DIYbio:Notebook/Open Thermal Cycler/Use Cases

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:
 * 2) Sequence the DNA -- more quantity is needed
 * 3) Send DNA to a friend
 * 4) Transform cells -- more quantity is needed
 * 5) Archive DNA
 * 6) A user wants to study their genome
 * 7) 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)
 * 8) A user wants to extract DNA sequence Z from organism O. The user knows short sequences surrounding the region (primers) -- unknown sequence is needed
 * 9) A user has DNA and wants to create copies that are each a little bit different
 * 10) Error prone PCR
 * 11) A user wants a sequence of DNA but doesn't want to synthesize it
 * 12) Use primers + sequence X to create more of sequence X
 * 13) A user wants to determine what tree is in their backyard using a simple test (~1 species/sample)
 * 14) Amplify species-specific DNA + digestion + gel electrophoresis + imaging ==> Webpage showing species
 * 15) A user wants to determine what bacteria are on a crosswalk button (100+ species/sample) (Jason Bobe)
 * 16) Amplify species-specific DNA + sequencing
 * 17) A user wants to combine a sequence onto a known sequence (tailing - per Jake)
 * 18) i.e. take a sequence and make add biobrick ends onto it
 * 19) A user wants to synthesize a gene (Alec Nielsen)
 * 20) Assemble shorter (~60bp), overlapping oligos into a large, contiguous strand of DNA
 * 21) A user wants to screen for successfully transformed cells (Alec Nielsen)
 * 22) Colony PCR: screen successful transformants from "background" colonies by PCRing many colonies with primers for the desired vector
 * 23) A user wants to incubate/heat inactivate/chill a culture/reaction (Alec Nielsen)
 * 24) I.e., non-PCR activities: For example, incubate a restriction digest at 37 C for a few hours, heat inactivate reaction at 80 C for ten minutes, then hold at 4 C indefinitely. Convenience!
 * 1) I.e., non-PCR activities: For example, incubate a restriction digest at 37 C for a few hours, heat inactivate reaction at 80 C for ten minutes, then hold at 4 C indefinitely. Convenience!

Advanced use cases:
 * 1) The user wants to observe gene expression in cells over a time period (Josh Perfetto)
 * 2) 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.