Tweet
Originally posted by maubp
View Post
-
I think that part needs a rewrite. things in <> are the ideas not the actual writing to be included.
Marco -
hi guys,
sorry for not looking into that for quite a while. The final draft looks very promising and the figures do look good as well.
I think the argument inside the <> is way too clumsy (I don't think mentioning an example here is helping the text).Especially connsidering the 300 word limit. This is still the plan right? Or did I miss something?
Apart from that, good work guys!!Comment
-
Why not leave this sentence (which is from long version of first draft), or at least the first half.:
However, the rate at which these technological advancements have come about has outpaced the speed of peer-reviewed publication and other traditional forms of information sharing in a burgeoning research field rapidly becoming known for 'big data'.Comment
-
I dont mean to include the example, i just mean to write an argument using that logicOriginally posted by ulz_peter View Post
MarcoComment
-
Because it is 95% identical to the wiki paper....is good to rewrite itOriginally posted by ulz_peter View PostMarcoComment
-
oh, that's a pretty good reason...Comment
-
Okay so spent some time looking at the data by date and by keyword frequency. There is clearly room to improve the analysis by omitting more of the common words, alternate versions of the same word, etc. but I have attached images for each quarter year since 2008. There are some trends I can see... for example in early 2008 there were terms like "capture" and "nimblegen" and these became less frequent later. There are also some interesting trends looking at terms like BWA, MAQ, and BOWTIE.
The images are not quantitative but we can use them to visually detect possible trends and then follow up by counting the occurrence of the terms in each dataset if we want to test for sure whether terms go in and out of fashion and also whether some terms become more prevalent than others.
So this is a first pass and I welcome comments/suggestions...
Here they are for everyone to look at:
Comment
-
Thanks for generating the tag clouds. It's kind of hard to find interesting trends that might be worth mentioning in the letter. If you could try to pick a few tags and generate some line charts over time then it might be easier to select some interesting trends or tags.
When I parsed the data, I converted everything to lower case to prevent counting e.g. Bowtie, bowtie and BOWTIE as three different words. Then I removed all the common English words that occurred in the top 50 list and generated the wordle. This might increase the size of some interesting words in your tag clouds.
Looking at the figures, we probably won't be able to put the tag cloud as a big figure. Maybe reducing the number of words (in wordle under Layout), or selecting a few and generating the cloud for those might be better. Especially if we want to add it to another figure, the top 20-30 words are probably the most that can still be read.
It might also be interesting to use phrases instead of single words. (You can upload pre-counted phrases under Advanced in wordle.) This might distinguish "read" from "I need to read" and "sequencing read".Comment
-
I agree. I certainly would not use the images as a big figure. Too messy. But I will play around and see if I can extract anything interesting...Comment
-
Good idea
I came across this forum accidentally while surfing, then forgot about it, and have now rediscovered it. It is so much better than comparable forums in LinkedIn which are close to useless. It would be good for everyone in this area to know about it.Comment
-
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
Commentary Letters: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
Any recent material about scientific community in Science?
Nature: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.
Correspondence:
Perspective: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.
Not sure how to submit.
There are some other possibilities, including PloS Comp Bio and genericforms suggested BMC Genome MedicinePerspective 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.
PLoS Comp Bio: perspective
BMC Genome Medicine: Opinion / CorrespondencePerspectives 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.
Opinion:
Correspondence: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
What do you think?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 considerationMarcoComment
-
I think Genome Biology is suitable too
Correspondence articles :
or Commentary EditorialGenome 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.
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.MarcoComment
-
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.Comment
-
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?Comment
-
Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.Today, 11:43 AM
-
I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before... -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
Comment