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==Strategic Summary: week of 11/09/08==
==Strategic Summary: week of 11/09/08==
* Genetically Encoded Memory
==Genetically Encoded Memory==
**General interest
*General interest
*** The big picture of my interests in this projects center around developing methods and managing guideline for discovering, characterizing, standardizing and presenting biological parts: enzymes, transcription factors, biochemical circuits, etc.  
** The big picture of my interests in this projects center around developing methods and managing guideline for discovering, characterizing, standardizing and presenting biological parts: enzymes, transcription factors, biochemical circuits, etc.  
***While the size of "registered biological Parts" library of BioBrick foundation is rapidly increase, there are two important facts one needs to keep in mind.  
**While the size of "registered biological Parts" library of BioBrick foundation is rapidly increase, there are two important facts one needs to keep in mind.  
****First, most of the registered parts came from specific studies from individual research groups. Synthetic biologists develop and characterize a set of parts they would like to used in the biological machines. Then, that data is put together and presented in BioBrick "standardized" format. Thus, the new Part arises in the library as a result from a specific engineering project.  
***First, most of the registered parts came from specific studies from individual research groups. Synthetic biologists develop and characterize a set of parts they would like to used in the biological machines. Then, that data is put together and presented in BioBrick "standardized" format. Thus, the new Part arises in the library as a result from a specific engineering project.  
****Second, billions years of evolutions have created huge diversity in living universe, which, of course, include the large library of naturally derived "parts"--enzymes, transcription factor, biochemical circuits, etc. Only a tiny fraction of these Parts are characterized well enough so that synthetic biology start using them to build something new. For instance, recall how many "transcription factors" and "promoters" have been identified...versus how many are frequently used by synthetic biologists to build a new living machine.  
***Second, billions years of evolutions have created huge diversity in living universe, which, of course, include the large library of naturally derived "parts"--enzymes, transcription factor, biochemical circuits, etc. Only a tiny fraction of these Parts are characterized well enough so that synthetic biology start using them to build something new. For instance, recall how many "transcription factors" and "promoters" have been identified...versus how many are frequently used by synthetic biologists to build a new living machine.  
***I believe that it would be very useful to have a synthetic biology project that focused on large-scale characterization of these natural parts for engineering purpose. I realized that there are three major issues to be addressed
**I believe that it would be very useful to have a synthetic biology project that focused on large-scale characterization of these natural parts for engineering purpose. I realized that there are three major issues to be addressed
****Prioritize question and information: we don't have to know everything about a part before using for engineering. Also, in practice, it might take natural scientist decades to dig deep into detailed mechanism of something. We engineer cannot wait that long!
***Prioritize question and information: we don't have to know everything about a part before using for engineering. Also, in practice, it might take natural scientist decades to dig deep into detailed mechanism of something. We engineer cannot wait that long!
****Data mining: if we wanna be tall, we need to stand on the shoulder of a giant! Generally, there are more or less valuable information about the Parts from previous studies. This information scatters around different database and publication. While not all conclusion and theories from the past are valid or usable for engineers, we shall not have to start learning things from scratch.  
***Data mining: if we wanna be tall, we need to stand on the shoulder of a giant! Generally, there are more or less valuable information about the Parts from previous studies. This information scatters around different database and publication. While not all conclusion and theories from the past are valid or usable for engineers, we shall not have to start learning things from scratch.  
****High-throughput assay and powerful measurement: we should be able to characterize multiple parts that belong to the same category all at once, under the similar standard conditions. This would allow engineers to compare and contrast items in the catalog. For instance, one might want to ask which transcription factors should I use in this circuit. Let's transciption X, Y, Z are all functions like inhibitors in nature..but different kinetic profiles, life time, etc. One may want to compare such information
***High-throughput assay and powerful measurement: we should be able to characterize multiple parts that belong to the same category all at once, under the similar standard conditions. This would allow engineers to compare and contrast items in the catalog. For instance, one might want to ask which transcription factors should I use in this circuit. Let's transciption X, Y, Z are all functions like inhibitors in nature..but different kinetic profiles, life time, etc. One may want to compare such information
****Data representation: after all, whatever we did will be useful only if those who come after can use it. There are many ways to represent the collective information about part that we know. Again, I believe that the very important features of our presenting schema is the capability to compare and contrast thing in the same category (like comparing one DNA polymerase to another DNA polymerase.. comparing one transcription inhibition system to another transcription inhibiting system) and same attribute (compare the speed of all DNAP in catelog... compare inhibiting kinetic of all transcriptional inhibitors in the catalog)
***Data representation: after all, whatever we did will be useful only if those who come after can use it. There are many ways to represent the collective information about part that we know. Again, I believe that the very important features of our presenting schema is the capability to compare and contrast thing in the same category (like comparing one DNA polymerase to another DNA polymerase.. comparing one transcription inhibition system to another transcription inhibiting system) and same attribute (compare the speed of all DNAP in catalog... compare inhibiting kinetic of all transcriptional inhibitors in the catalog)
****Synthetic studies
***Synthetic studies: it's important to demonstrate that the collection of data we present can facilitate the process of engineering a cells. In reverse, the result from an engineering project will also help us modify the methods and the management of the library of parts. Note that there can be many level of synthetic studies. Let's say we get the collection of information about DNA polymerase, that could help the protein engineering project on DNA polymerase..it could also help the circuit level projects that require DNA polymerase with specific properties.
 
