[ulz_peter]

I will contact Genome Medicine tomorrow. Can someone else take care of the other journal suggestions? I think from the thread people suggested:

Genome Biology
PLOS Biology
PLOS Computional Biology

Were there other journals I might have missed? Also we will obviously need to act quickly with respect to finalizing the authors, title, and content if we are pre-approved...

I could write an E-mail to GenomeBiology, although I don't know anyone there, but it won't hurt, right?. Genericforms: you could send me the E-mail you've sent via PM, just to see what you mentioned?

[marcowanger]

I could write an E-mail to GenomeBiology, although I don't know anyone there, but it won't hurt, right?. Genericforms: you could send me the E-mail you've sent via PM, just to see what you mentioned?

Would be nice to post the pre-inquiry email here before sending, so everyone know ;-)

[adaptivegenome]

Everyone,

Here is the response I got:

"In principle, we are interested in the manuscript you describe and we
think it might be suitable as a Correspondence article, although we
would need to see the full manuscript before making a decision. For this
manuscript to be considered by Genome Medicine, it would need to be
clear that it contains information that is not included in the recently
published Nucleic Acids Research issue and that it is applicable and
relevant to medical/clinical researchers as well as basic scientists.

Correspondence articles are open access, peer-reviewed articles that
include brief reports of particular interest to the community
(http://genomemedicine.com/authors/in...correspondence). To
submit the article, please go to http://genomemedicine.com/manuscript."

So we have two things to address:
1. Is the paper different than the NAR paper?

2. We need to clarify (if we publish in Genome Medicine) how this resources helps basic scientists as well as those that are interested in medical/clinical research.

I think these are both easy tasks. Question is: How do you want to proceed? We should finalize as soon as possible.

[marcowanger]

Everyone,

Here is the response I got:

"In principle, we are interested in the manuscript you describe and we
think it might be suitable as a Correspondence article, although we
would need to see the full manuscript before making a decision. For this
manuscript to be considered by Genome Medicine, it would need to be
clear that it contains information that is not included in the recently
published Nucleic Acids Research issue and that it is applicable and
relevant to medical/clinical researchers as well as basic scientists.

Correspondence articles are open access, peer-reviewed articles that
include brief reports of particular interest to the community
(http://genomemedicine.com/authors/in...correspondence). To
submit the article, please go to http://genomemedicine.com/manuscript."

So we have two things to address:
1. Is the paper different than the NAR paper?

2. We need to clarify (if we publish in Genome Medicine) how this resources helps basic scientists as well as those that are interested in medical/clinical research.

I think these are both easy tasks.

For 1>, I am not sure how should we argue. But I would say the NAR paper is MORE about the wiki (well, the title is The SEQanswers wiki). That was why I stressed not to copy the writings in the NAR paper. Before the actual publication, I have put the draft of the paragraph about SEQanswers into the wiki.

Briefly, in the wiki we described why SEQanswers is a credible community that lead to the wiki. In contrast, the correspondence/letter we are writing here want to say that SEQanswers is more than a scientific forum alone. SEQanswers, being a technical NGS focusd forum....served bioinformaticians.....

IS an example and advocate of OPEN SCIENCE...We want to focus on the IMPLICATION of SEQanswers rather than the technical stuff of SEQanswers

[marcowanger]

Everyone,

Here is the response I got:

"In principle, we are interested in the manuscript you describe and we
think it might be suitable as a Correspondence article, although we
would need to see the full manuscript before making a decision. For this
manuscript to be considered by Genome Medicine, it would need to be
clear that it contains information that is not included in the recently
published Nucleic Acids Research issue and that it is applicable and
relevant to medical/clinical researchers as well as basic scientists.

Correspondence articles are open access, peer-reviewed articles that
include brief reports of particular interest to the community
(http://genomemedicine.com/authors/in...correspondence). To
submit the article, please go to http://genomemedicine.com/manuscript."

So we have two things to address:
1. Is the paper different than the NAR paper?

2. We need to clarify (if we publish in Genome Medicine) how this resources helps basic scientists as well as those that are interested in medical/clinical research.

I think these are both easy tasks. Question is: How do you want to proceed? We should finalize as soon as possible.

Genericforms, may you post your pre-inquiry email here so that we can send email with comparable content to other editors?

[adaptivegenome]

Genericforms, may you post your pre-inquiry email here so that we can send email with comparable content to other editors?

Sent to you in a PM.

