Nature Protocols Discussion Forum: topic
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Bioinformatics protocols???
Kuljeet Sandhu
Monday, 25 February 2008 12:57 UTC
Recently, I saw few bioinformatics protocols published in Nature Protocols. It was disappointing to see how people are able to publish their ‘already published’ web-servers again and that too in Nature! The web-servers or the protocols are not very impressive too. I wondered even more when I find one of them does not even function properely. The methods used in those protocols are not novel either. I could mention all these articles here, but I don’t wish to offend anyone. I am not able to digest on what basis such articles are accepted in Nature Protocols. Any computaional biologist except the authors/reviewers themselves will find these articles no way better than any average routine bioinformatics paper!! I wish to see others’ opinion esp from established cmputational biologists. I wld be even more happier to see response from someone working with Nature Protocols editorial.
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Replies
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Dear Kuljeet,
Thank you caring about the quality of our content and for taking the trouble to contribute to our discussion forum. I will do my best to respond to the points that you have raised.
1) Publication of “already published” web-servers
The aim of Nature Protocols is to create a centralized resouce for high quality, reliable methods written in a protocols format. For this reason it is our policy to try to only publish protocols based on methods that have already been used to generate results that have been published in primary research papers.
2) Web-servers nor protocols are very impressive
We would very much value your input on which web-servers we should highlight in our content. Perhaps you would like to join the discussion here. Please bear in mind that our readership contains a lot of people who are not “computational biologists”, but would like to use web-servers and other programs to answer their research questions. That is: Different protocols might be necessary to satisfy the two types of researcher.
3) One of them does not even function properly
Technical problems with individual protocols would be very useful information to have on our site. Please would you use our commenting function to raise any questions or issues that you have with individual protocols. Both the authors and our readers would be very grateful for this contribution.
4) Request for opinions
A few months ago I made a list of our published protocols as a google document and this can be found here. We have published a few more in the meantime and I will make an effort to update this today! This forum thread would be an appropriate place to discuss ways in which we could make future protocols more useful to our readers – and we would be very grateful for such input! Nature Protocols is a relatively new journal and we are still in the process of learning how to best serve researchers.
Best wishes with your research.
Kind regards,
Bronwen
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