[DIYbio] Glowing Freshwater Algae?

Any ideas on how to go about splicing together glowing freshwater algae (preferably without all the toxic side-effects of naturally-biolumenescent-algae?)

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[DIYbio] Re: Richter or Merkel ?

Sorry, it's my mistake, it's not Merkel but Mercalli.

Le mercredi 17 août 2022 à 00:34:17 UTC, Steve Brown a écrit :
In the film San Andreas, do we use the Richter scale or the Merkel scale to measure earthquakes?

We should remember this information, after all, Americans don't make films for nothing, films are also an education.

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[DIYbio] Building Community Bio Momentum

Join us for a Global Community Bio Summit event, next week Saturday, 8amPST/11amEST/1600GMT

We'll work on ways to ask for help, build momentum, and start mutual aid networks

Join us for an event that will help you build momentum for your community labs and projects.

Have you had problems during the past 2+ years of the pandemic, building momentum on community bio projects?  We are hosting this 90 minute session to give some tips and tricks as well as helping folks get started.  We are also discussing the way we can build momentum and governance structures for our larger community - Bio Summit and beyond!

Register Here!

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[DIYbio] Re: Julia Language; are you using it?


A tabular view of Python versus Julia on many planning axis:
https://www.educba.com/julia-vs-python/

I'm working on a set of code that involves a interpreted portion to make it easy for users to tweak it without any fancy s/w management plan and a compiled side for speed. This is Python + Rust now.

For ref here are a few ways to get a compiler to fire up:

https://julialang.org/downloads/platform/

When I get a whiff of a language ( I think I know perhaps 35 or so Comp languages, easily ) I usually leave a hello world program and some IDE-ish thing on file. So it's by definition, a "maybe".

But large projects invariably span years if there even get into play seriously at all. So, it's a big decision to take a language seriously.

Not for me right now; Maybe for me, someday. 

Thanks for asking, I like to have material prepared.

Regards,
Daniel B. Kolis

 

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[DIYbio] Julia Language; are you using it?

Quick poll. Are you/your lab using or planning to use the Julia language for programming?  Or if you've investigated the language and decided not to use it, why or why not?




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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

You have a talking point that may help you with the people in San Diego that made that thing too.

Like I said, most motion control problems are slowly resolved, its unusual one observation does it. You have made some progress. You didnt mention it, but does the thing stop after the complaint entirely ?

A mere suggestion is DEFINITELY if you dont have one get a digital caliper like the cheap and just fine Mitotoyo. Maybe you have one in a tool bin, etc I mean one in the shoebox of maintenance stuff for this machine, specifically.

  Mitutoyo CNC 6in 8in 12in LCD Digital Caliper 150mm 200mm 300mm Vernier Calipers Gauge Electronic Stainless Steel Measuring Tool

I'm suggesting a wiggle and shim approach is a good line item step but not quite the bull's eye of a solution, For instance some little parallax in the frame, etc if it works sometimes and not other times, ( different XY position, etc ) that could cause a astonishing hole in some big experiment. 

Saying 'have a technician etc" is ok mostly to find out how it works in more detail. Once their gone, thats it, all you get for the moment is an invoice. That is Manager X has a nice copy and paste message for you for subsequent trouble: "We do not support tips from { fill in the blank }. Bam, that's that. 
 
A test of the shim for fun is to take it out and have a 1:1 correlation of error messages when its there or out. Your worry about the actual compliance of the material in the mix is far more ominous than positioning. Hopefully you are wrong...  Of course that's adjustable 'somehow', when they made it, they had no idea how that worked and just played with it like you are doing now. 

Non-wiggly shim stock might be good too, like brass you can cut with scissors, etc...

Good luck keep playing !

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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

***** UPDATE *****


We have tested 200 µl tips, which generate the "DiTi not mounted properly" error when taken from the SBS box, by placing them in the holes of the hanging racks. The arm mounted them from there without any problems. This way we have confirmed that the tip itself is not the cause of the problem.

