Update before the year's end

Hi everyone,

Sorry for the radio silence. I have had to focus on other work while we try and get a machine that’s easier for me to access and develop on. There are machines available on eBay in the UK but the prices are more than we could afford with our budget. I sent a lot of low-ball offers and several requests for sellers to contact me directly but none of it has worked.

(I also need to change my forum notification settings as I wasn’t notified that people were trying to get in touch here – sorry about that.)

The last significant work was undertaken at the end of September in Gaudilabs in Switzerland. I spent 5 days there working on stage movement, camera capture and trying to reproduce the initialisation process using python. I made some good progress but didn’t manage to get it to a point where I felt someone else could reliably make use of it (i.e. an alpha release).

Work has been pushed to Git though: https://github.com/kasbah/reseq-micro-manager and https://github.com/kasbah/reseq-python

The good news is: it’s looking much better for next year. We will have a HiSeq 2500 donated by @tboysen in Berlin in @bengtsjolen’s studio (has it arrived yet?). I can stay with my folks in Berlin for longer periods which should make things much easier. It should also be much easier for @bengtsjolen to contribute.

In non-software related news: @mamaya managed to win a photo competition with a scan made with the Gaudilabs HiSeq 2000. (Where can we see the scans @mamaya?)

So, in summary: hold tight and we should be able to make an alpha release in January 2020!

I’ve had a bunch of time to work with my HiSeq. I uploaded my version 2 code to my lab’s GitHub @ https://github.com/nygctech/PySeq2500V2. I think it may be useful enough for others to use.

Nice work @kunal. Looks like you made good progress! Can’t wait to try it out with the machine in Berlin.

What does the V2 refer to? Are there different hardware versions of the HiSeq 2500?

the V2 just refers to the version of the code. V1 was basically a set of scripts and functions for each piece of hardware. In V2, each piece of the hardware has a corresponding class object with relevant methods. Then everything is tied and stored together in a HiSeq object.

For example there is a y stage class named ‘y’ with a method named ‘move’ to move the y stage to an absolute position. A HiSeq object, named ‘hs’, stores the y stage class and other instrument classes. So to move the y stage in the HiSeq to position 0 you would use the command hs.y.move(0).

I’ll find some time in the coming weeks to update the GitHub with documentation on how to use the code.

Hey Kunal, that’s awesome! Thank very much for sharing. Is it worth us (as in all interested parties) trying to meet (virtually) some time to talk about our goals etc?

Oh ok, minor thing but your phrasing on GitHub reads like it’s for a HiSeq hardware V2 (“Control HiSeq2500 V2”).

@jmarkham, good idea! @kunal would be great if you could join us. I’ve made a poll. Can everyone fill it in to find the best time?

Good point, I just removed the V2 after HiSeq2500.

Apologies for my tardiness on the doodle poll. Done now. Tonight Melbourne time (GMT + 10) is still a possibility. Hopefully you will receive notifications in time and are not quite as hopeless as me at noticing them.



Hey, no problem. According to the Doodle the best time is:

2nd January 2pm UTC

Let’s use Zoom: https://zoom.us/j/973323757

Add it to your calendar!

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On my calendar! Talk to everyone then.