Joss-reviews: [PRE REVIEW]: GERMSbrowser: Proof of concept for interfacing between clinical samples and analyzed phylogenetic tree for infection relationship and possible outbreak detection

[whedon]

Submitting author: @chenjqp (Pauline Chen)
Repository: https://bitbucket.org/srcapps/germs-browser
Version: 1.0.0
Editor: @mgymrek
Reviewer: Pending

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[arfon]

Thanks for submitting this @chenjqp. It's not clear from your submission or the documentation here how complete this software is and whether it meets our submission guidelines. In particular we require that (quoting from http://joss.theoj.org/about#author_guidelines):

Your software should have a research application
Should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler)
Should be feature complete (no half-baked solutions)

Could you confirm that this submission meets all three of these criteria?

[chenjqp]

Thanks for starting the pre-review process!

Research application: It enables non-bioinformaticians to easily view strain relationships and zoom in to the raw data underlying the visualization. One application in particular that is clear is for the identification of clusters of related strains. In a potential outbreak setting, having an immediate answer to whether closely related strains by epidemiology (close personal contacts, close geographical location, and/or close temporal relationship) are in fact also closely related genetically. The finding of such a match in close epidemiology and close genome sequence is a solid basis for inference of transmission and therefore a potential outbreak. This software provides a platform for integrating all of these data types into an intuitive interface that is usable by clinicians or epidemiologists. Other applications are of course possible in food safety, animal health, or other areas.

Contributions: The primary benefit is making the above listed simpler. The software provides integration and some intuitive interface features such as enabling easy, click-enabled movement from the underlying data table to the phylogenetic tree and back.

Feature complete: Yes.

Do let me know if any additional information is required.

[chenjqp]

Hey there @arfon , just checking to see if I need to update the documentation to reflect the above information?

[arfon]

Hey there @arfon , just checking to see if I need to update the documentation to reflect the above information?

Yes that would be helpful @chenjqp. I'm currently looking for a JOSS editor to handle this submission so hopefully we won't have to wait too long to get this moving.

[mgymrek]

@whedon assign @mgymrek as editor

[whedon]

OK, the editor is @mgymrek

[mgymrek]

Hi @chenjqp, I noticed the wiki pages with install instructions say I don't have access to the wiki. Perhaps it is because I am unfamiliar with bitbucket and am missing something. Can you make sure those pages are publicly available so that a reviewer will be able to install the software?

[chenjqp]

Hi @mgymrek, my apologies, I've updated the settings to allow for public access to the Wiki.

[gymreklab]

Hi @chenjqp , I am still looking for reviewers for this. Feedback so far though: I and a colleague have gone through trying to get this set up and have found the installation process to be too cumbersome. There are many requirements (e.g. mysql, Google OAuth2, editing configuration documents) and I fear this precludes the software from accomplishing its goal for helping non-bioinformaticians visualize data. I consider myself a bioinformatician and have gotten stuck in trying to deploy it. I would suggest to compile as many as possible of the setup steps into a single script to install the package, rather than pointing to various wiki pages. I would also like to see a clear list of requirements needed to install. If this is something that runs over the web browser, it would be helpful to serve an example instance so people can see what it is before going through the steps to install.

[chenjqp]

Hi @mgymrek, thanks for the feedback! Let me work on that and I'll get back to you soon.

[arfon]

Hi @mgymrek, thanks for the feedback! Let me work on that and I'll get back to you soon.

👋 @chenjqp - do you have any update for us on this?

[chenjqp]

Hi @mgymrek , my sincerest apologies. I'm getting some help on writing the installation script so hopefully I can get this done soon.

[chenjqp]

Hi @mgymrek, I've committed a 'install.sh' bash script to aid in installation. Do let me know if this is ok for you.

At the moment, the script aims to assist in setting up the sample page. I'm in the midst of adding more functionalities to also assist in updating the configuration file.

[mgymrek]

Thanks @chenjqp. I'll take a look this week at the install script.

[mgymrek]

Thanks for the install script, this was helpful. I was able to get this installed, but still haven't successfully run it. I can get the webserver started with the sample data in the install script, but when I launch it I just see a Google login button. When I press I get a 400 error with the message "origin_mismatch." Any suggestions?

A couple other comments:

• There is still a significant part of the setup that involves entering commands in mysql. Could that not be added to the install script?
• It would be helpful to run an example instance, e.g. from AWS, so people can see how this works before deciding whether to install.

[arfon]

Ping @chenjqp - did you see @mgymrek's comments ☝️ ?

[chenjqp]

My apologies, i have been on maternity leave for the past 3 months. Let me look into this and i will get back ASAP.

[arfon]

@chenjqp - are you still interested in pursing this publication?

[chenjqp]

@arfon my sincerest apologies. yes, i am. i have made some changes to include a demo site on Heroku, details are on the 'Overview' page. However, I'm still working on a proper start script.

Sorry for the delay. Can i reopen this at a later time?

[arfon]

Sorry for the delay. Can i reopen this at a later time?

Sure, we can withdraw this submission for now if you like and you can re-submit in the future sometime when you're ready?

[chenjqp]

Yes please, i will resubmit when ready. Thank you so much!