Talk:Reviews:Directed evolution/Library construction: Difference between revisions
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Revision as of 07:46, 17 July 2007
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Mailing list for this review
General Comments
This is adapated more or less directly from the original text. The major modification is that Figure 2 has been removed as this was adapated from a paper in Nature Biotech. I could check up on the copyright issues but as this is a part of the review that needs modifications anyway I probably won't bother.
Todo List
Good place to list the things that need to be done on this review.
General presentation and logistics
References have been converted to biblio format. There is also now an Endnote style for generating a properly formatted text and reference list for biblio. The bibliography for the review has been placed on a separate page as I think this is probably the best way to do it as it will ultimately allow for linked bibliographies for a set of reviews in the area of directed evolution. The catch is that I've given them references that are just numbers (which correspond to record numbers in an Endnote file I have) so maintaining multiple bibliographies that are all cross compatible could get challenging.
Email appropriate editor at NAR to enquire about writing a short paper to get a primary citation for the WikiReview.
- Cameron Neylon 26 April 2007: Will wait on this until the review is more up to date before doing this.
Contact some directed evolution people to help out with curation.
- Cameron Neylon 26 April 2007: Done. Sent this email to people who cited the original review in papers describing new and improved methods for library construction.
It occurs to me it would be good to link the review to consensus protocols on OWW. Need to think about how to get a relatively large number of such protocols up on the system. If enough of the relevant people sign up as curators for the review then hopefully they can be persuaded to put up the relevant protocols as well.
Other issues?
Science and updating
Several areas need work to bring this up to date. If anyone has some particular references that they feel should be included it would be helpful to categorise them below. General criteria is that they need to give a good description of the methodology and any practical issues as well as apply it to a real experiment.
In vivo error prone methods
http://aem.asm.org/cgi/content/full/67/8/3645?view=long&pmid=11472942
Error-prone PCR methods
http://dx.doi.org/10.1016/j.ab.2004.11.032
pmid=15585138 - this link seems to be broken, currently checking
http://nar.oxfordjournals.org/cgi/content/full/32/22/e176
http://www.biomedcentral.com/1472-6750/7/18
http://dx.doi.org/10.1016/j.jbiotec.2004.10.016 - this may belong in RID methods below
Random insertion/deletion methods
Quite a lot to be done here. Need a new picture for this class.
http://nar.oxfordjournals.org/cgi/content/full/33/9/e80
Directed methods
Recombination methods
http://nar.oxfordjournals.org/cgi/content/full/33/13/e117
http://www.nature.com/nbt/journal/v20/n10/abs/nbt736.html
http://nar.oxfordjournals.org/cgi/content/full/29/20/e97
Other tools
http://bioinformatics.oxfordjournals.org/cgi/content/full/21/15/3314
http://dx.doi.org/10.1006/jtbi.2000.2082
Analysis of mutation methods
There is now a significant amount of work on analysis, both functional and theoretical of mutations methods and how this relates to results of the DE experiment. Perhaps a new section is required to cover this?
http://www.blackwell-synergy.com/doi/abs/10.1046/j.1462-2920.2002.00326.x
http://dx.doi.org/10.1016/j.jmb.2005.05.023
http://nar.oxfordjournals.org/cgi/content/full/33/11/3667
http://www.liebertonline.com/doi/abs/10.1089%2F10665270050081423
http://peds.oxfordjournals.org/cgi/content/full/16/6/451
http://peds.oxfordjournals.org/cgi/content/full/19/6/245 (?)