Thoughts on publishing - Revision history

Murray: /* Publishing in Controls and Robotics */

2023-09-30T17:06:41Z

Publishing in Controls and Robotics

← Older revision		Revision as of 17:06, 30 September 2023
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	* Most of the journals that we publish in are handled by technical societies (eg, the IEEE Control Systems Society) and the editors, associate editors and reviewers are all volunteers (active researchers in academia, industry or government). It is rare that a paper would not be sent out to review (unless it were clearly wrong, duplicative or trivial). A typical cover letter for a journal paper just says that we are submitting this paper to this journal and lists the authors.		* Most of the journals that we publish in are handled by technical societies (eg, the IEEE Control Systems Society) and the editors, associate editors and reviewers are all volunteers (active researchers in academia, industry or government). It is rare that a paper would not be sent out to review (unless it were clearly wrong, duplicative or trivial). A typical cover letter for a journal paper just says that we are submitting this paper to this journal and lists the authors.

	* Preprints of results are used at every stage. In my group, we typically post submissions to conference and journals on our web page at the time of submission. For conference papers these results are ~~usual~~ work that has occurred in the last 3-6 months => we let people know what we are doing almost at the same time as we are doing it. We typically don't use preprint servers; we just post on our web page. The results will eventually come out in the conference and then the journal, so we don't worry about DOIs for our preprints.		* Preprints of results are used at every stage. In my group, we typically post submissions to conference and journals on our web page at the time of submission. For conference papers these results are usually work that has occurred in the last 3-6 months => we let people know what we are doing almost at the same time as we are doing it. We typically don't use preprint servers; we just post on our web page. The results will eventually come out in the conference and then the journal, so we don't worry about DOIs for our preprints.

	The IEEE has written up some nice [~~http~~://ieeeauthorcenter.ieee.org/~~publish~~-~~with~~-ieee/publishing-ethics/~~publish-original~~-~~research~~/ author guidelines] that summarize their approach. Here's an excerpt:		The IEEE has written up some nice [https://journals.ieeeauthorcenter.ieee.org/become-an-ieee-journal-author/publishing-ethics/ethical-requirements/ author guidelines] that summarize their approach. Here's an excerpt:

	:It is ~~common in technical publishing for material to be presented at various stages of evolution. For example, early ideas may be~~ published in a ~~workshop; more developed work in~~ conference ~~proceedings; and the~~ fully developed ~~study may be published in~~ a journal. ~~However,~~ IEEE ~~guidelines require~~ that ~~authors fully cite their prior work~~. ~~authors must be able to demonstrate signicant advances from prior publications~~.		:IEEE recognizes that technical research is often published first as a conference article with preliminary findings. As those initial findings become fully developed, the conference article can evolve into a journal or magazine article which contains your more developed research and conclusions. IEEE supports this evolutionary publishing process provided that:

			:# Both the conference and journal articles undergo standard peer review.
			:# The journal article contains substantially more technical information than the conference article.
			:# The journal article cites the conference article and clearly indicates how the two articles differ.

	=== Publishing in Synthetic Biology ===		=== Publishing in Synthetic Biology ===

Murray at 17:03, 30 September 2023

2023-09-30T17:03:58Z

← Older revision		Revision as of 17:03, 30 September 2023
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	=== Publishing in Controls and Robotics ===		=== Publishing in Controls and Robotics ===

	Most of my career has been doing work in the area of control systems and robotics. Here is the way that publishing tends to work:		Most of my career has been doing work in the area of control systems and robotics. Here is the way that publishing in those fields tends to work:

	* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very small number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.		* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very small number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.

