[Open-bio-l] Toolkits and the new eutils policies

[Chris Fields]

To whom it may concern,

Just want to get some clarification from the eutils folks with the changes.  I'm a core developer for the BioPerl toolkit and and in collaboration with several other Bio* toolkits (BioPython, BioRuby, BioJava).  We all have interfaces to eutils, either via the standard interface, SOAP-based, or both.  

We're seeking a clarification regarding the new rules, specifically the rules concerning 'tool' and 'email'.  Per the rules proposed in Dec. 2009, many of us have already implemented changes to address them.  As we're basically language-specific toolkits (classes, modules, etc) that are used for developing other applications, we have taken the stance that the end-user will need to start providing at least the email in order to properly use the eutils-specific tools, with a warning issued otherwise.  This is based on several reasons, foremost being the toolkits are very widely used (so may be spread over potentially thousands of IPs) and are being used in a large number of downstream applications.  As an example of the latter, BioJava is used in several free and commercial applications, such as Taverna and Geneious.

Currently, with BioPerl and Biopython, we set the 'tool' parameter specifically to the toolkit name by default.  This parameter can be overridden.  However, from reading the newest rules it appears that each tool (and thus each toolkit) should have one common email, no more.  This also appears to make the assertion that users using these toolkits (with 'tool' set and using the relevant emails) may essentially be tied down if one IP decides to abuse the rules.

This unfortunately makes the incorrect generalization that each tool is created by one developer, and simply does not make sense in large collaborative projects such as ours, where the software is used primarily in downstream applications and scripts.  Setting the tool could be beneficial to the development team, but at the same time it could be a tremendous hindrance.

So, what exactly should we do?  Do we set the 'tool' by default, or leave it to the user?  Similarly, how do we treat 'email'?  If we do set them, would the entire group of users for that tool be blocked if one end-user abuses the system?  Should we leave it up to the user to register themselves (both tool and email)?  So, we're at an impasse and really need your help.  

Sincerely,

chris


Christopher Fields
Core Developer, BioPerl Project
IGB Postdoctoral Fellow
Genomics of Neural & Behavioral Plasticity
University of Illinois Urbana-Champaign
Institute for Genomic Biology
1206 W. Gregory Dr. , MC-195
Urbana, IL 61801