[adaptivegenome]

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)?

I would be willing to offset this if the journal does not.

[adaptivegenome]

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"

I am not a fan of putting dates into a title. Would everyone be okay with removing the "since 2007" part? I really like the title but it would optimal to make the paper title sounds less like an advertisement and more like a statement or conclusion.

Suppose:

"SEQanswers: Leveraging collective intelligence to decode biological sequences."

I envision the title would summarize our argument in a single sentence.

Or simply:

"Leveraging collective intelligence to decode genomic data."

These titles I think would help attract a broader audience and sound more formal in tone.

[andreas.sjodin]

I think "SEQanswers: Leveraging collective intelligence to decode biological sequences." is a nice title.

I would recommend to go for Genome Biology or PloS Biology. SEQanswers is widely used outside the medical field (plant sicence etc.) so I am worried that Genome Medicine has too narrow audience.

[Joann]

Sounds nice, but...

Title needs to be accurate and ring true, for my taste. "Read" is one of the terms used most often by the many experts who have posted regularly on the forum over the years. Clearly validated by genericforms' word counts. It is one of the terms emerging that specifically characterizes the field.
Just imagine if you will, "Short decode archive".


"As genericforms has mentioned, "Reading" is too generic." Not true. (see above) It is used as a new verb generated from the root word, read (see above).

As far as sounding like an advert--really, how likely in a scholarly journal? The factual nature of a title can extend well beyond the reach of any statement limit or aggrandized editorialized conclusion. Application of formality does not = solid/established science.

Please keep it factual and inclusive of any and every aspect of the extant uses of the technology. It's not enough to hit just parts of the field.

[adaptivegenome]

Title needs to be accurate and ring true, for my taste. "Read" is one of the terms used most often by the many experts who have posted regularly on the forum over the years. Clearly validated by genericforms' word counts. It is one of the terms emerging that specifically characterizes the field.
Just imagine if you will, "Short decode archive".


"As genericforms has mentioned, "Reading" is too generic." Not true. (see above) It is used as a new verb generated from the root word, read (see above).

As far as sounding like an advert--really, how likely in a scholarly journal? The factual nature of a title can extend well beyond the reach of any statement limit or aggrandized editorialized conclusion. Application of formality does not = solid/established science.

Please keep it factual and inclusive of any and every aspect of the extant uses of the technology. It's not enough to hit just parts of the field.

Your comments are noted however my analysis was not sufficient to solely base a title on and we have been warned that we need to distinguish ourselves from the NAR paper.

Our paper is not about word usage or even about the current topics of the forum. Its not about the Wiki or site at all, really. Our paper is about the fundamentally different approach to advancing and sharing science. And SeqAnswers is a case study in this new approach.

Therefore, while I do agree with you, to be true to the content of the paper we are drafting, I think the revised titles are better one-sentence summaries.

[Joann]

different

Our paper is about the fundamentally different approach to advancing and sharing science. And SeqAnswers is a case study in this new approach.

So far, the goal of this forum project has been simply to create a brief letter attempting to describe/summarize the forum as it has existed over the last 4 years, especially since it has given rise to the WIKI as a separate entity and has (in the manner of many databases over the years both extant and defunct) recently resulted in a brief, format driven description in the yearly NAR special issue. Hopefully this forum letter is to serve as the formal citation title for future articles wishing to reference the forum-based knowledge (outside of the WIKI), and also introduce the forum itself to a larger scientific audience.

While SEQanswers could be the subject of a case study about a fundamentally different approach to advancing and sharing science, this letter is an insufficient vehicle to represent a case study of it. Elaborating a case study is a much more detailed undertaking and would involve significant expansion of many topics only touched upon during our preliminary discussions over the letter.

[adaptivegenome]

So far, the goal of this forum project has been simply to create a brief letter attempting to describe/summarize the forum as it has existed over the last 4 years, especially since it has given rise to the WIKI as a separate entity and has (in the manner of many databases over the years both extant and defunct) recently resulted in a brief, format driven description in the yearly NAR special issue.

So if the above is your goal, I personally (and it is just my opinion) think that the revised titles are better. And I think the one that andreas.sjodin specifically picked (which is a variant of marco's suggestion): "SEQanswers: Leveraging collective intelligence to decode biological sequences." is my personal favorite. I think it is the best one-sentence summary of the forum.

Anyways, let's just get everyone's input and go from there. I think all these titles are nice.

We need to finalize a title, authors, abstract, etc. because PLOS journals do ask for a virtually complete submission (everything minus the actual text) before they will consider a presubmission inquiry.

[Joann]

Summary in letter, not title.

Again, I would caution that the summary--in the name of all SEQanswers forum participants--
is provided by the letter content, not any particular title. The job of the title should be to truly represent the actual forum, not editorialize, in a letter
signable by any member participant who wishes to do so.

Leveraging collective intellegence...can you even find that phrase on the forum...
is the title of a full article that might be written by a group of authors with a particular viewpoint. As such they would be responsible for founding their perspectives with concrete examples taken from the forum records. For example, who is leveraging what collective intelligence for what specific purpose or project. It will take many pages to answer this, not a title claiming it or the text of a letter.

[adaptivegenome]

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)

Marco,

Have you heard back from Genome Biology? Or is Genome Medicine our only response so far?

[marcowanger]

Marco,

Have you heard back from Genome Biology? Or is Genome Medicine our only response so far?

Not yet. No matter what. The correspondence has to be lengthen to 800-3000 words, which should not be difficult.

[ulz_peter]

Leveraging collective intellegence...can you even find that phrase on the forum...

I don't quite see why these words have to appear in the forum for being able to use them in the title. Anyways, I agree that the word "reading" might lead to a wrong perception of the article, as (at least most of us here) we are analyzing the data beyond mere reading.

Do you guys think we should start expanding the article already?

[marcowanger]

I don't quite see why these words have to appear in the forum for being able to use them in the title. Anyways, I agree that the word "reading" might lead to a wrong perception of the article, as (at least most of us here) we are analyzing the data beyond mere reading.

Do you guys think we should start expanding the article already?

Sure.

Keypoint: Write about Open Science, collaboration, how collective intelligence work. Joann is right, we need to demonstrate some cases for that. Please read the BioStar's paper to see how they describe the success case. We can learn from them (how to write).

[Joann]

"most of us here) we are analyzing the data beyond mere reading".

Yet all do work that starts from the basic unit, which is the "read". This is a key feature of high through put sequencing and its analyses. And unmistakably demonstrated from a whole analysis of the posts on this forum.

[marcowanger]

"most of us here) we are analyzing the data beyond mere reading".

Yet all do work that starts from the basic unit, which is the "read". This is a key feature of high through put sequencing and its analyses. And unmistakably demonstrated from a whole analysis of the posts on this forum.

sure, the "read" is the fundamental unit. Remember why the word "read" appear in the tagcloud is because it's frequently used. Usually in form of sequencing reads, how many reads mapped, unmapped reads, etc.

If it's used in the title "Reading the genome", then the word "read" is used in another context, which is not the original meaning used in the forum.

[Joann]

"Reading the genome" it is true, implies much more annotation past the initial raw dataset, which arrives in the form of reads--whether genomic or RNA, etc. Furthermore, there is much technical effort focused in this forum, and rightfully so, on the quality of the initial raw reads. One of the benefits of this forum is exposure to the many facets of the technology currently in the hands of many different investigators.