Publishing Group/Thoughts

Perhaps here we can try to formalize/synthesize the thoughts from the two meetings into a format that allows easier extension and improvement. I don't think this structure captures all that we want to say, so please improve it -Sri Kosuri 15:29, 6 Oct 2005 (EDT).

What kinds of information do we want to share?

1. characterization of parts
2. standards of characterization
   • approaches
   • protocols
   • operating conditions
3. ideas about how to engineer biology
   • i.e. idempotent assembly
   • i.e. abstraction hierarchies
4. process of design, decisions, tools, rational (comics?)
   • documentation of why people made the design decisions they did
5. failures
   • to avoid reinventing the wheel
6. critiques, comments, reviews, feedback
7. successful applications
8. societal issues

What features do we want to see in publishing mediums?

1. publishing versions
   • writing up of the same data/ideas for different target audiences
2. publishing collections that can pick up works from other places and push out works to other places (like journals)
3. open access
4. mechanisms for collaboration
   • useful for establishing community standards
   • RFC's (request for comments) to get feedback on proposals
   • wiki - anyone can contribute, establish community consensus on a topic
5. peer review?
   • thumbs up/down rating system
   • open reviews
   • signed reviews
   • author responses/revisions
6. a system that encourages people to share work early (prior to formal publication) rather than wait until their paper is written/accepted for publication
7. New wiki on collaboration established Oct 3, 2005 on wikicities. --Ilya 17:03, 11 Nov 2005 (EST)

Current publishing models

1. Currently the journals most amenable to work in synthetic biology are Nature Molecular Systems Biology and Synthetic and Systems Biology. It is unclear whether these journals are appropriate venues for publishing work related to parts in the Registry. While other journals accept the sort of papers we might want to publish (e.g. Biotechnology and Bioengineering), they are not open-access. NAR might be an option since it is open access.
2. DSpace synthetic biology publishing archive
3. WebCite is an on-demand archiving system for webreferences (cited webpages and websites, or other kinds of Internet-accessible digital objects), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future.

Possible models of moving forward

1. Wiki
   • fixed access?
2. coordination of DSpace and Wiki publishing
3. RFC (request for comment)
4. An Engineering Biology Letters journal has been proposed previously that would serve as a venue for papers describing work like development of new parts, parts characterization, assembly techniques etc. The primary advantage of such a journal is that it might motivate people to carry out and formally report on such work if there was a place where such work could be published. Currently, most biologically relevant journals evaluate submissions on the basis of scientific discovery rather than engineering advances. Without incentive (i.e. publications), it is unclear whether people will be willing to do this type of leg work necessary for parts development.