Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Spring 4 2022 Feb 14 - Feb 25, Spring 5 2022 Feb 28 - Mar 11
Description
Revise Frontiers in Bioinformatics manuscript as requested by Editor.
This is due by Friday Feb 25 at the latest.
Latest draft is: 2022-02-01-BiovizConnect.docx, in Dropbox / IGB / Manuscripts / biovizConnect / Frontiers
Editor's comments:
Thanks for addressing all reviewers concerns in the previous round. Whilst the manuscript is close to acceptance I noticed some minor issues:
R1. in 497-514 you outline a 'subtle' issue concerning indexed file formats like BAM. This paragraph, whilst informative, id not explain exactly what the subtle is.. for instance: as currently written, the undesirable aspect of the physician use case is not actually explained. I'm guessing the issue is that the 'whole genome' is exposed to the user who is only interested in a specific region ? If that is indeed the case, then I recommend mentioning the 'BEACONS' network (https://beacon-project.io/) which aims to allow secure dissemination of such personal genomic data without full disclosure (and it is conceivable, a beacon api instance could be spun up for a cyverse result .. ).
R2. Please provide a URL for the UCSC JSON interface
R3. Recommend that FIgure 2 could be omitted. Instead line 200-203 should refer to the menu shown in Figure 3 (which will become Figure 2 should you agree with this recommendation).
R4. Minor Typos/Grammar:
line 424: "we considered user several" .. sugg. 'user' should be omittedline 454-454: "However, since we first released BioViz Connect, the CyVerse development team have improved data throughput, making this design less problematic." - do you mean to say "those tools' design" ?
Line 468: I bashfully request you use the more modern "Jalview" rather than 'JalView', but greatly appreciate your citation of my work.
Line 489: "The first technical limitation has to do with how data flow from the CyVerse back end data store.." - sugg. 'flows'
Letter from Editor requests continue to track changes:
Dear Dr Loraine,
I'm contacting you to request your action on the manuscript "BioViz Connect: Web application linking CyVerse cloud resources to genomic visualization in the Integrated Genome Browser" submitted to Frontiers in Bioinformatics, section Data Visualization.
Please access the review forum using the link below to respond to the comments in the Editor's tab and resubmit the revised manuscript if necessary by 25 Feb 2022. We encourage you to submit your revised manuscript with tracked changes to facilitate the review.
http://review.frontiersin.org/review/764619/0/0
The review process is almost complete and we look forward to receiving your response in time. Should you require more time please do not hesitate to contact the editorial office.
With best regards,
Jim Procter
Guest Associate Editor, Frontiers in Bioinformatics
https://www.frontiersin.org/
Attachments
Activity
I think we can combine Figure 2 and Figure 3. Do you want to give that a try?
Hopefully we can submit the revised version on Friday after all!
attn: Nowlan Freese
Using latest code on https://bvctest7.bioviz.org to create new figure.
I have combined figure 2 and 3 (so they are now the new figure 2) and have updated the figure legend and references to figures 2-4. I have also updated figure 4B to reflect recent changes to BioViz Connect
The paper is in Dropbox > IGB > Manuscripts > biovizConnect > Frontiers > 2022-02-22-BiovizConnect.docx
The figures are in the same location as the paper.
[~aloraine] - Ready for review.
I have made all of the suggested edits by Dr. Procter except for R3. The file is in Dropbox > IGB > Manuscripts > biovizConnect > Frontiers > 2022-02-22-BiovizConnect.docx
R3. Recommend that FIgure 2 could be omitted. Instead line 200-203 should refer to the menu shown in Figure 3 (which will become Figure 2 should you agree with this recommendation).
I'm not sure it would make sense to omit figure 2 and refer to the current figure 3 instead. Figure 2 specifically refers to the manage link right panel with the manuscript section going into detail about the public links. Figure 3 refers to the main panel of BioViz Connect and also includes the metadata right panel.
Similar to the section on metadata in the design and implementation details, I think we could omit references to figure 2 and leave the text more or less the same. Or we could leave figure 2 as is.