[adaptivegenome]

Agree with genericforms: great title!!

Maybe we can work a discussion of the title into the paper?

[ulz_peter]

Agree with genericforms: great title!!

[adaptivegenome]

Hi genericforms,
The title is strictly data based, upon some top word counts from the forum. As a generalist, I like to promote wider scientific exposure. Also, I am wanting to see exactly how many times the question "What's a paired-end read?" gets posted on the forum by a newbie.

Clever title then!

[Joann]

Hi genericforms,
The title is strictly data based, upon some top word counts from the forum. As a generalist, I like to promote wider scientific exposure. Also, I am wanting to see exactly how many times the question "What's a paired-end read?" gets posted on the forum by a newbie.

[adaptivegenome]

Hi all,

For the section on implications--I could shorten it to:

"As the accelerated flow of technology development has dwarfted traditional peer reviewed information sharing, the computationally-abled HTS community has successfully connected itself by means of the electronic scientific forum, SEQanswers, since 2007."

The wonderful word data analysis give rise to a possible title:

"SeqAnswers, Reading Biological Sequences as a Community since 2007."

And I would like to see the letter in a general science journal such as Science because of its importance. Please submit and ask in the cover letter to waive the existing format.

I don't think that our paper will work in Science/Nature. But that is just my opinion. In addition to Genome Biology or Genome Medicine we could shoot for PLOS Biology which is both highly ranked and also widely read (not as much as Nature... but they could be sympathetic to our cause as they have obviously pushed for open science, etc.)

I agree with Marco we should simply send off presubmission inquiries to see who is interested. I would be willing to contact Genome Medicine if there is interest from everyone as I know someone people there...

BTW: Joann, I like that title. We might try for something a little more aggressive than "reading"... for example "decoding" or "interpreting", but it is a great title.

[adaptivegenome]

So my choice is for Genome Medicine or Genome Biology. You didn't state the limitations for publishing in one of those journals. Are there any regarding word count or number of authors?

Neither journal restricts authors and they are both open access journals so there would be a fee (depending on who submits the manuscript; and also this fee can be waived in some cases). An Opinion article would be 1500-3000 words which I think fits nicely for our topic. I would go for a shorter length (closer to 1500) and then go for more figures; particularly the two figures Rob came up with.

There are some other formats we could also shoot for, such as "Method" or "Database"; however given that the draft is more focused on showcasing a new way of doing science, I would think an "Opinion" would be a great format. A traditional "Review" format would be too long and I think ill-suited for our goals.

[Joann]

editing suggestions, text, title, cover letter

Hi all,

For the section on implications--I could shorten it to:

"As the accelerated flow of technology development has dwarfted traditional peer reviewed information sharing, the computationally-abled HTS community has successfully connected itself by means of the electronic scientific forum, SEQanswers, since 2007."

The wonderful word data analysis give rise to a possible title:

"SeqAnswers, Reading Biological Sequences as a Community since 2007."

And I would like to see the letter in a general science journal such as Science because of its importance. Please submit and ask in the cover letter to waive the existing format.

[ulz_peter]

So there is an article in Nature about community science:

Technology: The inspiration exchange

Chris Lintott

Nature, 478, 320–321 (20 October 2011) doi:10.1038/478320a

Published online
19 October 2011

Which is not too long ago, but there is the 3-author limit on the correspondence and I guess the letter doesn't really fit in the perspectives part. I'm looking for something similar in Science...

[marcowanger]

What do you think Marco?

I consider possibility.


original goal (1):
It seems either Nature / Science is hard. Unless we find some articles there that discuss community science. Then we can refer to that article and reply with what we have written.

If in case we find none, then (2):

I do not have personal preference. But of course, the wider the reader's base, the better. I think Genome Biology, Genome Medicine, PloS CompBio are both good choices.

Just leave the format or words limit alone first.

I suggest emailing the editors pre-inquiry emails.

[ulz_peter]

What do you think Marco?

[marcowanger]

Invited ECO via PM for his opinion on this.

Dear Eric,

Approaching the final phase of preparation to publish SEQanswers, we need your opinion in choosing the appropriate journal.

Would you please leave your comment in http://seqanswers.com/forums/showthr...7405#post57405

Thanks.

With regards,
Marco

[ulz_peter]

it seems that the Science commentary letter doesn't really fit for our problem...

Two things come to my mind: Do we want to adress the people who might cite SEQanswers because they use it or do we want to inform people who might have no idea what SEQanswers is about, that there is a place to exchange questions, ideas, experiments, etc. regardings HTS?

