Publishing Group/Meeting 10-4-05

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Time: 12p-1p Place: 68-580 Date: 10.4.05


  1. Drew
  2. BC
  3. Reshma
  4. Natalie
  5. Austin Che
  6. Jason
  7. Caitlin
  8. Julie Norville
  9. Sri Kosuri
  10. Ty
  11. Tom Knight
  12. Gerry Sussman


Added some notes from the Tuesday meeting for those who could not attend. Please expand. --Reshma

It seemed like there were two main areas of discussion (that aren't exactly mutually exclusive):

  1. What sort of publishing/reward structure makes sense for Synthetic Biology?
  2. What do we want to see out of a modern journal in general?

I grouped the discussion topics into these two areas (though some could fit in both), I think we mostly talked about the first area in the first meeting. Perhaps the second meeting should focus on the second area (this may also be more relevant for the conference call on Monday). --Jason

Synthetic Biology Publishing/Reward Structure

  1. Do we need a Synthetic Biology specific journal?
    • 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.
  2. What existing journals are the most appropriate/receptive venues for publication of SB work?
    • 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.
  3. How is publishing on SB topics different from any other field?
    • Many of the valuable contributions to be made in synthetic biology are not necessarily driven by scientific discovery but rather engineering-type work. There may be some value in examining the publication system and the reward structure in engineering fields as an alternative model to the biology field. See additional comments.
  4. Additional comments
    • It was pointed out that traditionally in computer science, conferences and the peer-reviewed proceedings associated with those conferences are usually more important than journal articles themselves. Since synthetic biology is relatively new, we could consider fostering a different type of reward structure. For instance, perhaps some recognition is given for being the original author of Registry parts.
    • It is not clear that a new journal is really needed. Perhaps existing journals would be receptive to publishing these kinds of work. One experiment we could try is writing up some of the work we've done and examine what form it takes and perhaps even see how our attempts to publish it goes.

Modern Scientific Information Dissemination

  1. Does the peer review process, as practiced work?
    • The peer review process is critical for two reasons. Firstly, it ensures that published content is of a consistently high standard. Secondly, to gain academic recognition contributions must be peer reviewed.
  2. Is peer review needed for engineering research articles?
    • See above.
  3. What features would we like for our papers? Reader comments? Reader Wiki?
  4. How should the structure of a paper be changed to reflect things like, well, the Internets?
    • There does not seem to be any reason why the journal should not have an online format. However, some care should be given to ensure that the work is preserved over time. Additionally, there is no real need to have a regular publication schedule. Papers can be published as they are accepted.
  5. What are the other (if any) alternate publishing models already out there?
  6. Non-synthetic biology improvement:Author IDs or URIs or something. Noticed this while trying to set up myNCBI searches for people with more common names, what a pain. I'm changing my name to xyuitk.
  7. Can we ensure that publishing and access to publications is equally open to all institutions regardless of rank?
    • Whatever forum we choose for our work should be online and open access. There is no compelling reason why it should not be.


This paper was published in Nucleic Acids Research in 1994. How different is this publication from the sort that was being discussed at the Tuesday lunch meeting? In a "B.E.Letters" model for publishing parts, would each author be independently credited for each of the ShineDalgarno/ATG spacings? That looks like 20 or more publications from this one.... (from Natalie)

- I think that since each of these parts is just a member of a part family, a publication might describe the family and the range of performance within that family rather than each part individually. One could envisage that "family characterization" will be the norm anyway since engineers will need access to a range of parts with similar function but different performance characteristics to suit different system designs.--BC
- That sounds like a valuable publication for lots of folks, even -- Natalie