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| ==Announcement==
| | It was decided at the retreat to set up a new publishing group (John, Julius, Drew and Jason) to look into a new mechanism for publishing pages on OWW. |
| <font color="green">There will be two "synthetic biology" publishing group meetings this week. <br>
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| One during Tuesday lunch, another during Thursday lunch.<br>
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| Attend one or both, as you like (I'll be attending both just to handle organization and take notes).<br></font>
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| '''Each meeting will begin at 12:10p at 68-577 (5th floor tea room) and move to a nearby room. | | ==Announcements== |
| Each meeting will end at 12:50p.'''
| | *'''8.7.06: '''Please see [[OpenWetWare:Information management/a model for novel publishing | recent discussion and ideas since retreat]] |
| | *'''8.7.06: '''Please see [[OpenWetWare:publishing group/Reddit idea| details on the reddit idea]] |
| | *'''10.20.07: ''' [http://materialtransfer.org Materialtransfer.org] launched as a user generated information repository for finding, sharing, and reviewing scientific materials. Self-archive feature allows you to inform the community about your work/materials without losing your rights to publish in journals like Science and JACS. |
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| '''Please add your ideas/questions below that you would like to discuss.'''
| | ==Past Meetings== |
| | *[[Publishing Group/Meeting 10-4-05|10/4/05]] <br> |
| | *[[Publishing Group/Meeting 10-6-05|10/6/05]]<br> |
| | *[[Publishing Group/old discussion items and comments]] |
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| ==Attending== | | ==Refs== |
| #[[Drew_Endy | Drew]]
| | [http://papers.nber.org/papers/W13272 Is peer review in decline?] (study of submissions to economics journals) |
| #[[Barry Canton|BC]]
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| #[[Reshma Shetty | Reshma]]
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| #[[Natalie Kuldell| Natalie]]
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| #[[Austin Che]]
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| #[[Jason Kelly|Jason]]
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| #[[Pam Silver]]
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| #[[Samantha Sutton|Samantha]]
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| #[[Caitlin Conboy|Caitlin]]
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| #[[Julie Norville]]
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| #[[User:Skosuri|Sri Kosuri]]
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| #[[Ty Thomson|Ty]]
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| ==Things to discuss==
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| #Do we need a Synthetic Biology specific journal?
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| #Does the peer review process, as practiced work?
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| #Is peer review needed for engineering research articles?
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| #What features would we like for our papers? Reader comments? Reader Wiki?
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| #How should the structure of a paper be changed to reflect things like, well, the Internets?
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| #What existing journals are the most appropriate/receptive venues for publication of SB work?
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| #How is publishing on SB topics different from any other field?
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| #What are the other (if any) alternate publishing models already out there?
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| #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.
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| #Can we ensure that publishing and access to publications is equally open to all institutions regardless of rank?
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| #<your question/idea>
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| ==Relevant material==
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| *Hal Abelson and John Wilbanks gave interesting talks on [http://mitworld.mit.edu/video/270/ Open Networks and Open Society: The Relationship between Freedom, Law, and Technology].
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| *An [http://www.oecd.org OECD] report on scientific publishing was published a couple of weeks ago and seems especially relevent. Here are links to the [http://www.oecd.org/document/55/0,2340,en_2649_34487_35397879_1_1_1_1,00.htm press release] and [http://www.oecd.org/dataoecd/42/12/35393145.pdf report]
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| ==Meeting notes==
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| Added some notes from the Tuesday meeting for those who could not attend. Please expand. --[[User:Rshetty|Reshma]]
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| #Do we need a Synthetic Biology specific journal?
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| #*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.
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| #Does the peer review process, as practiced work?
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| #*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.
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| #Is peer review needed for engineering research articles?
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| #*See above.
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| #What features would we like for our papers? Reader comments? Reader Wiki?
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| #How should the structure of a paper be changed to reflect things like, well, the Internets?
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| #*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.
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| #What existing journals are the most appropriate/receptive venues for publication of SB work?
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| #*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.
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| While other journals accept the sort of papers we might want to publish (e.g. Biotechnology and Bioengineering or NAR), they are not open-access.
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| #How is publishing on SB topics different from any other field?
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| #*Many of the valuable contributions to be made in synthetic biology are not necessarily driven by scientific discovery but rather engineering-type work.
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| #What are the other (if any) alternate publishing models already out there?
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| #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.
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| #Can we ensure that publishing and access to publications is equally open to all institutions regardless of rank?
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| #*Whatever forum we choose for our work should be online and open access. There is no compelling reason why it should not be.
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| #Additional comments
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| #*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.
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| #*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.
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| ==Discussion==
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| This [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7528374&query_hl=2 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 [[User:Nkuldell | Natalie]])
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| :- 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.--[[User:Bcanton|BC]]
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