to toogle between different references as well as zoom and pan. Peaks show SNP density of 1kb size bins. A change of SNP density can be observed around the 24M mark, with a slightly greater density of SNPs on the right, indicative of a potential introgression segment from another related species.
Third party browsers are also using
The
The
Zenodo: wigExplorer, a BioJS component to visualise wig data_v2, doi:
GitHub: BioJS,
We are grateful to all BioJS developers who have contributed their work under an open source license. We are grateful to David Swarbreck at TGAC for his advice on the data shown in
I am no JavaScript developer myself and I have not tested the described functionality, but I already can think of applications in my own work if the package is able to not only show predefined chromosomes in a wig file, but subsets in a chromosome too.
I will state all my issues like this first major one:
The link to your real example page (http://biojs.io/d/biojs-vis-wigexplorer) can only be found by reading your article, following to the rather unspecific GitHub link to the http://biojs.io web page. There one need to search for your wigexplorer - that is not acceptable! Make this link more prominent in the article and refer to the GitHub page as the main biojs.io GitHub page. I can not approve this article, if your package can not display any user defined region in a wig file. After having checked the functionality on the hidden demo page I get the impression that this javascript package does ONLY visualize whole chromosomes from a wig file. The user can not change the visualized region by e.g. interactively zooming in or at least stating a displayed area in the javascript function call? But if your package can visualize a user defined area in a wig file this functionality needs to be highlighted in the article.
In addition I have several minor 'complains':
Can the package be used stand alone? If yes, please extend your code example to a minimal, working html page. It would be perfect to have the javascript library loaded from your own web server together with the example data. Much like on the hidden demo page, but as plain html plainly stated in the article. You claim that your tool easily integrats into the third party TGAC Browser. Can you provide the example html there, too?
I hope I could add some additional points of view to your work and give a kind of positive feedback.
Reviewer Expertise:
NA
I confirm that I have read this submission and 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.
Dear Stefan
We would like to thank you for reviewing the manuscript and making some positive comments that could be used for your application.
Please find below our responses to your comments.
1) The link to your real example page (http://biojs.io/d/biojs-vis-wigexplorer) can only be found by reading your article, following to the rather unspecific GitHub link to the http://biojs.io web page. There one need to search for your wigExplorer - that is not acceptable! Make this link more prominent in the article and refer to the GitHub page as the main biojs.io GitHub page.
Answer: We can understand your concern, as this component was developed as a part of BioJS 1 and now BioJS is evolved to version 2, so some links are broken or redirected. We will update links in the article according. Link :
2) I cannot approve this article, if your package cannot display any user defined region in a wig file. After having checked the functionality on the hidden demo page I get the impression that this JavaScript package does ONLY visualize whole chromosomes from a wig file. The user cannot change the visualized region by e.g. interactively zooming in or at least stating a displayed area in the JavaScript function call? But if your package can visualize a user defined area in a wig file this functionality needs to be highlighted in the article.
Answer: I can understand your issue here about visualising user defined region, wigExplorer was already had a capability of allowing user to move around and zoom in and out for visualising region of interest, but due to compatibility issue with BioJS2 buttons were not visible. Now we had fixed the issue and you will notice some controls on top left corner which gives user flexibility to visualise any region. It is also possible to visualise user defined area using API provided.
3) Can the package be used stand alone? If yes, please extend your code example to a minimal, working html page. It would be perfect to have the javascript library loaded from your own web server together with the example data. Much like on the hidden demo page, but as plain html plainly stated in the article.
Answer: Yes, this package has been designed to work standalone, I have set up some example on my personal GitHub page to prove that. Here is the link to stand alone example for wigExplorer:
4) You claim that your tool easily integrates into the third party TGAC Browser. Can you provide the example html there, too?
Answer: Yes, we believe that it's easy to integrate into any third party application and TGAC Browser uses wigExplorer to visualise users’ wig data. Here is an example explaining procedure to visualise your own wig data using TGAC Browser.
Example:
Go to link
Click on the upload icon on the right (before ‘Save Session’) There is a link to example wig file, to save and upload to see example Upload the same file to the ‘Drop files here’ region and close the upload box You should see the uploaded wig file displayed with prefix of the filename you uploaded.
Regards,
Anil Thanki
The authors have provided answers to all my comments.
Reviewer Expertise:
NA
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
I have tried this piece of software and it does appear to do what it says and running the software was not too difficult. The link to the software on Zenodo in the Software Availability section (
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.
I ran the software from a GitHub checkout - here all the paths given in the documentation assume a specific configuration of directories (which is different from that of the GitHub repository). None of this is a show stopper, but it does make me rather doubt the validity of the statement: "Like any other BioJS component,
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?
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.
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
Reviewer Expertise:
NA
I confirm that I have read this submission and 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.
We would like to thank Phil for taking the time to review the manuscript.
Please find below our responses to your comments
1) The link to the software on Zenodo in the Software Availability section (
Answer: We have uploaded a new version of the code to Zenodo with dependencies provided (
2) It does make me rather doubt the validity of the statement: "Like any other BioJS component,
Answer: We understand that there are a number of required dependencies for this component, and not including these in the component’s 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:
4) 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”, 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 “BioJS code contains standard guidelines that how to use components and how API can be implemented to interact with other components.”
5) 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
Answer: We have reformatted the first statement to “Currently, this is the only BioJS component to show wig data” and we have changed the second statement as reviewer suggested, “Third party browsers are also using
The manuscript is well written, but it does not accurately describe the software in question.
I installed the software on my machine, and evaluated its behavior under several scenarios that I think would be commonly encountered by people using it. The major issues I found with the software are:
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. Most importantly, and I think this is a show stopper: wigExplorer does not actually support the Wiggle format as set forth by UCSC at
Unfortunately, I cannot approve this manuscript as it is currently written. It does not accurately describe the wigExplorer software.
Reviewer Expertise:
NA
I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.
Dear Robert
We would like to thank you for taking the time to review the manuscript.
Please find below our responses to your comments.
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. “Unknown format detected”, “No data for selected reference”, “File not found”, 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’s 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
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.