Originally posted by marcowanger
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1> Genome Medicine (positive feedback, see wiki for editor's reply)
2> Genome Biology (inquiry sent, 11-23-2011)
3> PLoS Biology (inquiry sent)
4> PLoS Computional Biology (inquiry sent)
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Originally posted by Joann View PostThese are examples of user-developer exchange. What other topics might be included in the expanded article under consideration? Standards development, modification, replacement? (for example the role of Sanger sequencing) Jobs and career advice (i.e. where to do an internship?) Topics in personal genomics (especially relevant to focus on the medical application side)? Personalized trouble shooting on your project by the experts? (how often is the word "help" used) Approaches to experimental design? International database repositories? These also are all important aspects of the forum as a whole.
Perhaps the generation of a consensus topics list could sort these out and help authors manage content within their alloted word count while meeting the topic requirements of a targeted journal--while preserving an accurate representation of the SEQanswers forum.
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user-developer exchanges, and...
These are examples of user-developer exchange. What other topics might be included in the expanded article under consideration? Standards development, modification, replacement? (for example the role of Sanger sequencing) Jobs and career advice (i.e. where to do an internship?) Topics in personal genomics (especially relevant to focus on the medical application side)? Personalized trouble shooting on your project by the experts? (how often is the word "help" used) Approaches to experimental design? International database repositories? These also are all important aspects of the forum as a whole.
Perhaps the generation of a consensus topics list could sort these out and help authors manage content within their alloted word count while meeting the topic requirements of a targeted journal--while preserving an accurate representation of the SEQanswers forum.
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Originally posted by genericforms View PostThanks. This is great!
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Originally posted by marcowanger View PostHere it is "Success case studies (word)"
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Originally posted by marcowanger View PostPreviously I have collected a not-so-exhaustive list of success cases in SEQanswers (that should be what Joann talks about). Those examples, IHO, are how people leverage collective intelligence to improve their works/tools.
I will go find it ...it is in my laptop..somewhere...
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Originally posted by genericforms View PostI agree. SeqAnswers is a success story and although we originally wanted to put together a letter in Science/Nature that simply advertised the existence of the forum, with our new target journals and article format, the focus should change slightly towards an argument for open science, collaboration, etc.
And that is how our draft currently reads. It is coming along nicely.
I will go find it ...it is in my laptop..somewhere...
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Originally posted by genericforms View PostYes. We have discussed the title enough! There are some good title suggestions on the Wiki page but now we need to advance the text. Marco says we need 800 to 3000 words. I would say if we assembled a brief commentary of about 1500 words and two figures from Rob, we would have a good document to submit.
We will also need a brief abstract and we can then submit. All of this needs to be assembled in a single document so as soon as everyone feels comfortable, we should migrate back to GDoc or something like that since eventually we will produce a document file anyways that gets submitted.
2> 800-3000 words is the impression I got from Genome Bio/Med journal correspondence type paper. I do agree 1500 word with 2 figures is reasonable enough.
3> Let's finalize the content before migrating to the Gdoc.
4> We still need robs to remove the raw data points in figure 2
5> good work so far. We need to concentrate on the main text now.
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Originally posted by ulz_peter View PostI 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?
We will also need a brief abstract and we can then submit. All of this needs to be assembled in a single document so as soon as everyone feels comfortable, we should migrate back to GDoc or something like that since eventually we will produce a document file anyways that gets submitted.
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Originally posted by marcowanger View PostSure.
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).
And that is how our draft currently reads. It is coming along nicely.
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"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.
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Originally posted by Joann View Post"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.
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.
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"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.
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Originally posted by ulz_peter View PostI 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?
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).
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