Difference between revisions of "User:Scmohr"

Revision as of 16:42, 13 March 2008

I am a chemist (biochemist, actually) from Boston University http://www.bu.edu/chemistry/faculty/profile/mohr.html Scott C. Mohr. I am currently working on a book about synthetic biology for a general audience and am also assisting with the curation and upgrading of the Registry Website.

Registry “Issues”/Agenda

Scott C. Mohr (11/29/06)

1. The “Search the Registry” should have an option to BLAST any sequence against the total set of sequences in the registry. I think this will require a table of all the registry sequences in flat-file format compatible with BLAST. With this function, someone with a gene of interest might be able to find it (or a close homolog) among the BioBricks even if its annotations are confusing or absent. (11/29/06)

2. I have a problem with the term “plasmid backbone.” [See the HELP page: Plasmids/Construction Plasmids.] A plasmid is just a DNA molecule, and the “backbone” of DNA consists of deoxyribose phosphate groups held together by phosphodiester bonds. That’s very different from the complete DNA molecule of the uncut plasmid (lacking an insert), or the linear DNA with breaks in both strands (backbones!) at the cut site. If that object is also to be referred to as a “backbone,” there’s a significant source of semantic confusion…. (11/29/06)

Having received no disagreements with this comment, I will proceed to edit out the term "plasmid backbone" and replace it with "plasmid core." (3/13/08)

(Suggested) Registry Style Sheet

Scott C. Mohr (11/20/06)

“A foolish consistency is the hobgoblin of little minds.” – Ralph Waldo Emerson (1803-1882)

I’m putting my preferences down here and encourage people to use them – or give me a hard time about why something different is better. Note that Emerson did not say “consistency is the hobgoblin of little minds” (as the quotation is so often reported). Only a foolish consistency!

Capitalization

BioBricks

Escherichia coli (genus name capitalized, species name not capitalized, both written in Italics).

Hyphenation

single-stranded/double-stranded

Italics

e.g.

E. coli, also Escherichia coli

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 . The “Search the Registry” should have an option to BLAST any sequence against the total set of sequences in the registry.  I think this will require a table of all the registry sequences in flat-file format compatible with BLAST. With this function, someone with a gene of interest might be able to find it (or a close homolog) among the BioBricks even if its annotations are confusing or absent. (11/29/06)
-. I have a problem with the term “plasmid ''backbone''.”  [See the HELP page: Plasmids/Construction Plasmids.]  A plasmid is just a DNA molecule, and the “backbone” of DNA consists of deoxyribose phosphate groups held together by phosphodiester bonds.  That’s very different from the complete DNA molecule of the uncut plasmid (lacking an insert), or the linear DNA with breaks in both strands (backbones!) at the cut site.  If that object is also to be referred to as a “backbone,” there’s a significant source of semantic confusion….
+. I have a problem with the term “plasmid ''backbone''.”  [See the HELP page: Plasmids/Construction Plasmids.]  A plasmid is just a DNA molecule, and the “backbone” of DNA consists of deoxyribose phosphate groups held together by phosphodiester bonds.  That’s very different from the complete DNA molecule of the uncut plasmid (lacking an insert), or the linear DNA with breaks in both strands (backbones!) at the cut site.  If that object is also to be referred to as a “backbone,” there’s a significant source of semantic confusion…. (11/29/06)
+'''Having received no disagreements with this comment, I will proceed to edit out the term "plasmid backbone" and replace it with "plasmid core."''' (3/13/08)