HiSeq2000 - Next Level Hacking

Imagine my surprise and joy! Well done everyone. Coincidentally I’ve just come back from work where I had to clad the franken-seq in Coreflute to make it removable, if necessary, from the PC2 lab where it now lives.

The cladding will need to be moved in order to do any surgery on the internals which is a pain.

If we get something working and into the MM distribution then we should do some promotional work. At a minimum, write a paper which then gives other media something to refer to. For example like the flypi guys did:
https://www.nature.com/news/open-hardware-pioneers-push-for-low-cost-lab-kit-1.19518
http://blogs.nature.com/naturejobs/2017/04/19/techblog-need-an-instrument-build-it/

I don’t know if anyone has noticed but MM has some Arduino integration.
https://micro-manager.org/wiki/Arduino
https://micro-manager.org/wiki/ArduinoNeoPixel

That second one drives X,Y,Z stepper motors and lighting. I was considering motorising and automating an old Olympus scope that I have.

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Hi!

my name is Lorenzo and I’m a researcher in Stockholm. This is a great project, and stunning results!

I was interested in repurposing the GAIIx illumina seq as the Burge lab did (https://www.nature.com/articles/nbt.1882) and I’m sure you are well aware of, for biophysics experiments.

I was wondering if you think this would be feasible on the HiSeq 2000 as well or if it’s something you wanted to implement beside fluorescence imaging.

@bengtsjolen I see you are in Stockholm? Would you mind meeting sometimes? I read you contacted someone from the NGI and they had some machines to give away?

Thanks!

Lorenzo

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Hi Lorenzo, it should be possible to do other kinds of experiments from within micro manager. It just needs DeviceAdaptors to be written for the devices controlled via the many serial ports. (DeviceAdaptors are C++ classes in MM that handle hardware abstraction and act as device drivers). Then the hardware can be controlled by Beanshell scripts to implement protocols from within MM. See here (https://micro-manager.org/wiki/Micro-Manager_Programming_Guide) for examples. In an ideal world someone would also write java plugins to provide user interface elements, as has been done for the microscope functionality. For example, for trouble shooting I think it would be useful to have a panel showing the status of everything.

John

Hello There

This is a bit short in Time, but there will be a next gathering at the gaudilabs for further research and hacks from the 20th - 27th of September and a first stunning appereance of the HiSeq as Mikroskopic Camera device at the public scientific photo contest in the Zoo of Zurich on the 27th September. (public opencall for participation) Kaspar will be here from the 20th - 24th and if any of you would like to join, pls feel welcome, also in remote.
All best
Maya
Maya

All best

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Dear Participants in the Science Photo-Marathon,

Many thanks for your interest.

We are looking forward to welcome you soon!

Four cash awards (CHF 500.- each), and four annual passes (to Zoo Zurich) are waiting for you.

You will be also granted some free entries to watch the screened films at the Global Science Film Festival (www.sciencefilm.ch).

The registration is still open, so you can bring your relatives and friends (registration is required https://www.sciencefilm.ch/photo-marathon).

All the very best,

Science Photo-Marathon Team

Dr. Samer Angelone

University of Zurich

https://www.ieu.uzh.ch/en/staff/member/angelone_samer.html

Festival Director
Global Science Film Festival www.sciencefilm.ch

Imfeldstrasse 25, 8037 Zurich

Telephone: +41 79 232 60 68; Mail: samer.angelone@gmail.com

Ph.D. sc. nat. Biology (Publications: Google Scholar and ResearchGate)
M.A. Film Directing (Films: www.vimeo.com/samerangelone)
M.A. Film Studies

Hi All,

I’ve been working on controlling a HiSeq2500 and this forum has been an immensely helpful resource.

I mainly want control of the instrument to do some spatial transcriptomics or proteomic imaging.

I successfully got images from the camera using TDIscan and the FPGA/Y-STAGE commands.

However I’d like to use the DCAM API instead of TDIscan.

I can talk to and configure the cameras with the DCAM API, but the cameras don’t seem to get triggered after using the FPGA/Y-STAGE.

The cameras report taking 0 frames after arming the TDI and moving the Y-STAGE.

Has anyone been successful in getting scans with the DCAM API instead of TDIscan?

You need to set it up to use hardware trigger. I’m away from a computer but can dig up some code on Monday. @kaspar may be able to help as he is working on this at the moment.

