Sunday, February 26, 2012

Future Bridges Lab Rules version 0.1

Lab Rules

Version 0.1.3 on July 14, 2012 by Dave Bridges

Remember when you were growing up and you would say, well when I’m older I will (or won’t) do that.
I have been thinking of that, for my future when I run my own group.
It is fairly easy (and as a bit of a blowhard I do this all the time) to say I would do this, or I would do that.
I think posting this publicly will encourage me to stick to these rules.
Below are some roles and a bit of rationale and caveats.
This is the first version of this post but future versions will include links to the previous versions.
The version numbering is described in the Lab Policies README.
Check out the GitHub Repository for more granular changes.

Supervision of Trainees

Trainee-Advisor Contract
Both myself and trainees (either mine, or co-supervised trainees) will read, discuss and sign a contract describing our roles and responsibilities both as a trainee/employee and a mentor. This will include data dissemination/publishing rules, expectations of productivity, note keeping and time commitment, rules for dealing with other members both in my group and in collaborations, rules for sharing of reagents and data, rules for adjucating disagreements and grounds and procedures for termination. These rules will be in conformity with any institutional rules. Exceptions can be discussed and the agreement can be modified throughout the term of the relationship. I will post a generic version of this agreement in a publicly viewable location.
Online Presence
All trainees will appear on the laboratory website and write a blurb about their research interests and goals. Trainees will be strongly encouraged to blog, tweet and otherwise engage in social networking tools regarding their research and the work of others, but this is not required. Links to their publicly available social network profiles will be posted on the laboratory website.
Open Access Policy
Trainees will be made aware of the open publishing, dissemination, software and data/reagent sharing policies of the laboratory at the outset and will have to agree to these standards.

Reagents, Software and Tools

Software Usage
Wherever possible, free open source software will be used for data acquisition, analysis and dissemination. Exceptions will be made if necessary, but trainees will be encouraged to use/incorporate/development free tools.
Software Development
If software, scripts or the like are generated they will be released under a permissible open source license such as CC-BY and the license will be attached explicitly to the source code. Scripts and programs will be uploaded to a public revision control database such as GitHub or similar (my GitHub profile is here).
Publishing of Protocols and Scripts
When not present in the published article, detailed step by step protocols, data analysis scripts and other things which cannot fit into either methods and materials sections or supplementary materials will be posted online and linked to the publication’s online presence (post or as a comment on the paper’s website).
Protocol Sharing
Protocols will be made available online in a wiki format in a publicly available location, whether they have been published on or not. Editing will be restricted to laboratory members and collaborators.
Reagent and Tool Sharing
Reagents generated by my group will be shared upon request without condition (aside from potential restrictions placed by other collaborators, funding agencies and the institution). These reagents will be shipped with an explicit statement of free use/sharing/modification. Once a reagent sharing license is generated/identified it will be linked to in this document. This policy includes unpublished reagents and will never require attribution as a condition. If a reagent is obtained from another group and modified, we will offer the modified reagent back to the originator immediately.

Publishing and Data Dissemination

Open Access Journals
I believe that all work should be available to the public to read, evaluate and discuss. I am strongly against the mentality that data/knowledge should be restricted to experts and the like. I will therefore send all papers in which I am corresponding author and have supervised the majority of the work to journals (or their equivalent) which are publicly available. The two major caveats will be for work in which I am a minor (less than 50% effort) collaborator and the primary group leader wants to submit the work elsewhere. This will not exempt any potential major impact publications, no matter how awesome they may be. Delayed open access does not count in this respect.
Open Peer Review
Journals will be selected which publish non-anonymous reviewer comments alongside the articles whenever possible. If this is not done, and if permissible by the publisher and/or reviewers I will re-post the reviewer comments online without any modifications.
Public Forum for Article Discussion
Although I will encourage discussion of articles to occur at the point of publication (for example via the posting of comments directly at the website of the publisher), I will also provide a publicly available summary of every published finding from which I am an author (corresponding or not) and allow commenting at that point too. This discussion post will also link to or contain the reviewer and editor comments where possible. This summary might be a blog post, a facebook post or a google plus post or anything else that might come up in the future. If I am not the primary author or corresponding author I will encourage the first or corresponding author to write the post and link/quote that directly.
All presentations of published data will be posted on an online repository such as Slideshare or something similar. My slideshare profile is here. If unpublished or preliminary data is presented privately and then is later published, then those slides will be presented upon publication. Similar to papers, an online blog post or the like will also accompany that upload. If audio or video of the presentation is available, that will be uploaded as well.
Data Sets
All datasets, once published will be made available in manipulable (preferably non-proprietary) formats for further analysis. Based on the scheme set out by the Linked Data Research Center Laboratory, all data will be provided at level 2 or above.

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