Re: [DIYbio] Fwd: [Biopython] Thermocycler program file format(ting)

On 05/13/2015 07:10 AM, Bryan Bishop wrote:
> the entire iterative aspect of PCR seems difficult for me to convey in a concise matter in a .csv file. Would you have any
> suggestions?


Are you meaning you would like to capture a dynamic iteration, or just the usual
static number of cycles and time and temp for each?

For the static case, I would use declarative programming's for loop format
with name:value pairs inside the loop.


If you want to get multi variable and dynamic, such as iterate
with one set of cycle parameters until a detector sees fluourescence,
then do "plan b" for a while, then do "plan c", there are two ways to go.

You could stick with declarative and use while loops, or go to
a functional programming language such as verilog. From verilog,
it's easy to choose various ways to implement it depending on your controller
being based on a compiled language, python interpreter, or what have you.

I think functional programming is rare with biologists, so I suggest sticking
with declarative, or "procedural" code, that is traditional, quick to understand.

The straight .csv file would have no possibility of ever iterating "until cooked", only
iterating statically for fixed time periods, and it will be long lists
that definitely are not concise.

Here's an example in pseudo C/Fortran style:

temp_unit="degree Celsius"
time_unit="seconds"
min_ramp_time=15
ramp_time=0
t=0

for i=1,120 (
ramp_time=0
while ramp_time<(3*min_ramp_time)
t=t+ramp_time
temp=95
control_output(t,temp)
done

ramp_time=0
while ramp_time<(5*min_ramp_time)
t=t+ramp_time
temp=46
control_output(t,temp)
done

ramp_time=0
while ramp_time<(4*min_ramp_time)
t=t+ramp_time
temp=72
control_output(t,temp)
done

)



That will generate a temperature control output list at 1 sec intervals.


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