By doing this I observed that the 96 tip hanging rack is a little more flexible than the rack in the SBS box. Therefore when the arm (or rather the finger) tries to mount the tip, it causes the rack to bend a little downwards because of the pressure applied, before mounting the tip securely and picking it up. In the SBS boxes the fitting or the "finger" in the tip is rather "hard". I wondered whether this difference in the last bit of the tip-mounting made a difference. Therefore I put a folded paper towel under the SBS box and repeated the experiment. This made the box a little unstable ( it tilted for a split second when the "finger" met the tip and pressed on it). AND WHAT DO YOU KNOW! THIS ACTUALLY WORKED. The tip was mounted without any problems.

I am not sure what is going on, but I am thinking that somewhere, somehow, there is a setting expecting this slightly bending/bouncing back movement right at the moment when the tip is being secured on the finger by application of pressure. The thing is, I do not know how to change this, but I will probalby have to get a TECAN technician have a look at this and repair or adjust the settings in the software .... 

Any ideas are very welcome......


On Thursday, 3 November 2022 at 19:18:50 UTC+1 dank...@gmail.com wrote:

Any thing packed with menus and a 490 page PDF writes a fat file someplace on XYZ attempts, which transducer doesn't like a thing.. Here's the manual and an extract hinting at a log file ( for example ):

https://www.tecan.com/hubfs/394802_en_V2_3%20Application%20Software%20Manual%20Fdm%20EVOlution-1.pdf

16.5.6 Log Files The log file contains information on configuration changes and other data which have been created, edited or saved. It documents pipetting and records user actions and changes to parameter values, etc. The log files are written to a specified directory (default location \Program Files\Common Files\Tecan\Logging\...)

Maybe try there as a start. poke around and find the file that changes everytime it does anything, etc. Horribly, this thing uses a MS operating system ( shudder ). But the above anyway gets you a spot in the DIR system to look, almost for sure.... the HHMMSS time stamp is the magic juice to focus your attention(s). Everybody assumes its just a Z position, well, who knows what they have dreampt up in that thing. Esp ! if it works at one end of the table and repeats this elsewhere in XY, now what. Understanding the thing is required and its a horror show when you don't have source code.

Obviously you can just carefully iterate the programmable positions you have, but a peek at the files is maybe fewer hours of tedious work. Even if/when you make it "go" the problem is nearly certain to reoccur, you cannot find the underlying logic completely via iteration without truly incredible amounts of experimentation.

Also, knowing file names by location and name is a huge leg up when talking to the phone help people. Instead of wishing you away with a click to their program, if you mumble out a specific filename, you might get 90 seconds more help before then click "Resolved" on their tracking program.

Motion control problems are usually moderately hard to really resolve. Even when you think its fixed, you usually wrong and it re- occurs sometimes. So what, keep notes and modify everything in truly "baby steps". ex: use the original tips and see if it fails with the new Cartesian settings, make a mixed system with lots of test moves and sub in the new tips one by one, etc.

and look for the file(s) !

You cannot trust even what appears to be success, anyway. There are too many things contingent on that thing to trust what appears to be a few try success. Maybe a highly specific test situation of a few tubes in a difficult to achieve 100 steps would be worth creating as a lab control, with or without this cheaper/different tip thing problem. Tap water will do, tap water with food colouring is maybe better. Most failures like this are total, not proportional, but that would show up hopefully in a last pass qualifying step you should elucidate and execute anyway. A really interesting qualifying step migth combine pH and color and give you a baseline five tubes with a ultra accurate mixed result either a colorimitter or pH tool could measure !

Finding the singular best file it makes with the most detail is surely a happy moment. If the experimenters make careful run records, tell them to make there batch files for file saving copy out that file buried in all the Microsoft noise....

Good luck, you will resolve it; ( First time, second time, etc ) but you will get the dragon slayed with effort.

Regards,
Daniel B. Kolis

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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa


Any thing packed with menus and a 490 page PDF writes a fat file someplace on XYZ attempts, which transducer doesn't like a thing.. Here's the manual and an extract hinting at a log file ( for example ):

https://www.tecan.com/hubfs/394802_en_V2_3%20Application%20Software%20Manual%20Fdm%20EVOlution-1.pdf

16.5.6 Log Files The log file contains information on configuration changes and other data which have been created, edited or saved. It documents pipetting and records user actions and changes to parameter values, etc. The log files are written to a specified directory (default location \Program Files\Common Files\Tecan\Logging\...)

