Major publishing groups should agree to bioboxes standard.

[michaelbarton]

I think a large portion of the success of the MIAME standard was publishers requiring submissions containing microarray data to include the required information. Therefore I believe we should discuss this standard with publishers as we move towards v1.0 and ask them to encourage editors/reviews to follow it when reviewing software.

[michaelbarton]

I think @ScottBGI at Gigascience can provide with useful suggestions and feedback on this process.

[ScottBGI]

Yes, let me know what I can do to help. We are already getting these types of submissions at GigaScience, so can use these test cases to work on best practices and fine tune and any standards. As we use open review as standard this will be transparent and can be referred back to in any developing documentation as well.

[michaelbarton]

Thanks for your response @ScottBGI. Could you share what sort of information you would need to implement a community standard from the publisher's point of view? This will help us shape the RFC as we start towards v1.0.

[ScottBGI]

Even though a depressing number of people will miss or ignore any guidelines, as you say making MIAME style minimal information checklists could help. For reviewers and editors to actually use it the more concise the better, defining essential/recommended information. Publishers would probably want flexibility on thresholds and licensing, although bioboxes/BOSC/OSI/etc. can express their own recommendations. Validation tools could also be useful too, as I think a few proteomics journals have done something similar, setting up pipelines with the EBI PRIDE database and made their curation and validation processes part of the review process.

[michaelbarton]

I spoke with @scottbgi, @pli888 and @bobbledavidson from @gigascience and they provided excellent ideas and feedback on how we could work with publishers. I will summarise the main points:

• A short editorial could provide a call-to-arms for the community to help provide feedback on how the spec and how the containers could be used in bioinformatics. The aim of an editorial would be to highlight the benefits of the project, and encourage people to participate. An editorial limited to 1200 words with 10 references.

  My initial thought is to get this done after v0.9 as having a website and working validators will provide a more concrete example of the direction the project is moving in.

• The BOSC conference would be an excellent place to spread the word about the project. The codefest would also be a great place to do perhaps a 'dockerthon' about using containers and the benefits for bioinformatics. Having the above editorial completed before this date would be ideal also. Some members from gigascience should be at BOSC so it will also be a good time to discuss in person.
• To encourate other publishers to adopt the standard, it should be as simple to use as possible and should have wide agreement and input from the bioinformatics community. If a proof of concept could be shown to add value to the publishing process, this would go a long way to helping the standard.
• AppSoma and Galaxy are interested in using containers and so could provide technical feedback once we have a working version of the spec.

[michaelbarton]

Discussed in meeting #67. Adoption of bioboxes standards by journals will become a greater priority once we have editor/reviewer instructions (#46) and working validators (#35).