HiSeq2000 - Next Level Hacking


#102

Imagine my surprise when I got stopped at the work lift yesterday by someone from unimelb who had seen me in the video. Didn’t get a chance to find out how they’d found it.

@tboysen, I think it’s best if you take some video of your sequencing machines because my request to use video taken at PM has not yet been answered, so I’m not hopeful.
Update: I just spoke to the communications manager and she’s fine with using the video.


#103

Hi @kaspar, how are you doing with setting up the campaign?

Here some ideas what could also be included in the text:

  • Description of Hackteria
    Hackteria is a global network of people practicing DIY (do-it-yourself) biology with an interest in art, design and interdisciplinary cooperation. As a community platform hackteria.org tries to encourage the collaboration of scientists, hackers and artists to combine their expertise, write critical and theoretical reflections, share simple instructions to work with life-science technologies and cooperate on the organization of workshops, temporary labs, hack-sprints and meetings.
  • Description of GOSH
    GOSH is a global open science hardware movement. The GOSH Gathering for Open Science Hardware serves the needs of the global Open Science Hardware community through convening meetings, publications, activities and providing a forum for the community.
    Link to Manifesto: http://openhardware.science/gosh-manifesto/
    Link to Roadmap: http://openhardware.science/global-open-science-hardware-roadmap/
  • Asking for machine donations :slight_smile:
  • Link to some papers. This one describing the tradition of open source standards in the genomics community: https://liorpachter.wordpress.com/2019/01/18/open-sourcing-bioinstruments/

Urs


#104

Sorry, I’m also dragging my feet writing copy. I was waiting to see what the website looked like but still haven’t been able to access it. I’ll just do something in google docs and send it.

This article makes me thing that it may be possible to DIY or recoondition a flow cell (of some sort).


#105

I had a couple of queries about the fluidics diagram (below). I only have my original pictures and the bits to work from, but it seems a little different to ours (which is likely my mistake). Where there is the PE primng pump, I suspect we had an isolation valve like this: https://biochemfluidics.com/products/isolation-valves

Where was the Lee pump situated? Just in case I have confused it with something.

We had a large noisy vacuum pump which is not shown on yours.
https://www.knf.com/?type=5600&fileref=6125

Also, what are the 3-way valves in the picture? Are they T-pieces or something different?

Ta,

J.


#106

The priming pumps (LPVX dispenser pumps) and valves (Bio-Chem isolation valves) are at the left near the syringe pumps.


#107

@gaudi: Have you downloaded the video - is this enough to replace the “foreign” photo or do you need a better/longer shot?


#108

I think that is different to us. I had presumed the syringe pumps delivered the required amount of reagent. They have a valve in them that switches between an inlet and an outlet tube. Perhaps that is a custom modification? @tboysen, can I ask what you have?


#109

Hi John,

The setup in my machines here is equal to the picture you posted, of course not all lines to the reagents on the 10port VICI valve and the additional set for the second flow cell is not shown there. But maybe the setup is slightly different between early and late machines of the HiSeq 2000/2500 product line.

The syringe pumps are used to pull the exact volume to sufficiently displace the fluid of the previous step from the flow cell. The setup with equally moved 8 syringes (one for every lane) and a binary flow splitter in the intake is used to ensure that every lane is flown through with identical volumes.

The 250µl pump is used to fill/flush the lines from the reagent chiller to the 10-port VICI pump without touching all the rest of the fluidic system. Maybe somebody can post a full sequence of pump/valve actions already extracted from the logs?

The parts are shown on the photo i posted, see the files “LPVX dispenser pump (www.theleeco.com).pdf” and “Bio-Chem Isolation Valves.pdf” in the Fluidic section of the documentation package i provided. I was happy about this pump/valve combination because i was able to reuse them for a setup with capillary electrophoresis.

Teide


#110

Hi Teide

Thank you for the videos. I am waiting for some feedback from Kaspar and will then update the video. The lightning situation in the video you uploaded is still not ideal. The machines are quite dark due to the light coming through the windows. Is something you can do about this (maybe shoot in the evening). Or then I will try to brighten things up a bit in the video edition.

Urs


#111

Hi @jmarkham , the vacuum pump is not shown in the diagram, only the fluidic system. The pump serves to hold down the two flowcells with a vacuum. Also the heating and cooling system for the flowcell (probably resistiv heating and liquid cooling or peltier, not sure) is not shown on the diagram. We know however commands to read and set the temperatures and to engage the vacuum.
Urs


#112

Hi @gaudi,

i will create a better video with better light, again with the
smartphone camera. I think it is not necessary to get the 4K cam and
gimbal, however, they have more wide-angle. If you have more seconds
for this shot i can do a full pass from the HighSeqs over the NovaSeqs
to a PacBio. Would be around 6-8 seconds.

The thermal control of the Flowcell holders is done with peltier
elements with watercooled conterside as used for the Chiller.

And a hint for some creative hacks: With peltier elements you can not
only make a temperatur gradient with a current but also a electric
current with a heat flow. With a sufficient delta-T such a element
produces enough current to drive a small motor. Mount the element
between a bigger heatsink (cooled by a fan powered from the element) and
a metal plate heated by a tea light (factor in Tmax) and - voila - you
have a candle-powered wind mill :wink:

Best,

Teide


#113

What further feedback do you need? Did you see my reply from above?

Just managed to add @bengtsjolen and @jmarkham as “project initiators”, still need to write a lot of the text, will try and incorporate your suggestions, thanks.


#114

Hi all,

i will make a new video with better light today for the “sequencer”
shot and provide them via dropbox.

Sorry for the delay, was too busy…

Teide


#115

Hi @kaspar - sorry, missed your earlier reply, that’s what I needed. So I will make the changes to the video and upload again.
Congratulations to the great media presence of the project, well done. Looking forward to the campaign. If you can give me access to the draft somehow, then I will communicate with the WeMakeIt people to see if this is acceptable in their terms.

Urs


#116

hoi zäme,

there could be a use of this “group” function on discourse? it’s kinda small maillist, or maybe better to leave it here under this topic, so it’s visible to the world.

greets,
marc


#117

Hi @gaudi

i uploaded a new video, a passby along several sequencers, HiSeq, NovaSeq and PacBio:

https:// www.dropbox.com/s/314xtgiql3kxqke/IMG_3538_20190125081806.MOV?dl=0

Please inform me when you downloaded the video and it’s OK. It’s done with the phone camera again because the professional gear is at a remote shooting location.

BTW - i can’t add new posts to this thread, only edit my last one, “new members are limited to three replys”… maybe somebody administer this forum can change this.

Best,

Teide


#118

Hello Team,
I had to say great work. I am sure many fellow enthusiasts will be beneficial from this. I am one such person with few questions about this work,

  1. Do all the pumps works with existing software you guys have developd ?

  2. If we ignore the camera operation is everything els working in the HiSeq2000 machine.

  3. Can all these pumps be controlled trough serial port commands?

I would really appriciate any insights for the above queries.

Thank you in Advance.


#119

Hi Uday, aside from the image data on the camera link cables, everything is via serial port. See the wiki documentation for port assignments and commands used during a sequencing run. Our intention is to write device adaptors so that they can all be controlled from within micromanager - hopefully from a custom plugin that we intend to write but certainly from the core api which can be called from a variety of languages. The pumps and microfluidic switches are all rs-232 and the command sets are similar (but not always identical) to the vendor data sheets.

Regards,

John


#120

@jmarkham, have you made any progress on the text about applications?

@gaudi, could you install the Signal app so I can send you login details?


#121

Hi all,
I just uploaded the updated campaign video.

See post below.

Urs