DIYbio:Notebook/Open Thermal Cycler

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Project Description/Abstract

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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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