HiSeq 2000 DNA Sequencer

Kaspar is part of the ReSeq project, within the Hackteria collective. We aim to write free and open source software for an older generation of Illumina DNA sequencers that are being de-commissioned en-masse: the HiSeq 2000/2500. These machines cost upwards of £400,000 about 8 years ago and can now be obtained below £1000 or even free. They contain an optical bench and fluorescence microscopic system with red and green lasers, advanced line cameras, a precision moveable stage, microfluidic flow-cells and a pump and even a fridge. They could be used for all sorts of automated experimentation and scientific inquiry if there was usable software to drive them.

Our aim is to allow these machines, through our software, to be used for all sorts of bio-hacking, research, workshops and education. So far we thoroughly documented a machine in Luzern, Switzerland and commissioned another one donated to us by the University of Kiel. It’s currently housed in a hacker/artist studio in Berlin. Software-wise the most impressive feat has been the Python library developed by a cancer researcher in New York.

We'd like to put a machine in the Hackspace for Kaspar to work on and to use for future workshops and other bio experimentation. We proposed this on the mailing list on the 12th of August 2020 in thread titled “Can I put a DNA sequencer in the Hackspace?”. Members responded with excitement, curiosity and some caution. I've decided to outline the plan and address common questions below.

Questions

How much space does it need, where are you going to put the machine?

The machine is 118.6 cm × 76.0 cm × 94.0 cm (WxDxH). I am going to place it on a roll-able platform and I am planning to re-arrange the bio-hack area to fit it in. Here is a layout plan:

Does it make a lot of noise?

  • the machine runs at 65db, a quiet vacuum cleaner, when on
  • it won't be on most of the time, even while I am working on it
  • we can also turn off the pump and fridge separately, which are the most noisy components, if it becomes a problem

Are you going to sequence DNA?

No, the cost of obtaining the chemical to do this is prohibitive. Our main goal is to use these amazing robotic microscopes and microfluidic systems for other scientific and artistic inquiry.

We may be able to obtain some microarrays and run scans on these.

What else can you do with it?

You can take scans and highlight fluorescing matter

e.g.:

reseq.hackteria.org_291px-daphniacompositescalecrop.jpg

(full-resolution )

Once we have more control over the machine, we can use the microfluidic system and PCR to do automated experiments/assays. Here are some of the experiments people on our project are interested in:

https://github.com/kasbah/reseq-website/blob/master/faq.rst#what-are-these-other-assays-that-you-speak-of

What will happen with it if it falls out of use?

Ideally it would go to another bio hack space / bio hacker. There is a great interest in these machines from the DIY bio community.

If that fails, we dismantle it for parts: it has nice lasers, actuators, pumps, etc. Possible applications/repurposing: milling machine for reversing chips or lithography applications.

Either way it will be Kaspar's and the ReSeq project's responsibility to make sure that Hackspace membership is happy with the solution.

  • equipment/dna_sequencer
  • Last modified: 3 months ago
  • by kaspar