Publishing Group: Difference between revisions
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==Announcement== | |||
<font color="green">There will be two "synthetic biology" publishing group meetings this week. <br> | <font color="green">There will be two "synthetic biology" publishing group meetings this week. <br> | ||
One during Tuesday lunch, another during Thursday lunch.<br> | One during Tuesday lunch, another during Thursday lunch.<br> | ||
Attend one or both, as you like (I'll be attending both just to handle organization and take notes).<br></font> | Attend one or both, as you like (I'll be attending both just to handle organization and take notes).<br></font> | ||
'''Each meeting will begin at 12:10p at 68-577 (5th floor tea room) and move to a nearby room. | '''Each meeting will begin at 12:10p at 68-577 (5th floor tea room) and move to a nearby room. | ||
Each meeting will end at 12:50p.''' | Each meeting will end at 12:50p.''' | ||
'''Please add your ideas/questions below that you would like to discuss.''' | '''Please add your ideas/questions below that you would like to discuss.''' | ||
==Attending== | |||
Attending | |||
#[[Drew_Endy | Drew]] | #[[Drew_Endy | Drew]] | ||
#[[Barry Canton|BC]] | #[[Barry Canton|BC]] | ||
| Line 25: | Line 23: | ||
#[[Ty Thomson|Ty]] | #[[Ty Thomson|Ty]] | ||
Things to discuss | ==Things to discuss== | ||
#Do we need a Synthetic Biology specific journal? | #Do we need a Synthetic Biology specific journal? | ||
#Does the peer review process, as practiced work? | #Does the peer review process, as practiced work? | ||
| Line 38: | Line 36: | ||
#<your question/idea> | #<your question/idea> | ||
Relevant material | ==Relevant material== | ||
*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]. | *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]. | ||
*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] | |||
==Meeting notes== | |||
Added some notes from the Tuesday meeting for those who could not attend. Please expand. --[[User:Rshetty|Reshma]] | |||
#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. | |||
#Does the peer review process, as practiced work? | |||
#*The peer review process is critical for those seeking academic recognition of their contributions. | |||
#Is peer review needed for engineering research articles? | |||
#*See above. | |||
#What features would we like for our papers? Reader comments? Reader Wiki? | |||
#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. | |||
#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. | |||
#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. | |||
#What are the other (if any) alternate publishing models already out there? | |||
#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. | |||
#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. | |||
#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. | |||
==Discussion== | |||
The following paper [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7528374&query_hl=2]] | The following paper [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=7528374&query_hl=2]] | ||
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.... | 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]]) | ||
:- 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]] | :- 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]] | ||
Revision as of 16:53, 4 October 2005
Announcement
There will be two "synthetic biology" publishing group meetings this week.
One during Tuesday lunch, another during Thursday lunch.
Attend one or both, as you like (I'll be attending both just to handle organization and take notes).
Each meeting will begin at 12:10p at 68-577 (5th floor tea room) and move to a nearby room. Each meeting will end at 12:50p.
Please add your ideas/questions below that you would like to discuss.
Attending
Things to discuss
- Do we need a Synthetic Biology specific journal?
- Does the peer review process, as practiced work?
- Is peer review needed for engineering research articles?
- What features would we like for our papers? Reader comments? Reader Wiki?
- How should the structure of a paper be changed to reflect things like, well, the Internets?
- What existing journals are the most appropriate/receptive venues for publication of SB work?
- How is publishing on SB topics different from any other field?
- What are the other (if any) alternate publishing models already out there?
- 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.
- Can we ensure that publishing and access to publications is equally open to all institutions regardless of rank?
- <your question/idea>
Relevant material
- Hal Abelson and John Wilbanks gave interesting talks on Open Networks and Open Society: The Relationship between Freedom, Law, and Technology.
- An OECD report on scientific publishing was published a couple of weeks ago and seems especially relevent. Here are links to the press release and report
Meeting notes
Added some notes from the Tuesday meeting for those who could not attend. Please expand. --Reshma
- 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.
- Does the peer review process, as practiced work?
- The peer review process is critical for those seeking academic recognition of their contributions.
- Is peer review needed for engineering research articles?
- See above.
- What features would we like for our papers? Reader comments? Reader Wiki?
- 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.
- 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.
- 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.
- What are the other (if any) alternate publishing models already out there?
- 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.
- 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.
- 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.
Discussion
The following paper [[1]] 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
