Biomek Guide

Streaming Biomek

Monday, November 26, 2007

Halo Pic

Halo plate for Steve I'm interested in the clear or black spots:

Here's what I can do with your function so far:

How can I align the grid such that the dots are in the center of each box? Thanks so much!

Saturday, October 13, 2007

New Video

Hey for anyone interested,

Here's a video of a recent application. I thought it was impressive so I decided to record it:

Enjoy, more super Biomek applications to come. Biomek training coming soon, ask David about details.

Monday, September 10, 2007

What NOT to do, Part 1 of a Multi-part series

Tip loader errors
The tip loader is the least reliable location on the deck because it is a moving part, is not screwed down and can be displaced by a stray tip or cable caught underneath. Positions which have conical pins rather than a rim around all corners (tip loader and fan) can be loaded incorrectly with the plate skirt over, rather than inside, one pair of pins (see picture). Therefore it is good practice to use these positions last, use for flat bottomed labware like troughs, which cannot be misplaced, or just always double-check for this error.

In addition always check the position of the notch. Some plates unfortunately have two notches, but most only have one. The notch should be on the upper left corner ALWAYS. Mis-alignment of the notch may cause a robot crash with either the span-8, pin tool or the multichannel head.

Friday, August 24, 2007

Post questions here


This is a place to vent and solve Biomek problems. If you want to make a post put a comment here with your email and I'll send you an invite.


Drops at top of well after pin tool aspirates liquid

This post was from David Carter

Pin Tool Position error in 384 well plates and solution
We had a problem with pins scraping on the edge of 384 wells, leaving droplets of liquid on the edge and depositing less than needed.

Discovery: Slowed the robot down to 10% (Instrument/ Hardware Setup/ Pod 1/ Additional settings/ Speed limit 10%)
Tripped the light curtain with the tips down. Shining a flashlight on the wells showed the pins were front and slightly left of center; pressed against the well edge. Several pins did not fully fall into wells during slower descent.

Possible Cause: labware definition was incorrect

Discovery: Manually moved head to determine good central position (Instrument/ Manual Control/ Advanced/ Pod 1/ Moved Right 0.02 then another 0.03. Moved back -0.05 then another -0.05 by typing numbers directly into fields rather than using arrow keys. Remember minus sign)

Solution: Edit labware definition (Project/Labware Type/ double click on in this case AB Gene 1055 384/Wells_1/Well offset changed from x=1.245 to 1.295 y=0.845 to 0.755)
After fix, tips hit center and day's work completed.

Outstanding problem: On 8/24/07 when writing up this post, x and y numbers had defaulted back to 1.245 and 0.845. Don't know how to make changes stick.

Outstanding problem: I think the labware definition offsets refer to distance from top left corner of plate, but we had wedged the plate bottom-right to eliminate the little bit of slop in placement. Should we always push the plates back and left instead?

Possible alternative: Framing error. I did not try re-framing the deck, which is running fine in all other applications.

end of post

Friday, July 20, 2007


1. I am now able to do a variable liquid level aspirate using a csv input
2. The robot is up and running on an agar dispense function and seed dispense for 96 well plates.

The first is only of interest to me or those who have to dilute a lot of powdered chemicals in a 96-well format. The second point is of interest to all.

In short the Biomek can make 96 well chemical screening assay plates from start to finish. This includes the addition of seeds to a desired final number per well (here 12-20 seeds per well).

The agar dispense was the hardest function to perfect. With a hot water wash of the tips after each agar aliquot the agar retension due to high viscosity (I use 0.67% agar) is overcome.

The 96-well seed dispense is achieved using wide bore tips. The 96-head aspirates from a seed suspension and then aliquots directly into the 96-well assay plate onto the hardened agar.

More interesting things to come:

1. single seed dispense to 96-well plates
2. dual seed dispense to 96-well plates. Side-by-side!
3. Pin tool chemical treatment of agar perfused with yeast.
4. ???

Technical updates from Phil's latest repair:

96 Multichannel Pod

1. pod was dropping in z axis following light curtain interuption/mag brake not
working/ I found a loose setscrew on the mag brake and resecured - fixed.

2. Pod not parallel to deck/ pod cocked towards rear in y axis a small amount/ I
releveled pod and reframed deck for MC pod

Span8 Pod

1. I realigned probes and reframed deck - much better alignment now. I also
realigned some of the tip detect black boxes which were slightly angled.

2. I did not experience any tip detect problems, but I ran relatively few tips.
Keep an eye on this and let me know if you have any more problems. Make sure
that none of the black shuck tubes or mandrel collars are loose.

3. I did not experience "probe spitting" (large droplets) but did notice "probe

I noticed what I call "probe misting" where very,very small droplets of system
fluid mist from the end of the mandresl. I believe these are unrelated to the
larger droplets of "probe spitting" generated within the mandrel and system
tubing, but result from droplets of fluid that form on the mandrel tip during
the purge cycle. and attach between the nipple and body of the mandrel.The
mandrels have a very short nipple, and purged fluid frequently bridges. I
believe the misting that I mention above is the result of this residual fluid
misting as the air quickly moves in and out of the nipple during and aspirate or
dispense cycle. See diagram below. You can minize this bridged fluid by cleaning
the ends with alcohol. Otherwise, I can't suggest anything.

Remember to use a slower asp/disp speed (50ul/sec?) to prevent probe spitting.

Wednesday, June 27, 2007


Well, in short Calibration is hell.

