Specifically:
"Software presubmission inquiries should explain how the proposed Software article meets the following criteria:
Article describes outstanding open source software of exceptional importance that has been shown to provide new biological insights.
Software must already be widely adopted, or have the promise of wide adoption by a broad community of users.
Software must be downloadable anonymously in source code form, with accompanying documentation, and licensed under an Open Source Initiative (OSI) compliant license.
"
Looks like PLoS Computational Biology requires a pre-submission inquiry: http://www.ploscompbiol.org/static/guidelines#software
The instructions are here: http://www.ploscompbiol.org/static/guidelines#presubs
Specifically: "Software presubmission inquiries should explain how the proposed Software article meets the following criteria:
We should start to put this together...