HiSeq2000 - Next Level Hacking


#122

Thanks Urs,

  • My title still says “Creative computer engineer” can you change it to “Software developer”?
  • Can you fade the audio in and out during transitions? I can hear some jarring clicks during transitions.

Happy to help if you put up the video editing project file.


#123

Uup, wrong old link in the post.
Here the new video:

** had to pull the video due to some non authorized sequences **

Urs


#124

@kaspar I have put what I have written (and some of what you have written) on drive.
https://drive.google.com/drive/folders/14NHPrUfoNUoTT2zfJD3_KIdxKeCL0V7P?usp=sharing

The powerpoint files can supply slide shows in the spots provided should you choose to use them. The site wants slide share and I have put them there. If you decide to use them I possibly should add some attributions.

I have moved some things to a partly-written FAQ in order to shorten the wemakeit text. I need to finish that and the mass email.

I have put links in my text which I fear cannot be rendered in wemakeit. If you use any of my text on the reseq site then they may be useful.

All suggestions welcome.

@gaudi, I have not had a chance to look at the video yet but will do so tomorrow.

Just got a look then. Looks good to me.


#125

Hi John,
Thank you so much.
Is that means it is possible to control the pumps without using the micromanager. In other words, can we control these pumps individually using an RS232 port enabled device to send the serial codes?

Regards,
Uday


#126


Getting a bit nostalgic… when building webcam microscopes was still “a thing” :slight_smile:


#127

Yep. If you use the main controller, then it provides many RS232 ports and makes them available via the USB port. Alternatively, you can provide your own. The Klohn pumps take 9 pin D-sub connectors but the VICCI switches just take a pair from memory. If you want I have some python code written by a student to implement our protocol on them. The port numbers are for an 8 serial port PCIe card but are trivial to change (we were unable to use our controller - likely due to an earth loop issue that we are in the process of tracking down). It may do something different to what you want but perhaps would be useful as prior art.

J.


#128

@kaspar I’ve done the FAQ.

I think @bengtsjolen and I need to fill in our profiles on wemakeit.com since they need to contain some sales content that is displayed on the project page.

As before, I’m happy to change anything or for others to do so.

J.


#129

Think we should start discussing more publicly what happened behind the scenes (by email) the last week and discuss how to proceed. @tboysen shot a video of the sequencing lab at his institute and I put it in the video for the campaign. Unfortunately not everyone was informed and happy about it and that caused some internal trouble. Everything is OK now. The remaining question is how to deal with possible undesirable side effects of a project involving reverse engineering…

We discussed about asking Illumina for permission. I am personally not sure now if this is realistic as it might be quite tricky to find the right person and quite unlikely to get a “go ahead hack our machines” :slight_smile: Still we might want to manage the risk. Eg. checking similar projects (kinect hacking, xbox hacking, iPhone hacking etc). And address the topic in the campaign eg: “if you have concerns about what we are doing, please contact us at…”

Urs

PS: @tboysen there is still a picture of your lab in one of your posts…:slight_smile:


#130

Hi all,

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.

Best,

Teide

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


#131

I have found nothing to indicate that tear downs are illegal and ifixit.com hasn’t been closed down by Apple yet. I had a look here and agree with Teide about reversing. We haven’t needed to dig inside or try to emulate any firmware or proprietary software. I don’t think we are publishing any copyrighted material. We have no agreement with Illumina and the documentation for all the API’s and hardware are available from the component manufacturers.

Having said all that, I am not a lawyer. The current institutional HiSeq owners will have ongoing relationships with Illumina and while I don’t wanna make life hard for them, I don’t imagine that what we’re doing is a threat to them.

How about I add this to the FAQ?

Thanks for the references Teide. I agree that it would be a good idea to contact a couple of the authors. Is anyone volunteering? Otherwise I’m happy to.

J.

PS. I added the issue to the FAQ.

html: https://drive.google.com/open?id=1H74nk1uQ1b6LtMeMfd8DFishu3_cFdOZ
text: https://drive.google.com/open?id=12S6HzsKEQW4ucZoibBytG6pg6Y-F2vmA


#132

Maybe just a simple catchy phrase somewhere:

We are repurposing not reverse engineering these machines.


#133

Just working on taking what you wrote @jmarkham and putting it on the campaign and the website. I think it would be good to have a video chat to sync up our efforts. Can people join a call on Friday at 14:00 at 10:00 am GMT, especially @jmarkham, @bengtsjolen and @gaudi?


#134

If need be. Melbourne is 11 hours ahead at the moment so that’s at 1am. Something before 12:00 or after 21:00 GMT would be better for me.


#135

Ok, just picked it because that’s the time we picked last time. Let’s say 10 am GMT instead. If there are more objections then we should probably do a Doodle poll.


#136

If anyone is looking for line scan cameras/optics and the cpci based controllers for Hiseq 2000. I have about 90 sets I purchased from illumina which were removed from working or new machines. See SRLSALES on ebay or contact me for bulk sales. Selling cheap. Camera set and optics with a controller card for 250 USD. or best offer. I have some of the other parts like the objective piezo systems (about 100 of those) and some miseq parts but mostly the cameras and controllers left. Thx Mark


#137

Hey, I will be on a train then, on my way from Berlin to
Copenhagen/Malmö then :frowning: Unfortunately internet on the train is a bit
too shaky for video through the German countryside - can barely ssh…
Can do tomorrow, or any day until next Friday except this Friday and
Monday - I guess that might call for a doodle?

/b


#138

Made a doodle poll.


#139

@jmarkham is this a test to see if anyone is actually reading what you wrote? :laughing:

If you give over €100 we will send you a certificate in the mail as a token of our appreciation. Those who give less than €100 will receive a pdf of the certificate daily by email until they pay the difference.

Oh, and the slides need to be made public somehow? I can’t add them as they are :confused:


#140

FAQ is now on GitHub, please continue to edit there rather than on Google Docs.


#141

I put them on some slide sharing thing that wemakeit.com wanted. Here’s the power points.

https://drive.google.com/file/d/11WFsTn55LghCaN3SXn9Ru4PLZFhqfwrI/view?usp=sharing

https://drive.google.com/file/d/1OTPs7HBjkFiRUjEjsoN6QLJY4Dt2NaAs/view?usp=sharing

https://drive.google.com/file/d/1sPRjhq2taAa0wenfSY2fJjjbxSiuRDg_/view?usp=sharing