Is SEQanswers worthy of publication in a journal?

[samanta]

Before I start, congratulations for getting the forum and the wiki published in top journals.

Last August, people of Seqanswer were discussing about publishing the wiki and I commented -

http://seqanswers.com/forums/showthread.php?t=13103&page=2

Why do you guys care ??????

When I was an undergraduate in India, email was new thing and only one professor in the whole university had email access. So, he received emails for everyone and printed them in papers in front of his office. We had to sort through reams of paper to find out anything useful.

If you enjoyed that story, I can also tell you about riding a horse-buggy in Haridwar (a small town near the Himalayas).

Marcowanger, one of our kind and helpful senior members, commented -

To answer your question, I care because I benefit from the forum from the first day of my graduate study. I learn and keep track of papers from here (the generous persons who share their insight of paper and the authors who promote their tools and the newsbots). When I have gained so much from here, I think it is time to give back something.

And people here are nice too.

and I responded -

I am not doubting the power of this forum, but the power of Nucleic Acids Research. My original comment was written to suggest that paper journals are the horse buggy technology now

Why do we need endorsement from them? Just my take.....

I apologize for being short and cryptic in my previous message, but my point was this. In these days of google and internet, researchers in all parts of the world do a google search first, when they have any question. When I search in google with NGS-related questions, Seqanswers comes first. From that point of view, seqanswers is more successful 'journal' than even the most high-profile ones including Science and Nature. Does this forum need an endorsement from 'them'? To me, publishing seqanswers in regular journal was similar to Steve Jobs and Bill Gates going back to finish their college degrees to prove that they were smart (little too late for Jobs now ).


I wrote this commentary based on my experience from another experiment with online media.

http://www.homolog.us/blogs/2012/03/19/does-citation-index-count/

Does Citation-index Count in the Era of Google?

"In late 2006, we were working on the honey bee genome paper and I noticed an interesting pattern in the AT-rich and GC-rich parts of the genome. So, I wrote up a short commentary and tried to get a few ‘experts’ excited about my findings. However, based on their reaction, I gave up any thought of publishing it in a regular journal. I did not have any doubt about the merits of the findings. However, at that time, we were working on several Science and Nature papers (all published now), and few other papers in ‘lesser’ journals. I could not take the headache of another round of arguments with editors, anonymous reviewers, resubmission and so on."

More at https://href=http://www.homolog.us/b...n-index-count/
Enjoy !!

[chadn737]

Try to make that argument to any hiring committee, tenure committee, grant panel......

[samanta]

Try to make that argument to any hiring committee, tenure committee, grant panel......

...but those guys were initially skeptical about shotgun sequencing, microarrays, short read sequencing, utility of bioinformatics and many other things at major turning points.

If nothing works, please show them the attached image

[Heisman]

It's nice to have a paper to cite when referencing this website in papers any of us want to publish (if we feel it is merited to reference SEQanswers). That alone is nice. It will also lead to increased exposure to the website. Additionally, for the authors on the paper who heavily contributed to the forum, they have done an excellent job, so it's nice to have them acknowledged for it in some capacity.

[rskr]

Not to hi-jack the thread, but maybe a more appropriate question would be, "Is Bioinformatics a very good journal?" As of late I have not been very impressed by the quality of the papers in that journal, it seems that most of the citations Bioinformatics gets are from a few high profile papers, and the rest are simple web resources or simple academic java applications, and in that journal SEQanswers certainly does fit.

[samanta]

Prior to 2002, the word 'bioinformatics' was respectable and described serious researchers developing biological algorithms. Then around 2002-2003, CS people hijacked the word and started to describe database maintenance and all other junks as bioinformatics. Biologists themselves could not tell the difference, because they had no understanding of how computers worked. So the people working on algorithm development picked different names such as 'computational biologists', 'system biologists', etc. The journal 'Bioinformatics' came in around 2002-2003 and had hard time defining its audience.

Eventually algorithm development became respectable again with NGS sequencing, because biologists could not cope with the volume of data with their excel spreadsheets. By this time, serious researchers moved on to Genome Research leaving Bioinformatics with a mixed audience.

That's the history.

P. S. the topic title is no way meant to undermine the work of contributors of this forum, who has done excellent work to build up the community. It is rather a tounge-in-cheek comment about the traditional journals.

[adaptivegenome]

Before I start, congratulations for getting the forum and the wiki published in top journals.

Last August, people of Seqanswer were discussing about publishing the wiki and I commented -

http://seqanswers.com/forums/showthread.php?t=13103&page=2

Marcowanger, one of our kind and helpful senior members, commented -



and I responded -




I apologize for being short and cryptic in my previous message, but my point was this. In these days of google and internet, researchers in all parts of the world do a google search first, when they have any question. When I search in google with NGS-related questions, Seqanswers comes first. From that point of view, seqanswers is more successful 'journal' than even the most high-profile ones including Science and Nature. Does this forum need an endorsement from 'them'? To me, publishing seqanswers in regular journal was similar to Steve Jobs and Bill Gates going back to finish their college degrees to prove that they were smart (little too late for Jobs now ).


I wrote this commentary based on my experience from another experiment with online media.

http://www.homolog.us/blogs/2012/03/19/does-citation-index-count/

Does Citation-index Count in the Era of Google?