Maybe try there as a start. poke around and find the file that changes everytime it does anything, etc. Horribly, this thing uses a MS operating system ( shudder ). But the above anyway gets you a spot in the DIR system to look, almost for sure.... the HHMMSS time stamp is the magic juice to focus your attention(s). Everybody assumes its just a Z position, well, who knows what they have dreampt up in that thing. Esp ! if it works at one end of the table and repeats this elsewhere in XY, now what. Understanding the thing is required and its a horror show when you don't have source code.

Obviously you can just carefully iterate the programmable positions you have, but a peek at the files is maybe fewer hours of tedious work. Even if/when you make it "go" the problem is nearly certain to reoccur, you cannot find the underlying logic completely via iteration without truly incredible amounts of experimentation.

Also, knowing file names by location and name is a huge leg up when talking to the phone help people. Instead of wishing you away with a click to their program, if you mumble out a specific filename, you might get 90 seconds more help before then click "Resolved" on their tracking program.

Motion control problems are usually moderately hard to really resolve. Even when you think its fixed, you usually wrong and it re- occurs sometimes. So what, keep notes and modify everything in truly "baby steps". ex: use the original tips and see if it fails with the new Cartesian settings, make a mixed system with lots of test moves and sub in the new tips one by one, etc.

and look for the file(s) !

You cannot trust even what appears to be success, anyway. There are too many things contingent on that thing to trust what appears to be a few try success. Maybe a highly specific test situation of a few tubes in a difficult to achieve 100 steps would be worth creating as a lab control, with or without this cheaper/different tip thing problem. Tap water will do, tap water with food colouring is maybe better. Most failures like this are total, not proportional, but that would show up hopefully in a last pass qualifying step you should elucidate and execute anyway. A really interesting qualifying step migth combine pH and color and give you a baseline five tubes with a ultra accurate mixed result either a colorimitter or pH tool could measure !

Finding the singular best file it makes with the most detail is surely a happy moment. If the experimenters make careful run records, tell them to make there batch files for file saving copy out that file buried in all the Microsoft noise....

Good luck, you will resolve it; ( First time, second time, etc ) but you will get the dragon slayed with effort.

Regards,
Daniel B. Kolis

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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

Ah, I see. I'm afraid it's been too long since I've been in front of an EVO to be of much help, then.

On Thu, Nov 3, 2022 at 6:37 AM Panagiotis Chanos <panoshanos@gmail.com> wrote:
Hello Rikke,

thank you for your email.. I will try your suggestion, although I am pretty sure that this is not the problem. I clearly remember that at least once I slowly adjusted the Z value so that I come to the point where a crash error appeared. Then I used the Z value corresponding to that just before the crash error appeared. What I have also not mentioned is that the same problem comes up with the original 10 µl SBS tips from TECAN. Furthermore, the funny thing is that after disounting the tip from the LiHa with my hand, the system "thinks" that is a DiTi is still mounted (see second error below) which makes no sense anyway if it thinks that the DiTi is not properly mounted in the first place anyway.



On Thursday, 3 November 2022 at 01:02:36 UTC+1 Rikke wrote:
Have you tried dropping the Z height by another couple of tenths? That has worked for me on the past when using off-brand tips.

On Wed, Nov 2, 2022, 11:05 Panagiotis Chanos <panos...@gmail.com> wrote:
Hello all,

I have seen that within the group there is quite some expertice on TECAN liquid handling systems so I thought I'd give it a try.

We have a TECAN Evo Clinical liquid handling system and we have purchased 1000 μl and 200μl tips from a provider and fitting SBS tip boxes. The tip positions of the SBS tip boxes did not quite correspond to the ones from the original manufacturer (from TECAN) therefore I had to initiate a teaching of the LiHa, regarding the x, and y positions of the tips in the box as well as the z position for securely mounting the DiTis.

After finishing the teaching session I tried to pick one tip from the SBS box using the "Get DiTi" direct command from the Evoware standard menu. Although the cone went in the tip, mounted it and lifted it up without any problems, I got the following error message from Evoware standard.

error tecan.png

I have tried to talk to TECAN helpdesk but after a lot of emails bak and forth it seems they do not have an idea and they suggested we order one of their technicians to look into it on site.

I was wondering whether anyone has had a similar experience and whether there is a way to overcome this problem.

Thank you for your time. 

