Quick DemoΒΆ
To run a quick demo to test that the installation works:
Change to the
dnastackdirectory and activate the Python virtual environment (if not already activated):cd dnastack source venv/bin/activate
Then run a stochastic simulation of adding DNA strands in order start - push - X (each at 300nM concentration and separated by a wait time of 30 minutes) by typing:
python3 washing.py example 3
After around 1 minute of computation, output similar to the following should be produced:
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STOCAL stochastic simulation of stack washing
spX
example lane 3
PHI_0 = 33% volume fraction of supernatant species SURVIVE each wash via non-specific bead binding initially, when normalised bead mass = 1.0
MU = 10% of remaining beads LOST on each wash
VOL = 1.50000e-13 litre (100nM = 9033 particles, 300nM = 27099 particles)
Bead mass remaining: 1.00
Incubating linker (200 nM) with beads, waiting sufficient time to get 100% binding
--- Wash ---
Bead mass remaining: 0.90
Adding s (300 nM) to reaction, waiting sufficient time to get 100% reaction completion
--- Wash ---
Bead mass remaining: 0.81
Adding p (300 nM) to reaction, waiting 30.00 mins
(Recording chemistry state, supernatant state, and supernatant state after a releaser)
--- Wash ---
Bead mass remaining: 0.73
Adding X (300 nM) to reaction, waiting 30.00 mins
(Recording chemistry state, supernatant state, and supernatant state after a releaser)
Done.
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Final state: (not directly observable by electrophoresis)
8 nM ks 725
0 nM s 30
0 nM p 4
6 nM ksp 576
0 nM sp 33
123 nM X 11126
119 nM kspX 10772
0 nM Xp 52
0 nM pX 14
6 nM spX 569
10 nM XpX 982
0 nM kspXp 56
10 nM kspXpX 951
0 nM spXp 2
0 nM spXpX 58
0 nM pXpX 1
0 nM XpXp 2
0 nM kspXpXpX 75
0 nM XpXpX 72
0 nM kspXpXp 8
0 nM spXpXpX 4
0 nM XpXpXpXpX 1
0 nM XpXpXpX 5
0 nM kspXpXpXpX 5
0 nM kspXpXpXpXpXpX 1
Supernatant of final state:
0 nM s 30
0 nM p 4
0 nM sp 33
123 nM X 11126
0 nM Xp 52
0 nM pX 14
6 nM spX 569
10 nM XpX 982
0 nM spXp 2
0 nM spXpX 58
0 nM pXpX 1
0 nM XpXp 2
0 nM XpXpX 72
0 nM spXpXpX 4
0 nM XpXpXpXpX 1
0 nM XpXpXpX 5
Supernatant state AFTER further wash, and releaser applied: (released stacks present)
7 nM s 658
3 nM sp 320
110 nM spX 10001
0 nM spXp 26
10 nM spXpX 910
0 nM spXpXpX 70
0 nM spXpXp 6
0 nM spXpXpXpX 4
24 nM X 2194
0 nM Xp 6
2 nM XpX 195
0 nM XpXpX 16
0 nM XpXpXpX 1
68 nM z 6219
The numerical data reported are the final concentrations (and particle numbers) of all species in the stack chemistry. Note that the output you obtain will probably vary slightly due to the simulation being stochastic.
See the Running a Simulation page for more detailed running instructions.
Also, see the Virtual Gel Image page for how to turn numerical simulation results into a more intuitive virtual polyacrylamide gel image.