Until we perform a calibration test on the AP96, and the Span-8 we do not know what volumes are being moved around. After two days of failed efforts with Fluorescein dye I reluctantly switched to a more simple, but less fancy, gravimetric method of volume estimation.

In the end I got the following results:

the second method name is gravimetric calibration june 27 07 ii, the first is without the "ii"

It is important to consider pipetting techniques when doing a calibration. The first gravimetric test I performed prior with different settings yielded different results. One must also consider evaporation as a significant source of error.

Tips to get the volume you desire

Let's start talking about methods where the aspiration is from a reservoir. It is important to aspirate at the proper height. When dispensing, the dispense velocity must be appropriate to expel the fluid without leaving a remaining amount in the tip or on the tip surface. A tip touch may or may not be useful in these instance. If no tip touch is allowed you can increase your blowout volume, but your largest aspiration volume will limit this. Any blowout around 50ul is considerable, but depending on the situation you may want to increase or decrease it.

More tips later.

Also you'll get a different behavior depending on fluid type.

Updates and lessons learned

Sofware upgrade story

Well lots has gone on with the robot recently.

To make a long story short the tech support guy, Phil, suggested to update the Biomek software to build 14. He couldn't do it since he didn't have the software on him, but had the software sent to me.

I did it on my own, since he was on vacation, and it was a learning experience. I called into phone support for guidance, and here is how it went.

So it is important to know that the "export all" funciton under the file option does not really mean "export all". This only exports methods. So they should call it "export methods" rather than "export all". So if you are doing a re-install remember to do a separate export for methods, instrument files, decks, hardware, etc. Otherwise you have to start from scratch.

I got lucky and found some files to recover, but it took me a whole day to rebound from the "export all" mishap.

Also, since Norton's Ghost is on the Biomek computer I suggest that you clone the whole drive on DVD and recover in the event of disaster.

Other news--Probe Replacement

Probe 7 of the span-8 was leaking ever so little, so Phil sent a replacement part and I replaced the whole probe. The leaking has gone away. If you experience any leaking be sure to call tech support. The liquid is from the inside of the machine and will contaminate your sample as well as cause a pipetting error.

Dilution of powdered chemicals and Tranfer from file feature.

The Cutler lab has a new library, but it came in powders. The library requires dilution with DMSO. Lots of lessons were learned about the tranfer from file feature.

Each chemical has a unique molecular weight, and as such requires a unique volume of DMSO to achieve a constant molarity. This task requires tranfer from file. It took me about four days to figure out how to do this, and with some intervention from Beckman forum users I discovered that if one wants to use a reservoir as a source they must call all the wells "1".

Don't bother looking in the manual, as it does not even support a source reservoir.

Monday, June 11, 2007

Suped-up Biomek


It's time to get Biomek to do interesting and complex things.


1. Get Biomek to handle Filled chemical plates from the hotel

2. Have Biomek dilute a powdered chemical library using a variable filling function from an input csv (excel sheet)

3. Use liquid level sensing to "discover" the liquid level and therefore the top of the liquid to accomplish variable aspiration from plates that have been cherry picked or have variable volume.

4. Combinatorial mixing. Taking two compound plates and mixing them in a combinatorial fashion to yield a plate that is a mix (synthesis) of two or more compounds.

5. Use barcode reader to inform the method what the incoming labware is and how to handle it. Use this function to have each library plate dealt with accordingly.

6. Remote Viewing. I would like to set up the Biomek computer on the network to be accessable via Windows remote desktop. With this capability the progress of an automation run can be periodically checked from a user's remote computer. In short you don't have to run to the Biomek room to see if the robot has screwed up or has stalled.

Solutions in progress:

1. Slow down the belt speed to prevent splashing, also define a new labware type and restrict handling to a low speed (5% or lower)

2. Use the Quant/Normalization wizard.

3. Perhaps some mix of the qant/normalization wizard with LLS output.

4. May be as simple as a generated csv input

5. Dunno, will work on it with Phil

6. Get CPU on network and install windows remote desktop.

Friday, May 18, 2007

Biomek Seed Dispense


And the Biomek can also dispense seed for two ecotypes into a single well of a 24-well plate. Pics will be posted.

Span-8 Tip eject errors

The span-8 had a tip ejection error. The tip detectors said tips were still loaded after a tip eject, but they were not. Phil the Beckman guy was called to fix the problem.

The problem was specifically with probe 1, and it occured intermittently. Phil opened the system up and replaced the tip detection switch, but that wasn't necessarily the problem. He also opened up some board and reseated the tip detect wires. This rectified the problems and the span-8 has run without tip detect errors since then.

Wednesday, April 11, 2007

First Post

Note: This blog will be in a rudimentary form until it proves utility.

Issues of concern for Biomek:

Precision and accuracy have been in question for the Biomek by new Users. It pays to be skeptical, but it's more work. I recently received an email from conerning this issue. Both the 96-channel and the span-8 pod should be tested before the machine is used for aliquoting and dilutions.

The technician detailed the following info concerning the Span-8:

Span-8 Pipettor %CV Precision Accuracy
- 60mm probe 1uL dispense (wet well) 1mL syringe 8% 10%
- 60mm probe 5uL dispense 1mL syringe 4% 6%
- P20 tip 1uL dispense 1mL syringe 6% 7%
- P20 tip 1uL dispense 250uL syringe 6% 7%
- P200 tip 5uL dispense 1mL syringe 4% 6%

96-Multichannel pod

This issue will be verified independently and continuously investigated.

Links to check out:

Pics from my first large scale aliquot: