DIYbio:Notebook/Open Thermal Cycler/Requirements

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Current revision (03:02, 24 April 2009) (view source)
 
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Use cases of a thermal cycler:
 
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# A user has X DNA and wants to increase the quantity of X, or quantity of Y (a subsequence of X) in order to:
 
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## Sequence the DNA -- more quantity is needed
 
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## Send DNA to a friend
 
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## Transform cells -- more quantity is needed
 
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## Archive DNA
 
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##
 
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# A user wants to study their genome
 
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## Small SNP-sensitive sets of primers are used to amplify DNA. Electrophoresis is used to image PCR product, where short bands indicate SNP match/mismatch (Kay Aull)
 
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# A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
 
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# A user has DNA and wants to create copies that are each a little bit different
 
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## Error prone PCR
 
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# A user wants a sequence of DNA but doesn't want to synthesize it
 
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## Use primers + sequence X to create more of sequence X
 
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# A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
 
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## Amplify species-specific DNA + digestion + gel electrophoresis + imaging ==> Webpage showing species
 
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# A user wants to determine what bacteria are on a crosswalk button (100+ species/sample) (Jason Bobe)
 
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## Amplify species-specific DNA + sequencing
 
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# A user wants to combine a sequence onto a known sequence (tailing - per Jake)
 
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## i.e. take a sequence and make add biobrick ends onto it
 
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Advanced use cases:
 
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# The user wants to observe gene expression in cells over a time period
 
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##User is presented with a graph showing the change in expression over time, or other desired result (RT PCR)
 
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The Pain of Current Thermal Cyclers:
 
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Price - thermal cyclers
 
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Interface - current models are
 
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Application -
 
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The Open Thermal Cycler:
 
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Design something a great number of current non-thermocycler users will use.
 
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Current revision

In progress...


High Level Requirements

  1. The Open Thermal Cycler (OTC) shall allow users to replicate DNA
  2. "" software must allow users to load settings manually
  3. "" hardware must support a range of temperatures from X to Y
  4. "" may be accessible through a web interface
  5. "" may allow users to load pre-configured settings
  6. "" may allow users to know if the machin


  1. Perhaps the operator doesn't know (or care) how the machine is actually cycling - if the protocol has been verified, the task is to run it, get the result & move on. -- Jonathan Cline

Response: Many PCRs are more complicated than that unfortunately, the melting temperature (Tm) of the primer-DNA is just an estimate and often the annealing temp. needs adjusting with each template and primer used. Likewise the extension time is also often adjusted depending on the product length in order to speed up the total time it takes to run, -- John Cumbers

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