Transferring Digitally Encoded Information through Bacterial Nanonetworks

Hi,
I am working on reproducing this DNA Molecular Storage System and Transferring Digitally Encoded Information through Bacterial Nanonetworks:
Published https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8792165
Arxiv if you don’t have access https://arxiv.org/pdf/1801.04774.pdf

I am still playing with attaching plasmid to the Ecoli, but I am wondering about thow to make this thing more accessible from the ending part or reading the data, as it requires DNA sequencing.
Any experience in doing this not in DIY biology settings? Cheap sequencer? Alternatives?

Ale

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Dear Alessandro

Your work is much interesting about the Bacterial Nanonetworks. I think this is an interesting aproache since I am experimenting a lot with my Kombuch and Kefir. A bacterial and fungal community network that continiously adapts itself to new conditions and environment. I am a biohacker from the more naturalside doing hands on experiments. It would be really nice if you could come one time to Gaudilabs where we are currently working with a highseq 2000 machnine. There are some anticipations to create a workshop and gather some interesting people to talk more specifique on the possibilities of what a sequencer in a DIYbio environment could bring.

best

Maya

Maya Minder

Hi,
I realized the only way to sequence cheaply is to use the MinIon Sequencer.
Though I am still at the level of insering plasmids (as IT data) into bacteria. Is the Gaudilabs in Basel or Zurich?

@alecrimi, Gaudilabs is in Lucerne.

Given that you are sequencing such small amounts of DNA then you may be able to get away with a smaller/cheaper ONT sequencer:
https://nanoporetech.com/products/flongle

Sequencing errors will be an issue. See for example here:

The error rate is quite high (compared to other sequencers) and it’s non-uniform - that is, it’s sequence dependent. Some sequences (homopolymer runs for example) are not well handled. However, for your application you are free to choose an encoding scheme that avoids such sequences. Furthermore, if you characterise the error profile it should be possible to optimise the encoding to minimise the read error rate. You could potentially also encode to do some sort of forward error correction. Or you could just sequencing more deeply. Possibly a simulation could tell you which is cheaper.