DIYbio:Notebook/Open Thermal Cycler

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==Project Description/Abstract==
==Project Description/Abstract==
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* Place short description of project or notes regarding this project
 
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:Draft:
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==Why quantitative thermal cycling?==
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How do you go from a spit sample to  - or from a crosswalk swab to a map of the bacterial populations of the world? Can $1,000 get you there? quantitative thermal cycling can be an all-in-one device capable
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==Notes==
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==Comparisons to standard thermal cycling==
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* Place some notes here for visitors
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The following is the outline of quantitative thermal cycling, its advantages over traditional thermal cycling,
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* Example: This project is currently on hold until further notice.
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There are 2 general areas of thermal cycler use:
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#(strong) Synthesis/copying of DNA
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#(weak) Analysis of DNA
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Since thermal cycling itself is not an analytical tool, thermal cycling is not the final step in most processes. Gel electrophoresis, transformation into cells, and/or sequencing of the sample follow.
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There are 2 general areas of quantitative thermal cycler use:
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#(strong) Synthesis/copying of DNA
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#(strong) Quantitative and qualitative analysis of DNA/RNA sample
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qPCR on the other hand can be an all-in-one tool for analysis, both qualitatively and quantitatively. In addition to the functionality of a standard thermal cycler, a quantitative thermal cycler includes an imaging device to record the florescence of samples. Florescent markers added to each sample indicate the presence of a particular sequence (replacing gel electrophoresis and short sequencing) or measure gene expression (supplementing other analysis of modified cells)
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==Cost of current products==
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# Licensing -- [http://www.patentstorm.us/patents/6814934/fulltext.html florescent analysis is patented] although one key patent, [http://www.patentstorm.us/patents/6814934/fulltext.html US6814934], is under [http://www.genomeweb.com/pcrsample-prep/uspto-rejects-life-techs-thermal-cycler-patent-initial-ruling challenge] in a case before the [http://www.uspto.gov US Patent and Trademark Office]. The European equivalent to US6814934, [http://ep.espacenet.com/publicationDetails/biblio?adjacent=true&KC=A1&date=19981021&NR=0872562A1&DB=ep.espacenet.com&locale=en_GB&CC=EP&FT=D EP872562], has been confirmed by the [http://ep.espacenet.com/ European Patent Office] after [http://www.genomeweb.com/pcrsample-prep/uspto-rejects-life-techs-thermal-cycler-patent-initial-ruling-epo-upholds-europe challenges were dropped.]
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#Hardware -- developed in house
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#Software -- developed in house
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==Details==
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[[DIYbio:Notebook/Open_Thermal_Cycler/Use_Cases | Use Cases ]]- experiments involving a thermal cycler
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[[DIYbio:Notebook/Open_Thermal_Cycler/Requirements | Requirements]]- what a user might want to do with an Open Thermal Cycler (i.e. get more DNA)
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[[DIYbio:Notebook/Open_Thermal_Cycler/Specifications | Specifications]] - what hardware, software, GUI-ideas we might use to build it (i.e. Arduino, or a checkbox interface for entering temperatures)
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[[DIYbio:Notebook/Open_Thermal_Cycler/Conference Calls/2009/4/26 | 4/26/2009 Conference Call]] - Details for connecting to the conference call.
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Project Description/Abstract

Draft:

Why quantitative thermal cycling?

How do you go from a spit sample to - or from a crosswalk swab to a map of the bacterial populations of the world? Can $1,000 get you there? quantitative thermal cycling can be an all-in-one device capable

Comparisons to standard thermal cycling

The following is the outline of quantitative thermal cycling, its advantages over traditional thermal cycling,

There are 2 general areas of thermal cycler use:

  1. (strong) Synthesis/copying of DNA
  2. (weak) Analysis of DNA

Since thermal cycling itself is not an analytical tool, thermal cycling is not the final step in most processes. Gel electrophoresis, transformation into cells, and/or sequencing of the sample follow.

There are 2 general areas of quantitative thermal cycler use:

  1. (strong) Synthesis/copying of DNA
  2. (strong) Quantitative and qualitative analysis of DNA/RNA sample

qPCR on the other hand can be an all-in-one tool for analysis, both qualitatively and quantitatively. In addition to the functionality of a standard thermal cycler, a quantitative thermal cycler includes an imaging device to record the florescence of samples. Florescent markers added to each sample indicate the presence of a particular sequence (replacing gel electrophoresis and short sequencing) or measure gene expression (supplementing other analysis of modified cells)

Cost of current products

  1. Licensing -- florescent analysis is patented although one key patent, US6814934, is under challenge in a case before the US Patent and Trademark Office. The European equivalent to US6814934, EP872562, has been confirmed by the European Patent Office after challenges were dropped.
  1. Hardware -- developed in house
  2. Software -- developed in house

Details

Use Cases - experiments involving a thermal cycler

Requirements- what a user might want to do with an Open Thermal Cycler (i.e. get more DNA)

Specifications - what hardware, software, GUI-ideas we might use to build it (i.e. Arduino, or a checkbox interface for entering temperatures)

4/26/2009 Conference Call - Details for connecting to the conference call.

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