Regards,

John

Hi,
Gilad E. contacted me with the following request:

I’m interested in using different kinds of polymerases during clustering to cluster more complex kinds of DNA with secondary structures that do not cluster on standard Illumina clustering. Do you have any information on: 1) the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell? 2) How to purchase stand-alone Illumina flow cells? 3) Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering?

Anyone has an idea?
Urs

Right, so as far I can tell I can set the trigger 2 ways.

  1. I can use dcam_settriggermode with the mode = 1 for internal or the mode = 128 for TDI.

  2. I can use dcam_setgetpropertyvalue with the property id for trigger mode and the property value of either 1 (normal), 3 (PIV/ fast repeat mode), 7 (multigate), or 8 (multiframe).

I think I’ve tried all the different combinations. Logically, I thought it would have just been dcam_settriggermode = TDI, but I haven’t been successful.

Here is a source file circa 2008 (around the time the camera was released) where you can see how MM did it. Does that help?

I’m not sure if this is DCAM-API v4 or not. From memory there may be differences between v4 and what MM used back then. I’m on holiday but can dig harder when I get back next week. Possibly @kaspar can say something more sensible since (hopefully) he is currently working on this.

Regards,

John

Regarding 2), I think you can buy flow cells from Illumina still. Is that what he meant? Can’t comment on the others.

Looking here I’m guessing you’re using v3? I think think this is the version being used in the 2008 code that I linked to.

If he doesn’t want to use Illumina stage for the flow cell to world interface, I’ve plasma bonded PDMS donuts to glass flow cells to stick tubing into.

Hi,

It sounds to be a good idea to try to sequence DNA that cannot be sequenced properly with the standard Illumina technology. Sometimes it is difficult to know if the problem comes from the library preparation step, the clustering step, the sequencing step or if it is a mixture of all that…

In case it may help to start with, we have here in Paris some old Illumina consumable & reagents for HiSeq2500 mainly and also MiSeq (list below)

  1. the basic materials (syringes, ports) needed for flowing reagents in and out of the flowcell?

In the rehyb kits (TruSeq Rapid Rehybridization kit) there are seringes and capillaries to fill th flowcells

  1. How to purchase stand-alone Illumina flow cells?

Usually not possible to buy without the reagents to do the clonal amplification

We have some old not used FlowCell (8 lanes for HiSeq2500)

  1. Info on swapping different reagents instead of Illumina reagents in the cBot instrument during clustering?

Never try to do that…

Let me know if some of these reagents may be usefull, because it takes space in our freezers.

Best,

Christine


Reagents Illumina Reference Expiration date Quantity

TruSeq Rapid Rehybridization kit 15038899 03/04/2015 2

HiSeq PE Cluster Kit V4 cBot Box2 of2 15049947 2019/06/21; 2019/06/25; 2019/06/07 3

TruSeq Rapid Duo cBot sample Plate Box 15037579 18/12/2014 4

TruSeq Rapid PE Cluster Kit HS 15033394 03/07/2015 2

HiSeq Rehybridization V4 15049948 13/10/2015 2

TruSeq rapid SBS Kit HS (200Cycls) 15033386 26/05/2015 2

TruSeq Multiplex Sequencing Primer 15017557 18/06/2015 4

MiSeq Reagent kit V3 (150 Cycles) Box 1 of 2 15043893 01/09/2019 1

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Dear All

Finally I found out who this ominiouse Christine is. A Meeting in Paris at La Generale with Emanuel Rebus and an enlighting insight in her practice. Hope to see you again. Best to keept good contact with the people in resource. Christine is working for the Institute for rare genetic illnesses, so her offer of all the equipment leftovers is not a scam, she has great experiences.
Would be great to somehow involve here in further processes. And, Paris, Lausanne is very close.
Nice things to come. all best
Maya

Hei Christine
Have you ever heard about the geneediting comission?
http://nationalacademies.org/gene-editing/international-commission/index.htm
would be interested about your opinion on this.
all best

let’s start to seperate this stream into new topics…

hei hei,

By the end of the year I am updating my last projects and I made some nice documentation on how to hack a science photo marathon. YES WE WON A PRICE!

check out the pics here:
https://www.hackteria.org/wiki/ReSeq2000:_Science_Photo_Marathon_2019#How_we_got_noticed_and_came_up_with_the_idea:

See you all in Leipzig,
motherfuckers!

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A post was split to a new topic: Editing Illumina recipes/run files