Joss-reviews: [PRE REVIEW]: bio-go: A flexible tools Bioinformatics library

[whedon]

Submitting author: @RHagenson (Ryan Hagenson)
Repository: https://github.com/bio-ext/bio-go
Version: v1.0.0
Editor: @lpantano
Reviewers: @kortschak, @will-rowe

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

👋 @RHagenson - please add to your paper an explantation of what research problems your software can help with (which is another way of saying who will cite your software). Perhaps add a little about how they would use your software. When you have done so, please enter @whedon generate pdf as a new comment here to regenerate the pdf.

[rhagenson]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[danielskatz]

👋 @lpantano - would you be willing to edit this?

[lpantano]

@whedon assign @lpantano as editor

[whedon]

OK, the editor is @lpantano

[lpantano]

Hi @RHagenson, thanks for submitting to JOSS. I look around but I couldn't find any documentation of the tool. One of the mandatory requirement is to have full documentation with examples. If it is already done, can you put the link in the readme of the repo?

Cheers

[rhagenson]

@lpantano Documentation can be built through godoc, for online access to documentation visit: https://godoc.org/github.com/bio-ext/bio-go/bio

I have been using property tests to serve as both tests and examples. These can be run and seen from the repo root through go test via go test -v ./... (I have also just now added the -v flag to produce this output in TravisCI). In my opinion, code that is not automatically validated with each push to master is less useful than strict properties that can be expected from the library. The intent of the property tests (perhaps not as well as I had hoped) is to show potential users what properties they can expect from an implementation. All this said, I agree that explicit examples have value so I will add an examples/ directory alongside bio/ at the root. The separate directory would allow running everything all at once in CI and let potential users clearly see where examples are housed without all the property-testing framework around them.

I will add all the above directive information on viewing documentation and running tests to the README later today.

In your opinion, are there other additions I need to make?

[lpantano]

Thank you for the detailed explanation, I think that would help a lot to show potential users how they can use your tool, and then the goDoc can get into details.

Thanks for making the changes.

[rhagenson]

@lpantano I added the documentation and testing sections to the README. However, due to my immediate schedule I will not be able to add examples/ quite yet. I will tag you again in this thread when I have examples/ added. If there are any other additions/changes I need to make, let me know.

[lpantano]

@adavidzh, would you be interested in reviewing this tool?

[adavidzh]

@adavidzh, would you be interested in reviewing this tool?

Hi @lpantano. I'm afraid I'm tight for time these coming weeks and the topic is a little too far away from my comfort zone.

[rhagenson]

@lpantano Not done with the examples (they are being developed on examples branch), but I wanted to update you that I will be doing two types of examples:

1. Individual documentation example, i.e. examples that will display in the documentation built with godoc that show usage of individual elements
2. Aggregate examples, i.e. examples that use multiple elements together

[lpantano]

@krother, do you think you would have time to review this new tool? Thanks

[lpantano]

@mskwark, would you be interested in reviewing this tool?

[peterjc]

I was asked (by email) to review, but declined:

Sadly I know nothing about Go, and the project's current state of documentation leaves too steep a learning curve for me or any other bioinformatician curious to try it.

It needs a quick start, I would think even a trivial example like loading a given DNA sequence (be it with IUPAC ambiguity codes or just A, C, G, T bases) from a FASTA file, translating it into an amino acid sequence, and then writing out this protein sequence as a new FASTA file would be useful. Looking at the module names I think this functionality would be covered already.

[rhagenson]

@peterjc Thank you for the advice on a helpful and explanatory aggregate example of usage reading in a given DNA FASTA, translating it to protein, and writing it out as a new FASTA. In your opinion, are there any other rough edges about the project in its current state that need smoothing?

[peterjc]

@RHagenson the beginner documentation was the main thing lacking - beyond that it was hard to say more, sorry.

[rhagenson]

@peterjc Thank you for the help you provided. I will add more documentation at the beginner level.

[lpantano]

@kortschak, would you like to review this tool?

[kortschak]

Sure.

[will-rowe]

Happy to review this too if needed

[lpantano]

@whedon assign @kortschak as reviewer

[whedon]

OK, the reviewer is @kortschak

[lpantano]

@whedon add @will-rowe as reviewer

[whedon]

OK, @will-rowe is now a reviewer

[lpantano]

Thank you both to agree on reviewing this tool. I will wait until docs are updated to start the review.

[rhagenson]

@lpantano, I finished writing the beginner documentation (available at https://bio-ext.github.io/bio-go/) and the updated version number is v1.1.3.

[lpantano]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1741. Feel free to close this issue now!