All the best,
Panos













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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

Hello Rikke,

thank you for your email.. I will try your suggestion, although I am pretty sure that this is not the problem. I clearly remember that at least once I slowly adjusted the Z value so that I come to the point where a crash error appeared. Then I used the Z value corresponding to that just before the crash error appeared. What I have also not mentioned is that the same problem comes up with the original 10 µl SBS tips from TECAN. Furthermore, the funny thing is that after disounting the tip from the LiHa with my hand, the system "thinks" that is a DiTi is still mounted (see second error below) which makes no sense anyway if it thinks that the DiTi is not properly mounted in the first place anyway.

log.png

On Thursday, 3 November 2022 at 01:02:36 UTC+1 Rikke wrote:
Have you tried dropping the Z height by another couple of tenths? That has worked for me on the past when using off-brand tips.

On Wed, Nov 2, 2022, 11:05 Panagiotis Chanos <panos...@gmail.com> wrote:
Hello all,

I have seen that within the group there is quite some expertice on TECAN liquid handling systems so I thought I'd give it a try.

We have a TECAN Evo Clinical liquid handling system and we have purchased 1000 μl and 200μl tips from a provider and fitting SBS tip boxes. The tip positions of the SBS tip boxes did not quite correspond to the ones from the original manufacturer (from TECAN) therefore I had to initiate a teaching of the LiHa, regarding the x, and y positions of the tips in the box as well as the z position for securely mounting the DiTis.

After finishing the teaching session I tried to pick one tip from the SBS box using the "Get DiTi" direct command from the Evoware standard menu. Although the cone went in the tip, mounted it and lifted it up without any problems, I got the following error message from Evoware standard.

error tecan.png

I have tried to talk to TECAN helpdesk but after a lot of emails bak and forth it seems they do not have an idea and they suggested we order one of their technicians to look into it on site.

I was wondering whether anyone has had a similar experience and whether there is a way to overcome this problem.

Thank you for your time. 

All the best,
Panos













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Re: [DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

Have you tried dropping the Z height by another couple of tenths? That has worked for me on the past when using off-brand tips.

On Wed, Nov 2, 2022, 11:05 Panagiotis Chanos <panoshanos@gmail.com> wrote:
Hello all,

I have seen that within the group there is quite some expertice on TECAN liquid handling systems so I thought I'd give it a try.

We have a TECAN Evo Clinical liquid handling system and we have purchased 1000 μl and 200μl tips from a provider and fitting SBS tip boxes. The tip positions of the SBS tip boxes did not quite correspond to the ones from the original manufacturer (from TECAN) therefore I had to initiate a teaching of the LiHa, regarding the x, and y positions of the tips in the box as well as the z position for securely mounting the DiTis.

After finishing the teaching session I tried to pick one tip from the SBS box using the "Get DiTi" direct command from the Evoware standard menu. Although the cone went in the tip, mounted it and lifted it up without any problems, I got the following error message from Evoware standard.

I have tried to talk to TECAN helpdesk but after a lot of emails bak and forth it seems they do not have an idea and they suggested we order one of their technicians to look into it on site.

I was wondering whether anyone has had a similar experience and whether there is a way to overcome this problem.

Thank you for your time. 

All the best,
Panos













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[DIYbio] TECAN Evo Clinical - DiTi not properly mounted on LiHa

Hello all,

I have seen that within the group there is quite some expertice on TECAN liquid handling systems so I thought I'd give it a try.

We have a TECAN Evo Clinical liquid handling system and we have purchased 1000 μl and 200μl tips from a provider and fitting SBS tip boxes. The tip positions of the SBS tip boxes did not quite correspond to the ones from the original manufacturer (from TECAN) therefore I had to initiate a teaching of the LiHa, regarding the x, and y positions of the tips in the box as well as the z position for securely mounting the DiTis.

After finishing the teaching session I tried to pick one tip from the SBS box using the "Get DiTi" direct command from the Evoware standard menu. Although the cone went in the tip, mounted it and lifted it up without any problems, I got the following error message from Evoware standard.

error tecan.png

I have tried to talk to TECAN helpdesk but after a lot of emails bak and forth it seems they do not have an idea and they suggested we order one of their technicians to look into it on site.

I was wondering whether anyone has had a similar experience and whether there is a way to overcome this problem.

Thank you for your time. 

All the best,
Panos













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