DIYbio:Notebook/Open Thermal Cycler/Requirements

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
m
m
Line 3: Line 3:
Use cases of a thermal cycler:
Use cases of a thermal cycler:
# A user has X DNA and wants to increase the quantity of X, or quantity of Y (a subsequence of X) in order to:
# A user has X DNA and wants to increase the quantity of X, or quantity of Y (a subsequence of X) in order to:
-
# Sequence the DNA -- more quantity is needed
+
## Sequence the DNA -- more quantity is needed
-
# Send DNA to a friend
+
## Send DNA to a friend
-
# Transform cells -- more quantity is needed
+
## Transform cells -- more quantity is needed
-
# Archive DNA
+
## Archive DNA
-
#
+
##
# A user wants to study their genome
# A user wants to study their genome
-
# 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)
+
## 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)
# A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
# A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
 +
# A user has DNA and wants to create copies that are each a little bit different
 +
## Error prone PCR
# A user wants a sequence of DNA but doesn't want to synthesize it
# A user wants a sequence of DNA but doesn't want to synthesize it
-
# Use primers + sequence X to create more of sequence X
+
## Use primers + sequence X to create more of sequence X
# A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
# A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
-
# Amplify species-specific DNA + digestion + gel electrophoresis + imaging/Encyclopedia of life
+
## Amplify species-specific DNA + digestion + gel electrophoresis + imaging ==> Webpage showing species
-
# A user wants to determine what bacteria are on a crosswalk button (1+ species/sample) (Jason Bobe)
+
# A user wants to determine what bacteria are on a crosswalk button (100+ species/sample) (Jason Bobe)
-
# Amplify species-specific DNA
+
## Amplify species-specific DNA + sequencing
 +
# A user wants to combine a sequence onto a known sequence (tailing - per Jake)
 +
## i.e. take a sequence and make add biobrick ends onto it
 +
 
 +
 
 +
Advanced use cases:
 +
# The user wants to observe gene expression in cells over a time period
 +
##User is presented with a graph showing the change in expression over time, or other desired result (RT PCR)
The Pain of Current Thermal Cyclers:
The Pain of Current Thermal Cyclers:
Line 25: Line 34:
-
The ideal solution:
+
The Open Thermal Cycler:
-
A user places their sample into Device X. The user picks Device X replicates a desired sequence of DNA.
+
Design something a great number of current non-thermocycler users will use.
-
 
+
-
Problems the Open Thermal Cycler solves:
+
-
Price -  
+

Revision as of 03:01, 24 April 2009

In progress...

Use cases of a thermal cycler:

  1. A user has X DNA and wants to increase the quantity of X, or quantity of Y (a subsequence of X) in order to:
    1. Sequence the DNA -- more quantity is needed
    2. Send DNA to a friend
    3. Transform cells -- more quantity is needed
    4. Archive DNA
  2. A user wants to study their genome
    1. 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)
  1. A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
  2. A user has DNA and wants to create copies that are each a little bit different
    1. Error prone PCR
  3. A user wants a sequence of DNA but doesn't want to synthesize it
    1. Use primers + sequence X to create more of sequence X
  4. A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
    1. Amplify species-specific DNA + digestion + gel electrophoresis + imaging ==> Webpage showing species
  5. A user wants to determine what bacteria are on a crosswalk button (100+ species/sample) (Jason Bobe)
    1. Amplify species-specific DNA + sequencing
  6. A user wants to combine a sequence onto a known sequence (tailing - per Jake)
    1. i.e. take a sequence and make add biobrick ends onto it


Advanced use cases:

  1. The user wants to observe gene expression in cells over a time period
    1. User is presented with a graph showing the change in expression over time, or other desired result (RT PCR)

The Pain of Current Thermal Cyclers: Price - thermal cyclers Interface - current models are Application -


The Open Thermal Cycler: Design something a great number of current non-thermocycler users will use.


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

Personal tools