Murray at 01:13, 23 February 2018

2018-02-23T01:13:59Z

← Older revision		Revision as of 01:13, 23 February 2018
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	* Preprints of results are used at every stage. In my group, we typically post submissions to conference and journals on our web page at the time of submission. For conference papers these results are usual work that has occurred in the last 3-6 months => we let people know what we are doing almost at the same time as we are doing it. We typically don't use preprint servers; we just post on our web page. The results will eventually come out in the conference and then the journal, so we don't worry about DOIs for our preprints.		* Preprints of results are used at every stage. In my group, we typically post submissions to conference and journals on our web page at the time of submission. For conference papers these results are usual work that has occurred in the last 3-6 months => we let people know what we are doing almost at the same time as we are doing it. We typically don't use preprint servers; we just post on our web page. The results will eventually come out in the conference and then the journal, so we don't worry about DOIs for our preprints.

	The IEEE has written up some nice [~~https~~://~~www~~.ieee.org/~~publications_standards~~/~~publications~~/~~authors~~/~~author_guide_interactive.pdf~~ author guidelines] that summarize their approach. Here's an excerpt:		The IEEE has written up some nice [http://ieeeauthorcenter.ieee.org/publish-with-ieee/publishing-ethics/publish-original-research/ author guidelines] that summarize their approach. Here's an excerpt:

	:It is common in technical publishing for material to be presented at various stages of evolution. For example, early ideas may be published in a workshop; more developed work in conference proceedings; and the fully developed study may be published in a journal. However, IEEE guidelines require that authors fully cite their prior work. authors must be able to demonstrate signicant advances from prior publications.		:It is common in technical publishing for material to be presented at various stages of evolution. For example, early ideas may be published in a workshop; more developed work in conference proceedings; and the fully developed study may be published in a journal. However, IEEE guidelines require that authors fully cite their prior work. authors must be able to demonstrate signicant advances from prior publications.

Murray at 14:49, 7 July 2017

2017-07-07T14:49:27Z

← Older revision		Revision as of 14:49, 7 July 2017
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	* [http://www.nature.com/news/beat-it-impact-factor-publishing-elite-turns-against-controversial-metric-1.20224 Beat it, impact factor! Publishing elite turns against controversial metric], Ewen Callaway. ''Nature News'', 08 July 2016.		* [http://www.nature.com/news/beat-it-impact-factor-publishing-elite-turns-against-controversial-metric-1.20224 Beat it, impact factor! Publishing elite turns against controversial metric], Ewen Callaway. ''Nature News'', 08 July 2016.
	* [http://biorxiv.org/content/early/2016/07/05/062109 A simple proposal for the publication of journal citation distributions], V. Lariviere, V. Kiermer, C. J. MacCallum, M. McNutt, M. Patterson, B. Pulverer, S. Swaminathan, S. Taylor, and S. Curry. bioRxiv, 2016.		* [http://biorxiv.org/content/early/2016/07/05/062109 A simple proposal for the publication of journal citation distributions], V. Lariviere, V. Kiermer, C. J. MacCallum, M. McNutt, M. Patterson, B. Pulverer, S. Swaminathan, S. Taylor, and S. Curry. bioRxiv, 2016.

			=== Other useful information ===

			* [https://en.wikipedia.org/wiki/List_of_academic_journals_by_preprint_policy List of preprint policies for journals]

Murray at 06:50, 7 July 2017

2017-07-07T06:50:42Z

← Older revision		Revision as of 06:50, 7 July 2017
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	* When we submit an abstract to a conference, we write a technical report with the results that we are going to present. The title, authors and abstract of the conference submission match the technical report, and the report contains all of the data you would find in a paper. The results are still preliminary and we may not have all of the explanation and controls. We post the report on a web page or (more commonly) on the bioRxiv preprint server at the time of submission (usually).		* When we submit an abstract to a conference, we write a technical report with the results that we are going to present. The title, authors and abstract of the conference submission match the technical report, and the report contains all of the data you would find in a paper. The results are still preliminary and we may not have all of the explanation and controls. We post the report on a web page or (more commonly) on the bioRxiv preprint server at the time of submission (usually).

