Difference between revisions of "Help talk:Regulatory"
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A 'regulatory element' is often simplified into a 'promoter' but in the Registry it also includes (in addition to the RNA-polymerase binding site) the repressor/activator binding site. My suggestion is that these two (or three) regions which have well-defined characteristics and functions should be separated into distinct physical areas and carry different symbols. It might at this stage go too far into the BioBrick concept, but I believe it makes more sense making this development now than in a few years.<br> | A 'regulatory element' is often simplified into a 'promoter' but in the Registry it also includes (in addition to the RNA-polymerase binding site) the repressor/activator binding site. My suggestion is that these two (or three) regions which have well-defined characteristics and functions should be separated into distinct physical areas and carry different symbols. It might at this stage go too far into the BioBrick concept, but I believe it makes more sense making this development now than in a few years.<br> | ||
Additionally, I wish to suggest ;-) that the repressor binding region is depicted as --[R]-- (eg. red box with an R in it) and the activator binding region as --[A]-- (green box with an A). Further, since regulatory proteins are very important in SB, they could have separate icons as well, e.g. a red arrow --[R]--> for a repressor coding region. It would certainly add to easier understanding of composite regulatory networks. Try to explain fig. 1 in the recent Cell SB [http://www.cell.com/content/article/abstract?uid=PIIS0092867407006848 article] with currently used BioBrick icons and I am convinced you will agree with my proposals. [[http://parts.mit.edu/wiki/index.php/User:MDolinar MDolinar], July 30, 2007] | Additionally, I wish to suggest ;-) that the repressor binding region is depicted as --[R]-- (eg. red box with an R in it) and the activator binding region as --[A]-- (green box with an A). Further, since regulatory proteins are very important in SB, they could have separate icons as well, e.g. a red arrow --[R]--> for a repressor coding region. It would certainly add to easier understanding of composite regulatory networks. Try to explain fig. 1 in the recent Cell SB [http://www.cell.com/content/article/abstract?uid=PIIS0092867407006848 article] with currently used BioBrick icons and I am convinced you will agree with my proposals. [[http://parts.mit.edu/wiki/index.php/User:MDolinar MDolinar], July 30, 2007] | ||
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| + | This point is well-taken, though it tends to reflect the difference between the conceptual aspects of the molecular biology and the practical issues of engineering. Basic scientists seek to define DNA binding sites at high resolution in terms of their precise roles -- in this case transcription-related roles. Thus the repressor-binding site of the lac operon | ||
Revision as of 20:19, 30 July 2007
A 'regulatory element' is often simplified into a 'promoter' but in the Registry it also includes (in addition to the RNA-polymerase binding site) the repressor/activator binding site. My suggestion is that these two (or three) regions which have well-defined characteristics and functions should be separated into distinct physical areas and carry different symbols. It might at this stage go too far into the BioBrick concept, but I believe it makes more sense making this development now than in a few years.
Additionally, I wish to suggest ;-) that the repressor binding region is depicted as --[R]-- (eg. red box with an R in it) and the activator binding region as --[A]-- (green box with an A). Further, since regulatory proteins are very important in SB, they could have separate icons as well, e.g. a red arrow --[R]--> for a repressor coding region. It would certainly add to easier understanding of composite regulatory networks. Try to explain fig. 1 in the recent Cell SB [http://www.cell.com/content/article/abstract?uid=PIIS0092867407006848 article] with currently used BioBrick icons and I am convinced you will agree with my proposals. [[http://parts.mit.edu/wiki/index.php/User:MDolinar MDolinar], July 30, 2007]
This point is well-taken, though it tends to reflect the difference between the conceptual aspects of the molecular biology and the practical issues of engineering. Basic scientists seek to define DNA binding sites at high resolution in terms of their precise roles -- in this case transcription-related roles. Thus the repressor-binding site of the lac operon