Getting ReSeq out of hibernation

Hey folks, let’s have a discussion on how to restart the ReSeq project.

Just after the COVID pandemic hit I was trying to buy a HiSeq here in Bristol and set it up in our Hackspace. This didn’t work out for several reasons:

  1. I couldn’t get a machine with the PC for a reasonable price, the ebay seller kept rejecting my offers
  2. While the local Hackspace agreed to give me some space for it, the Hackspace itself decided to move somewhere else in the meantime (so all of that would need to be re-negotiated with the Hackspace members)
  3. I had too many other obligations, including my part-time work at the University of Bath
  4. The pandemic made everything harder

My availability is looking up a little at the end of this month when my contract with Uni of Bath runs out. However I do still have a lot of other projects ongoing.

The money available for ReSeq is still as it was May 2020 (CHF 5693.74 remaining). At this stage, I would like to try and sub-contract someone with the skills to take on the remaining programming work and use my own time to set the goals and manage the transition.

In the meantime @kunal has been steadily improving PySeq. The last discussion we had about ReSeq moving forward was here where we were talking about using the LabThings stack and making a GUI for it.

So what I would like to do is make a clear brief of what work should be done, what people want the HiSeq’s to do that they can not currently with PySeq. Feel free to respond below, also let’s have a call to discuss (@jmarkham @gaudi @bengtsjolen @kunal)

https://doodle.com/poll/gt3wadggucf35yfw

2 Likes

Hi @kaspar, good to hear from you. I’m happy to meet and discuss. I have a bit of time now and will have more next year I suspect. Looking at the previous post I’m still in agreement with everything that was said there.

John

@kaspar – If you will need to pay to sub-contract the programming work, I would like the opportunity to help pay for some of the costs. Thank you

Do we have a quorum for tomorrow? There seems to only be one time that everyone who has filled in the poll is available (9pm Melbourne which I think is 1pm in Europe).

John

I think so, @kaspar do you want to send out a link?

This is a great time to get restarted, our preprint has generated a decent amount of interest in the project.

Hey guys, sorry for the slow response, been setting up https://asunder.earth/ at Ars Electronica the last days and just on my way back to Berlin. Just as Kaspar I have had pandemic related issues, in my case the machine sitting in Berlin and me stuck in Stockholm for the most part of the pandemic. I’m back in in Berlin since June but also intend to finally get things sorted so that it can be remotely powered up/down and controlled as well. A Reseq reboot sounds great! And the suggestion of basing it on more accessible and expressive languages such as python and js does indeed sound attractive and much more productive. Anyway let’s talk tomorrow or so!

OK, here’s a zoom meeting we can use. Kaspar, if you would prefer to use something else, that’s fine with me too.

Join from PC, Mac, iOS or Android: https://unimelb.zoom.us/j/87515852227?pwd=MzJsTHg2QlZUTE9qa3VRb1VOL3FzQT09
Password: 144045

Or join by phone:
Dial (Australia): +61 3 7018 2005 or +61 2 8015 6011
Dial (US): +1 669 900 6833 or +1 646 876 9923
Dial (Hong Kong, China): +852 5808 6088 or +852 5803 3730
Dial (UK): +44 203 481 5240 or +44 131 460 1196
Meeting ID: 875 1585 2227
International numbers available: https://unimelb.zoom.us/u/ketaUHDU66

Or join from a H.323/SIP room system:

Dial:87515852227@zoom.aarnet.edu.au
or SIP:87515852227@zmau.us
or 103.122.166.55
Meeting ID: 87515852227
Password: 144045

Are we on for 13:00 CET? Bad timing here with builder supposed to come between 10 and 12 now will arrive just before 13:00. Should just return keys and discuss a small thing but I guess I will be ca 10-15 minutes late :frowning:

I was assuming so. I’m here now.

Too late? Or noone showed up?

Bit of both. Kaspar wasn’t there. We need to organise another time I think. @kaspar do you wanna make another doodle poll or do you want me to?

I am missing out
So sorry

Gesendet von Yahoo Mail auf Android

So sorry, I didn’t realise everyone had filled out the Doodle in time to schedule the meeting. Let’s do it this Friday if people can make it:

2021-09-17T11:00:00Z

link: Jitsi Meet

Hey, it seems the motherboard on our painstakingly installed computer for the Hiseq in Berlin just died :frowning: Maybe we just replace the motherboard but we thought we’d first have a go at setting up a virtualized system with win7, win8 and perhaps an ubuntu as guests - if that works we can switch os, “power cycle” and what not at will from the host while also not having to rely on vpn on windows etc.

can we image the win8 we set up and use that as the virtual system?

I really hope so, worst case otherwise I guess it would be a lot less fighting with physical hardware, drivers and related catch 22’s if using virtualized hardware to install.

A little update: we set up a Proxmox Virtual Environment (debian-based) with our SATA SSD with w7 as guest and gave that access to the frame-grabber card and that booted fine and sees the card. I haven’t tried connecting it to the cameras yet but we made disk-images of both the w7 and w8 installations to put them on the nvme-ssd on the machine instead of using the SATA disk so when that is up we will try hooking it up to the Hiseq - hopefully tomorrow. The plan is to add an Ubuntu guest also and then be able to reassign the framegrabber and usb to the one we want to run at the moment and only have one of them up. I also added a TP-Link Kasa wifi power plug with energy meter to the Hiseq so can switch it on/off command-line on the local network.