the problems are solved, i missed out to get the right approval before publishing it - my fault. Another problem was the fact that “hacking” is not a thing well received by everyone. No need to post further details open to the public.
In principle reversing and hacking quickly cause trouble if you publish it, a problem everyone has who is doing security research. For example when reversing software you usually have a breach of contract if you look in the licensing conditions. So in this case reversing the firmware of the ARM controller or FPGA inside the machine or reversing their software would be a problem. However, this is important, analyzing the protocols between the computer and the HiSeq is not legally relevant (here in germany) just as the analysis of network communication from a piece of software. More importantly most if not all of the information you need to control the machine you can read in the documentation provided by the components manufacturers.
I don’t see a significant risk of a collision of interest with illumina as long we are not beginning to produce our own chemicals for sequencing and therefore intruding their market and interests. So the “OpenSeq / Discussion” part of the FAQ could trigger some critics from them. But i don’t see reusing a decommissioned sequencer for microscopy is problematic, especially if used for science, not profit.
There was a series of publications involving “hacked” Illumina GAIIx machines, a list is below. I remember some of them had help from Illumina - at least from their responsible Illumina technical service. I would propose asking one of these authors if they had some reply from illumina about their doing.
Papers with reused sequencers:
Nutiu, R. et al. Nature Biotechnol. 29, 659-664 (2011). Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument.
Buenrostro, J. D., Giresi, P. G., Zaba, L.C., Chang H. Y. & Greenleaf, W. J. Nature Meth. 10, 1213-1218 (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Buenrostro, J. et al. Nature Biotechnol. 32, 562-568 (2014). Quantitative analysis of RNA-protein interactions on a massively parallel array reveals Biophysical and evolutionary landscapes
Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H. & Bartel, D. P. Nature 508, 66-71 (2014). Poly(A)-tail profiling reveals an embryonic switch in translational control
Svensen, N., Peersen, O. B. & Jaffrey, S. R. ChemBioChem 17, 1628-1635 (2016). Peptide Synthesis on a Next-Generation DNA Sequencing Platform
Sweeney, T. E., Braviak, L., Tato, C. M. & Khatri, P. Lancet Respir. Med. 4, 213-224 (2016). Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis
Jung, C. et al. Cell 170, 35-47 (2017). Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips
Boyle, E. A. et al. Proc. Natl Acad. Sci. USA 114, 5461-5466 (2017). High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding
Layton, C. J., McMahon, P. L. & Greenleaf, W. J. Preprint at bioRxiv https://doi.org/10.1101/342808 (2018). Large-scale, quantitative protein assays on a high-throughput DNA sequencing chip