[adaptivegenome]

For 1>, I am not sure how should we argue. But I would say the NAR paper is MORE about the wiki (well, the title is The SEQanswers wiki). That was why I stressed not to copy the writings in the NAR paper. Before the actual publication, I have put the draft of the paragraph about SEQanswers into the wiki.

Briefly, in the wiki we described why SEQanswers is a credible community that lead to the wiki. In contrast, the correspondence/letter we are writing here want to say that SEQanswers is more than a scientific forum alone. SEQanswers, being a technical NGS focusd forum....served bioinformaticians.....

IS an example and advocate of OPEN SCIENCE...We want to focus on the IMPLICATION of SEQanswers rather than the technical stuff of SEQanswers

Yes this absolutely correct and it is the angle I took in the letter to the editor. I argued this a fundamentally different way of doing collaborative science.

[marcowanger]

Regarding how to proceed

[My opinion]

Consider
(1) reader's base
(2) impact to the field (impact factor?!?)
(3) Open Access journal? Is kind of weird to publish a OPEN SCIENCE forum in a closed source journal
(4) difficulty to publish in that journal.

[/My opinion]

[action]
send inquiry email to all editors. See how they say. And make the rational choices given all the choices.
[/action]

Everyone,

Here is the response I got:

"In principle, we are interested in the manuscript you describe and we
think it might be suitable as a Correspondence article, although we
would need to see the full manuscript before making a decision. For this
manuscript to be considered by Genome Medicine, it would need to be
clear that it contains information that is not included in the recently
published Nucleic Acids Research issue and that it is applicable and
relevant to medical/clinical researchers as well as basic scientists.

Correspondence articles are open access, peer-reviewed articles that
include brief reports of particular interest to the community
(http://genomemedicine.com/authors/in...correspondence). To
submit the article, please go to http://genomemedicine.com/manuscript."

So we have two things to address:
1. Is the paper different than the NAR paper?

2. We need to clarify (if we publish in Genome Medicine) how this resources helps basic scientists as well as those that are interested in medical/clinical research.

I think these are both easy tasks. Question is: How do you want to proceed? We should finalize as soon as possible.

[adaptivegenome]

Sounds good. Sometimes editors are not as quick to reply as the one I contacted. Go ahead and email other editors but we should set a final date at which we do not wait any further for replies and make a choice assuming there is one.

In the meantime I think we should aim to wrap the paper up next week if possible.

[marcowanger]

I will help contact the rest.

PLoS Biology seems to be a good choice because they specifically has a article type called "Community Page" !

But they need abstract, cover letter , etc.. for pre-submission inquiry

[adaptivegenome]

I will help contact the rest.

PLoS Biology seems to be a good choice because they specifically has a article type called "Community Page" !

But they need abstract, cover letter , etc.. for pre-submission inquiry

Let's just finish the paper so we have all these things and a final author list and paper title. Then we can delay submission for a couple days while we inquire about submission. But really if they need all that, we might as well just submit. Turn around time at PLOS is quick.

I still vote for Genome Medicine.

[marcowanger]

Current status:

1> Genome Medicien (positive feedback, see wiki for editor's reply)
2> Genome Biology (inquiry sent)
3> PLoS Biology (to be done)
4> PLoS Computional Biology (to be done)

[marcowanger]

Let's just finish the paper so we have all these things and a final author list and paper title. Then we can delay submission for a couple days while we inquire about submission. But really if they need all that, we might as well just submit. Turn around time at PLOS is quick.

I still vote for Genome Medicine.

That's great. We can do these in parallel. Author list is pretty obvious now. Paper's title is emerging. Figures are ready (how about the raw dots in fig 2?). Texts are almost done, we have to go nth pass text polishing again. Need to convey the right message.

[ulz_peter]

Great stuff going on here...
Another question: How do we cover the publication fees (as far as I've seen it, it would be 2900$ for the PLoS journals and $2490 for the Genome* journals)?

And how do we select the title?
My vote goes for Joann's title:

SEQanswers, Reading Biological Sequences as a Community since 2007.

[marcowanger]

Great stuff going on here...
Another question: How do we cover the publication fees (as far as I've seen it, it would be 2900$ for the PLoS journals and $2490 for the Genome* journals)?

And how do we select the title?
My vote goes for Joann's title:

SEQanswers, Reading Biological Sequences as a Community since 2007.

As genericforms has mentioned, "Reading" is too generic.

I would in favor in replacing "reading" with "Collective Intelligence in decoding", so.

"SEQanswers, Collective Intelligence in Decoding Biological Sequences since 2007"