	* When we submit a paper to a journal, we acknowledge that the results have appeared in preliminary form in one or more preprints. ~~With the possible exception of ''Cell'', all~~ journals we publish in allow preprints and so this is not a problem. We do have to be careful about publishing results that have appeared in a peer-reviewed form (such as a traditional controls conference). Typically we would include those results only in the supplementary materials and that seems to be fine with everyone (and we are upfront about the fact that the results have appeared elsewhere).		* When we submit a paper to a journal, we acknowledge that the results have appeared in preliminary form in one or more preprints. All journals we publish in allow preprints and so this is not a problem. We do have to be careful about publishing results that have appeared in a peer-reviewed form (such as a traditional controls conference). Typically we would include those results only in the supplementary materials and that seems to be fine with everyone (and we are upfront about the fact that the results have appeared elsewhere).

	* The first author on a paper is typically the corresponding author on the paper. This is usually a graduate student or postdoc, and we did get some questions from journals about this in the beginning. It seems OK and generally hasn't been a problem. Senior authors still appear at the end, just without the dagger or whatever annotation is used for the corresponding author.		* The first author on a paper is typically the corresponding author on the paper. This is usually a graduate student or postdoc, and we did get some questions from journals about this in the beginning. It seems OK and generally hasn't been a problem. Senior authors still appear at the end, just without the dagger or whatever annotation is used for the corresponding author.
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	* A: Nope. I’m a fan (and have been publishing this way for 30 years).		* A: Nope. I’m a fan (and have been publishing this way for 30 years).

	: I routinely tell my students that with the possible exception of Cell and its journals, preprints are now embraced by all of the journals that we publish in. I currently discourage my students from publishing in Cell and its journals due to the lack of an explicit policy allowing preprints.
	</blockquote>		</blockquote>

Murray: /* Publishing in Synthetic Biology */

2016-09-13T20:34:06Z

Publishing in Synthetic Biology

← Older revision		Revision as of 20:34, 13 September 2016
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	My two cents:		My two cents:

	* I don’t care about impact factor and would suggest that we not bother with that as a metric. I’ll spare you the long version of the rant, but the considerations should be (a) fit of the journal to the primary contributions of the paper, (b) quality of the review process, (c) speed of the review process (submission → acceptance). Also, we should not submit to any journal that doesn’t allow free distribution of preprints ~~(this only rules out Cell, which doesn’t meet consideration (a), in my opinion)~~.		* I don’t care about impact factor and would suggest that we not bother with that as a metric. I’ll spare you the long version of the rant, but the considerations should be (a) fit of the journal to the primary contributions of the paper, (b) quality of the review process, (c) speed of the review process (submission → acceptance). Also, we should not submit to any journal that doesn’t allow free distribution of preprints.

	* To me, this is a paper whose contributions are related to engineering (how to effectively engineer biological circuits) and not about science (understanding the natural world). Hence, I would suggest submitting to journals that are dedicated to advances in engineering (along with science is OK, but not dominated by science).		* To me, this is a paper whose contributions are related to engineering (how to effectively engineer biological circuits) and not about science (understanding the natural world). Hence, I would suggest submitting to journals that are dedicated to advances in engineering (along with science is OK, but not dominated by science).

Murray: /* Publishing in Synthetic Biology */

2016-09-13T20:32:46Z

Publishing in Synthetic Biology

← Older revision		Revision as of 20:32, 13 September 2016
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	=== Publishing in Synthetic Biology ===		=== Publishing in Synthetic Biology ===