"In late 2006, we were working on the honey bee genome paper and I noticed an interesting pattern in the AT-rich and GC-rich parts of the genome. So, I wrote up a short commentary and tried to get a few ‘experts’ excited about my findings. However, based on their reaction, I gave up any thought of publishing it in a regular journal. I did not have any doubt about the merits of the findings. However, at that time, we were working on several Science and Nature papers (all published now), and few other papers in ‘lesser’ journals. I could not take the headache of another round of arguments with editors, anonymous reviewers, resubmission and so on."

More at https://href=http://www.homolog.us/b...n-index-count/
Enjoy !!

It is silly to argue about the power of a google search versus a search in a journal, etc. Peer-reviewed publication is a major avenue for communication in the sciences and reporting SEQanswers in Bioinformatics/NAR therefore made sense. However, if you search "SEQanswers" in google (and this obviously assumes you are already aware of the site), the manuscripts we published are the 2nd and 3rd site you see after seqanswers.com (not counting Eric's twitter feed); and the PubMed record is 4th.

I think SEQanswers has benefited from exposure in both Google and the traditional journals. No need to pick sides.

[samanta]

It is silly to argue about the power of a google search versus a search in a journal, etc. Peer-reviewed publication is a major avenue for communication in the sciences and reporting SEQanswers in Bioinformatics/NAR therefore made sense. However, if you search "SEQanswers" in google (and this obviously assumes you are already aware of the site), the manuscripts we published are the 2nd and 3rd site you see after seqanswers.com (not counting Eric's twitter feed); and the PubMed record is 4th.

I think SEQanswers has benefited from exposure in both Google and the traditional journals. No need to pick sides.

I think what you guys did is likely the best decision in making the forum popular and more visible. My arguments are more philosophical and not criticism about publishing your work. I hope there is some room for philosophical discussions here.

The way I see things, even 15 years back, there were only two methods of communication between scientists -

(i) publishing a paper and hoping that others would notice you.
(ii) giving talk about the (published) research in scientific conferences.

Communication channels also existed between small groups of scientists through letters, emails, departmental meetings, but the above two were the only ways of reaching large audiences.

Internet and social media changed everything about how we communicate in general, but so far the scientists are trying to merely extend the boundaries of (i) and (ii) with peripheral support from everything else.

Let us discard all pre-conceived notions developed from a bygone era, and think fresh by going to the root of everything. Why do we pay attention to 'impact factor'? It is because the paper journals with high impact factor have supposedly been read by more people. That works, only if we restrict ourselves within the confines of old media. What is the 'impact factor' of something unpublished in traditional media, but has been used by everyone? Taking the example of NGS, what is the 'impact factor' of transcriptome assembler 'OASES', which has been used by almost everyone working on RNAseq data but has not been published?

To me, SEQanswers is a journal by itself. It should start issuing its own impact factor !!! Also I am anticipating that sooner or later, traditional journals will start to see it as a competition to their existence, and start acting accordingly.

[rskr]

To me, SEQanswers is a journal by itself. It should start issuing its own impact factor !!! Also I am anticipating that sooner or later, traditional journals will start to see it as a competition to their existence, and start acting accordingly.

Actually I think it will go the other way, where journals will have blogs associated with them. If you look at it they already do you can for example comment on articles in bioinformatics. The blogs don't appear to be very popular though. There was recently a movement by popular Mathematics editors to boycott Elsevier. They seemed to think that being paid nothing for their services while the journal was a for profit institution wasn't fair, so I guess it can go either way.

[steven]

Hi,

I agree that there are a lot of issues with the current "Impact Factor" criteria. This said I would not consider a Google rank as an acceptable way to assign a "value" to a scientific work -for obvious reasons.

On the other hand, I am really looking forward to some open-source community-based scientific social network that could really challenge the current system, embody the undeniable shift that has been occurring and propose a valid, alternative, reliable, fair and recognized communication channel.

I would say a mix between google, facebook, mendeley, seqanswers, ted and others.
In the meantime i fear that we are inevitably stuck with journals, publication fees, anonymous peer-reviews and impact factors..

[rskr]

Now that you mention it the "Pagerank" criterion does resemble the citation model used in the impact factor. If Google only parsed out the citations in the pdf instead of the URL's on the page, then the Pagerank algorithm would be pretty good, but as far as I am aware, Pagerank doesn't actually look at the references.

[steven]

Now that you mention it the "Pagerank" criterion does resemble the citation model used in the impact factor. If Google only parsed out the citations in the pdf instead of the URL's on the page, then the Pagerank algorithm would be pretty good, but as far as I am aware, Pagerank doesn't actually look at the references.

Well, I have a couple of serious concerns regarding the google page rank as a metric for scientific papers/work in general. It is totally obscure, not disclosed, it can be -and is frequently- modified with no visibility nor control on the public side. And it is only a way to measure global popularity, not relevance. Plus there is no normalization: to find a brilliant but recent paper you would need to define yourself the time interval, self referencing (same authors, same journal) is not taken into account, you can "trick" or at least "play" with the algorithm to "mechanically" change the rank of a page, google bombing, etc etc.

Note that Google Scholar already provides a number of citations for your paper of interest.

I am sure that with a (couple of) proper metric(s), a relevant network model, a couple of smart algorithms and of course a general adoption it could be possible to propose a new system.. just dreaming

[rskr]

It is totally obscure, not disclosed, it can be -and is frequently- modified with no visibility nor control on the public side.

Actually pagerank is pretty straight forward, as described in Brin and Page's paper.

http://ilpubs.stanford.edu:8090/361/1/1998-8.pdf

I am sure whatever the Google search engine uses now is shrouded in voodoo.

[steven]

Yes, i was referring to the actual google ranking (cf samanta's link), not to the original pagerank algorithm.