====
====
* Bacterial Cell shape
* Bacterial Cell shape

Revision as of 17:01, 9 November 2008

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Strategic Summary: week of 11/09/08

Genetically Encoded Memory

  • General interest
    • The big picture of my interests in this projects center around developing methods and managing guideline for discovering, characterizing, standardizing and presenting biological parts: enzymes, transcription factors, biochemical circuits, etc.
    • While the size of "registered biological Parts" library of BioBrick foundation is rapidly increase, there are two important facts one needs to keep in mind.
      • First, most of the registered parts came from specific studies from individual research groups. Synthetic biologists develop and characterize a set of parts they would like to used in the biological machines. Then, that data is put together and presented in BioBrick "standardized" format. Thus, the new Part arises in the library as a result from a specific engineering project.
      • Second, billions years of evolutions have created huge diversity in living universe, which, of course, include the large library of naturally derived "parts"--enzymes, transcription factor, biochemical circuits, etc. Only a tiny fraction of these Parts are characterized well enough so that synthetic biology start using them to build something new. For instance, recall how many "transcription factors" and "promoters" have been identified...versus how many are frequently used by synthetic biologists to build a new living machine.
    • I believe that it would be very useful to have a synthetic biology project that focused on large-scale characterization of these natural parts for engineering purpose. I realized that there are three major issues to be addressed
      • Prioritize question and information: we don't have to know everything about a part before using for engineering. Also, in practice, it might take natural scientist decades to dig deep into detailed mechanism of something. We engineer cannot wait that long!
      • Data mining: if we wanna be tall, we need to stand on the shoulder of a giant! Generally, there are more or less valuable information about the Parts from previous studies. This information scatters around different database and publication. While not all conclusion and theories from the past are valid or usable for engineers, we shall not have to start learning things from scratch.
      • High-throughput assay and powerful measurement: we should be able to characterize multiple parts that belong to the same category all at once, under the similar standard conditions. This would allow engineers to compare and contrast items in the catalog. For instance, one might want to ask which transcription factors should I use in this circuit. Let's transciption X, Y, Z are all functions like inhibitors in nature..but different kinetic profiles, life time, etc. One may want to compare such information
      • Data representation: after all, whatever we did will be useful only if those who come after can use it. There are many ways to represent the collective information about part that we know. Again, I believe that the very important features of our presenting schema is the capability to compare and contrast thing in the same category (like comparing one DNA polymerase to another DNA polymerase.. comparing one transcription inhibition system to another transcription inhibiting system) and same attribute (compare the speed of all DNAP in catalog... compare inhibiting kinetic of all transcriptional inhibitors in the catalog)
      • Synthetic studies: it's important to demonstrate that the collection of data we present can facilitate the process of engineering a cells. In reverse, the result from an engineering project will also help us modify the methods and the management of the library of parts. Note that there can be many level of synthetic studies. Let's say we get the collection of information about DNA polymerase, that could help the protein engineering project on DNA polymerase..it could also help the circuit level projects that require DNA polymerase with specific properties.

==

  • Bacterial Cell shape



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