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 omitted

line 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/