View source for User:Scmohr

I am a chemist (biochemist, actually) from Boston University [[http://www.bu.edu/chemistry/faculty/profile/mohr.html Scott C. Mohr]].  I am working on a book about synthetic biology for a general audience and also assisting with the curation and upgrading of the Registry Website. My current Registry project consists of to compiling a set of [[RSBP Draft Documentation Standards]].  That effort will, in turn, contribute to the [[Part Promotion Process]] that the Registry hopes soon to implement.  Another useful summary of preliminary ideas about part documentation and promotion has been prepared by Mac Cowell [[http://parts.mit.edu/igem07/index.php/User:Macowell/Part_Documentation_Guidelines here]].  Since the concept of a "part" in synthetic biology has close connections to that of a "gene," I have also written a short document that deals with [["Gene" Definition(s) for Synthetic Biology]].


'''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)


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'''(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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*[[Part_Type:Protein_Coding_Regions | Protein Coding Regions]] 
*[[User:Scmohr/ProtCode_Summary | Protein Coding Region Summary]]
*[[User:Scmohr/ProtCode_Repressors_&_Activators | Repressors and Activators]]
*[[User:Scmohr/ProtCode_Enzyme | Enzymes]]
*[[User:Scmohr/Enzyme_background | Enzyme Details]]
*[[User:Scmohr/Reporters | Reporters]]
*[[User:Scmohr/Part_Evaluation | Part Evaluation]]
*[[User:Scmohr/Documentation_Score | Documentation Score]]
*[[User:Scmohr/Specialized_Doc_Score | Specialized Doc Score]]
*[[User:Scmohr/Gene_Definition | Gene Definition]]
*[[User:Scmohr/Part_Doc_Score_Tally | DocScore Tally]]
*[[User:Scmohr/Part_Doc_Guide | Guide to Registry Documentation]]
*[[User:Scmohr/Glossary | RSBP Glossary]]
*[[User:Scmohr/Gray_box | "Gray-box" Plans]]
*[[User:Scmohr/Sample Protein Gray_boxes | Sample Protein Facts Boxes]]
*[[User:Scmohr/Sample RNA Parts Gray_Boxes | Sample RNA Parts Facts Boxes]]
*[[User:Scmohr/RBS's | Ribosome-binding Sites]]