Make tip reuse optional

[EvanKirshenbaum]

Steve Barcelo pointed out that for some protocols, the risk of contamination may be too high to allow the OT-2 to reuse tips for multiple transfers of the same reagent, so this should probably be made something that can be controlled by the setup JSON file (or, when generalized RunConfig is there (#123) by command-line parameter).

I'm not sure whether it will be necessary/desirable to do this on a per-reagent basis. I presume that in any case, reusing tips for waste will be fine. I'll have to ask him whether this means that if a fill takes multiple trips, we need to get a new tip for every leg.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Jun 13, 2022 at 11:10 AM PDT.

[EvanKirshenbaum]

Just to get it on the record, here are Steve's comments.

Thinking through it some more, I think the contamination concern is not a big one for our R&D scale system, so for now we can operate in a less wasteful way and reuse tips. We may need to run small demonstrations that contamination is not an issue, but can hopefully scale the experiments so that they can be achieved with our existing setup.

As for the long term, see my comments below.

Steve:

I want to make sure that I understand the point you brought up in today's meeting about protocols needing to avoid tip reuse in order to avoid contamination.

In particular,

1. What is the source of the contamination you're worried about? Is it contact with the edge of the hole, contact with the fluid in the chip, or something else?

Contact with the well and fluid are the biggest issues for reuse of tips. When tips are stored, are they sealed off from the open air somehow? It’s unlikely, but there is a small chance that the aspiration could lead to airborn DNA contamination.

2. If it's contact with the hole, is there still a risk if we reuse a tip for multiple transfers to a hole (e.g., a well) that is only used for that reagent?

I think this is probably not an issue, but we would probably need to prove it. In my experience there is a bias towards throwing away tips after use to avoid any possibility, even a small one, of contamination.

3. Is it a problem to use a single aspiration (with a single tip) to fill multiple wells with the same reagent?

This seems OK to me.

4. Could it be the case that the sensitivity to contamination only applies to certain reagents used by a protocol or is it an all-or-nothing kind of thing?

Some reagents, especially those going into a DNA amplification routine, will be much more sensitive to contamination than others. There are also likely entire workflows that are less sensitive than I am describing above.

5. If the problem is contact with the fluid, would it suffice to knock the tip against the side of an empty well (an operation Opentrons provides)?

No, especially for DNA amplification, even a few molecules remaining on the tip can be a problem.

6. Is there anything else that can be done (e.g., dunking the tip into a cleaning solution before aspirating the reagent) to reduce the level of contamination to acceptable levels?

Maybe, but then I think you would introduce other concerns, probably not worth it.

I'm trying to figure out how to provide hands-free operation for long-running protocols in the face of limited slot availability. With Bilby taking up six of eleven slots, that only leaves us five. We'll need one for an input well plate and one for a product well plate, so there are three available for tip racks, and we'll need two sizes of tip for large and small transfers.

As I said above, I think we should be OK reusing tips for our existing system, no need to make design changes to accommodate this yet.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Jun 13, 2022 at 3:11 PM PDT.

[EvanKirshenbaum]

the transfer method has a new_tip argument which can be set to pick up new tips once, never or always. There's also the option of throwing the tip into the trash or putting it back into the tray.

This has to be set for each transfer step though, so the first transfer (meaning the pipettor doesn't have a tip yet) cannot be never cause otherwise it would never pick up the tip.

Migrated from internal repository. Originally created by Mark Huber on Aug 03, 2022 at 2:38 PM PDT.

[EvanKirshenbaum]

Unfortunately, we can't use high-level operations like transfer, as we need finer control over when it's safe to actually interact with the DMF board. Also, it's not a question of whether we can simply reuse whatever tip we happen to have (the answer is always going to be "no") but rather whether we can reuse the last tip that we used for the reagent we're about to transfer.

The current logic is:

• For transfers of generated products off the board, always grab a new tip and dump it in the trash when you're done.
• For all other reagents (including waste), grab the tip you used last time for that reagent (or, if this is the first time, grab a new one), and when you're done, put it back where you found it.

We don't do it yet, but (#170) at the end of the run, all tips that we used should (unless otherwise specified), be dumped into the trash.

Migrated from internal repository. Originally created by @EvanKirshenbaum on Aug 03, 2022 at 2:50 PM PDT.