In the first case it doesn't really matter where we are trying to put it (regarding the possible readers) as it will be found, however if we would like to have people have a look at it, which are previously uninformed we should pick a Biology/medicine journal...

I personally would prefer the latter...

So my choice is for Genome Medicine or Genome Biology. You didn't state the limitations for publishing in one of those journals. Are there any regarding word count or number of authors?

[adaptivegenome]

I think that Genome Medicine and Genome Biology are great choices. PLOS CompBio is highly ranked but probably not a good target unless we focus the article on the informatics aspect to genomics. I think I already voted in favor of Genome Medicine...

And this is not necessarily a bad thing to do. Just commenting here. Informatics is definitely one of the primary discussion points on the board.

[marcowanger]

I think Genome Biology is suitable too

Correspondence articles :

Genome Biology publishes Correspondence articles on all aspects of political, scientific, and medical issues relating to genomic, post-genomic and genome-scale analyses, as well as to molecular, cellular, organismal or population biology studied from a genomic perspective.

Correspondence items discuss material published in Genome Biology or issues of general interest to the readership. They may be edited for clarity or length. Correspondence are short, freely available, peer-reviewed items of correspondence. They should describe material of exceptional interest to the broad readership of Genome Biology and include data, guidelines, or policies for which free availability is a key consideration. To contribute, contact the editors.

or Commentary Editorial

The second form is more editorial in nature and covers an aspect of an issue that is relevant to the journal's scope. Examples of this type of Commentary - Editorial could be a discussion of the impact of new technology on research and treatment, or a discussion of changes in peer review or grant application procedures and their effect on research. By their nature, the second form of Commentary - Editorial articles is less frequent.

[marcowanger]

Hi all again,

Current initial effort is to publish SEQanswers in the form of letter to Science / Nature.

Science
Commentary Perspectives:

We need to submit inquiry first. Ask (1) if interested and (2) more than 2 authors

Perspectives (up to 1000 words plus 1 figure) highlight recent exciting research, but do not primarily discuss the author's own work. They may provide context for the findings within a field or explain potential interdisciplinary significance. Perspectives commenting on papers in Science should add a dimension to the research and not merely be a summary of the experiments done in the paper. Although many of the Perspectives that comment on research published in Science are solicited, we welcome inquiries regarding new advances and fresh insights. As these are meant to express a personal viewpoint, with rare exceptions, Perspectives should have no more than two authors

Commentary Letters:
Any recent material about scientific community in Science?

Letters (up to 300 words) discuss material published in Science in the last 3 months or issues of general interest. Letters should be submitted online (www.submit2science.org). Letters are subject to editing for clarity and space. E-letters are online-only, 400-word contributions for rapid, timely discussion.

Nature:

Correspondence:

These items are 'letters to the Editor': short comments on topical issues of public and political interest, anecdotal material......A Correspondence is usually signed by no more than three authors; this is because Correspondence is a forum for readers' reactions, not for statements by organizations or groups of individuals.

Perspective:

Not sure how to submit.

Perspective articles are intended to provide a forum for authors to discuss models and ideas from a personal viewpoint. They are more forward looking and/or speculative than Reviews and may take a narrower field of view. They may be opinionated but should remain balanced and are intended to stimulate discussion and new experimental approaches.

Perspectives follow the same formatting guidelines as Reviews. Both are peer-reviewed and edited substantially by Nature's editors in consultation with the author.

There are some other possibilities, including PloS Comp Bio and genericforms suggested BMC Genome Medicine

PLoS Comp Bio: perspective

Perspectives in PLoS Computational Biology typically reflect an author's viewpoint on a particular development in science and how, based on current knowledge of the field and the progress in it, this development evidences or can lead to change in how science is conducted or interpreted. Perspectives are intended to be more prospective than retrospective but require sufficient background to place the points made in context. Perspectives are intended to invite debate and further comment as appropriate. The length is ideally around 2000 and limited to 2500 words. Suggestions for topics may be forwarded to ploscompbiol [at] plos.org and are usually handled by the Editor-in-Chief.

BMC Genome Medicine: Opinion / Correspondence

Opinion:

opinion articles are to provide systematic and substantial coverage of mature or emerging topics as well as a discussion of possibly controversial views, different models and theories in the field

Correspondence:

Correspondence items discuss material published in Genome Medicine or issues of exceptional interest to the broad readership of the journal. They are short, freely available, peer-reviewed articles and include data, guidelines, or policies for which free availability is a key consideration

What do you think?