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7 replies to this topic

#1 wswr

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Posted 27 July 2015 - 04:54 PM

Hi everyone. Is there a standardized format for writing a design before conducting actual research? How specific should a design be? For example, does it include a list of materials as well as detailed steps on how to do certain protocols, or just materials (like what substrate[s] and enzyme[s] will be used)? I'm not sure if this is the right place to post my question, but if it's not, I will be happy to move it. Thanks in advance.



#2 bob1

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Posted 28 July 2015 - 01:05 AM

There isn't a standardized format for writing protocols, but they should be detailed enough for someone to be able to replicate the steps that you have taken. If you want to look at good protocols, have a look at Nature protocols and Current Protocols journals.

 

Don't worry about the place, I have moved you to the correct one.



#3 wswr

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Posted 28 July 2015 - 10:26 AM

Thanks!



#4 phage434

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Posted 31 July 2015 - 04:30 AM

The Antha language being built by Synthace is intended to formally describe protocols, which can then be executed robotically or by hand.



#5 hobglobin

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Posted 31 July 2015 - 08:20 AM

A diverse collection (and diverse formats) you find here and might be helpful as a starting point:

http://www.protocol-online.org/

(unfortunately several links are dead now)


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...except casandra's that belong to the funniest, most interesting and imaginative (or over-imaginative?) ones, I suppose.


#6 wswr

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Posted 31 August 2015 - 04:36 PM

Thanks for the answers so far. Just wondering, when you're doing research that is related to your peers with the exact bacteria and plasmid they worked with, do you come up with your own design, follow their protocols, or follow protocols from the papers that focused/worked with the bacteria and plasmid (but your peers for some reason didn't follow them and hence came up with their own protocols)? I see my peers referring to the paper about the bacteria and plasmid they're using and what enzyme is yielded as well as the enzyme's characteristics, but as to the protein overexpression and purification, they deviate from the paper and came up with a different design. Why is that?


Edited by wswr, 31 August 2015 - 04:47 PM.


#7 phage434

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Posted 31 August 2015 - 05:40 PM

You should also check out the software being built by Transcriptic, which is intended to allow you to define protocols which they will run on their fully automated platforms.



#8 wswr

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Posted 01 September 2015 - 08:43 AM

Thanks for the recommendation. But how do you go about with coming up with your design? Does it just depend on each different case?






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