	When I first started publishing in journals that are more science oriented, I was surprised to find that papers were handled very differently. This is particularly true in the biological sciences, where conferences consist mainly of invited talks by PIs, there are no conference papers or preprints, and some groups are very secretive about their results until they are published in journal form (so often presentations at open conferences are results that have already appeared in a journal). The notion of being "scooped" is quite prevalent and there is a lot of emphasis about publishing in "~~glamor~~" journals (high impact factor). Since this doesn't fit the style of the work that we do in my group, I have adopted the following approach to publishing in this environment:		When I first started publishing in journals that are more science oriented, I was surprised to find that papers were handled very differently. This is particularly true in the biological sciences, where conferences consist mainly of invited talks by PIs, there are no conference papers or preprints, and some groups are very secretive about their results until they are published in journal form (so often presentations at open conferences are results that have already appeared in a journal). The notion of being "scooped" is quite prevalent and there is a lot of emphasis about publishing in "glamour" journals (high impact factor). Since this doesn't fit the style of the work that we do in my group, I have adopted the following approach to publishing in this environment:

	* When we submit an abstract to a conference, we write a technical report with the results that we are going to present. The title, authors and abstract of the conference submission match the technical report, and the report contains all of the data you would find in a paper. The results are still preliminary and we may not have all of the explanation and controls. We post the report on a web page or (more commonly) on the bioRxiv preprint server at the time of submission (usually).		* When we submit an abstract to a conference, we write a technical report with the results that we are going to present. The title, authors and abstract of the conference submission match the technical report, and the report contains all of the data you would find in a paper. The results are still preliminary and we may not have all of the explanation and controls. We post the report on a web page or (more commonly) on the bioRxiv preprint server at the time of submission (usually).

Murray: /* Publishing in Controls and Robotics */

2016-09-13T20:31:55Z

Publishing in Controls and Robotics

← Older revision		Revision as of 20:31, 13 September 2016
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	* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very small number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.		* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very small number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.

	* Collections of conference papers are pulled together into journal papers. The results in journal papers have typically appeared in preliminary form in conference papers, but the journal paper has a more complete set of results. Journals are relatively slow to publish: from first submission to final publication as a paper (typically after 1 major review and a second minor revision) might take 1-2 years (but remember that the results are probably available in conference paper well before they are submitted to the journal => people in the field know what everyone is working on years before the final results come out in a journal).		* Collections of conference papers are pulled together into journal papers. The results in journal papers have typically appeared in preliminary form in conference papers, but the journal paper has a more complete set of results. Journals are relatively slow to publish: from first submission to final publication as a paper (typically after 1 major review and a second minor revision) might take 1-2 years (but remember that the results are probably available in conference paper form well before they are submitted to the journal => people in the field know what everyone is working on years before the final results come out in a journal).

	* Most of the journals that we publish in are handled by technical societies (eg, the IEEE Control Systems Society) and the editors, associate editors and reviewers are all volunteers (active researchers in academia, industry or government). It is rare that a paper would not be sent out to review (unless it were clearly wrong, duplicative or trivial). A typical cover letter for a journal paper just says that we are submitting this paper to this journal and lists the authors.		* Most of the journals that we publish in are handled by technical societies (eg, the IEEE Control Systems Society) and the editors, associate editors and reviewers are all volunteers (active researchers in academia, industry or government). It is rare that a paper would not be sent out to review (unless it were clearly wrong, duplicative or trivial). A typical cover letter for a journal paper just says that we are submitting this paper to this journal and lists the authors.

Murray: /* Publishing in Controls and Robotics */

2016-09-13T20:30:09Z

Publishing in Controls and Robotics

← Older revision		Revision as of 20:30, 13 September 2016
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	Most of my career has been doing work in the area of control systems and robotics. Here is the way that publishing tends to work:		Most of my career has been doing work in the area of control systems and robotics. Here is the way that publishing tends to work:

	* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very ~~few~~ number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.		* Graduate students and postdocs write short papers on preliminary results as conference papers. Conference papers are submitted as 6-8 page papers and peer-reviewed to determine what is accepted for presentation. Most talks at conferences are given by graduate students and postdocs and all but a very small number of talks are based on review of submitted papers. At a big conference, there might be 2000 people with 800 papers presented (in 15 parallel sessions, 20 min/talk). Every paper will appear in the proceedings. Papers are submitted about 9 months before the conference, reviews come back after 3-4 months and final versions (addressing the reviewer comments, but not re-reviewed) are due a few months before the conference. Acceptance rates at big conferences are 50-60%, at small (single track) conferences about 20-30%.

	* Collections of conference papers are pulled together into journal papers. The results in journal papers have typically appeared in preliminary form in conference papers, but the journal paper has a more complete set of results. Journals are relatively slow to publish: from first submission to final publication as a paper (typically after 1 major review and a second minor revision) might take 1-2 years (but remember that the results are probably available in conference paper well before they are submitted to the journal => people in the field know what everyone is working on years before the final results come out in a journal).		* Collections of conference papers are pulled together into journal papers. The results in journal papers have typically appeared in preliminary form in conference papers, but the journal paper has a more complete set of results. Journals are relatively slow to publish: from first submission to final publication as a paper (typically after 1 major review and a second minor revision) might take 1-2 years (but remember that the results are probably available in conference paper well before they are submitted to the journal => people in the field know what everyone is working on years before the final results come out in a journal).
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	The IEEE has written up some nice [https://www.ieee.org/publications_standards/publications/authors/author_guide_interactive.pdf author guidelines] that summarize their approach. Here's an excerpt:		The IEEE has written up some nice [https://www.ieee.org/publications_standards/publications/authors/author_guide_interactive.pdf author guidelines] that summarize their approach. Here's an excerpt:

	:It is common in technical publishing for material to be presented at various stages of evolution. For example, early ideas may be published in a workshop; more developed work in conference proceedings; and the fully developed study may be published in a journal. However, IEEE guidelines require that authors fully cite their prior work. authors must be able to demonstrate signicant advances from prior publications.		:It is common in technical publishing for material to be presented at various stages of evolution. For example, early ideas may be published in a workshop; more developed work in conference proceedings; and the fully developed study may be published in a journal. However, IEEE guidelines require that authors fully cite their prior work. authors must be able to demonstrate signicant advances from prior publications.

	=== Publishing in Synthetic Biology ===		=== Publishing in Synthetic Biology ===

Murray: /* Some articles about impact factor (and why you shouldn't use it) */

2016-08-25T17:31:47Z

Some articles about impact factor (and why you shouldn't use it)

← Older revision		Revision as of 17:31, 25 August 2016
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	=== Some articles about impact factor (and why you shouldn't use it) ===		=== Some articles about impact factor (and why you shouldn't use it) ===

	* [http://www.sciencemag.org/content/340/6134/787 Impact Factor Distortions], Bruce Alberts. Science, 340(6134):787		* [http://www.sciencemag.org/content/340/6134/787 Impact Factor Distortions], Bruce Alberts. Science, 340(6134):787, 2013.
	* [http://www.nature.com/news/beat-it-impact-factor-publishing-elite-turns-against-controversial-metric-1.20224 Beat it, impact factor! Publishing elite turns against controversial metric], Ewen Callaway. ''Nature News'', 08 July 2016.		* [http://www.nature.com/news/beat-it-impact-factor-publishing-elite-turns-against-controversial-metric-1.20224 Beat it, impact factor! Publishing elite turns against controversial metric], Ewen Callaway. ''Nature News'', 08 July 2016.
	* [http://biorxiv.org/content/early/2016/07/05/062109 A simple proposal for the publication of journal citation distributions], V. Lariviere, V. Kiermer, C. J. MacCallum, M. McNutt, M. Patterson, B. Pulverer, S. Swaminathan, S. Taylor, and S. Curry. bioRxiv, 2016.		* [http://biorxiv.org/content/early/2016/07/05/062109 A simple proposal for the publication of journal citation distributions], V. Lariviere, V. Kiermer, C. J. MacCallum, M. McNutt, M. Patterson, B. Pulverer, S. Swaminathan, S. Taylor, and S. Curry. bioRxiv, 2016.