Database storing common Labware (DWPs, etc.) specifications

62

Hi Christine, I and surely others would love to join. We already had a meeting with a couple people in here and it was great. We also decided to discuss things on this Slack: Slack. Next meeting was planned to be around next week, but we could additionally meet end of this month.

63

Hello, all! To find a good time for an ongoing biweekly meeting, starting next week, I have set up a when2meet poll. If you are interested in participating in labware catalog development, please indicate when could work for you for meeting once every two weeks: Biweekly Labware Meeting - When2meet

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64

Based on the responses to the poll, we will be meeting biweekly starting this Thursday, September 29th at 1pm Central / 2pm Eastern / 11am Pacific / etc. I have sent at calendar invitation to all poll respondents whose email address I could find. If you would like to be invited, send me a DM. The invitation information is also posted in the #collab-labware-database channel on the Bits-in-Bio Slack (See: https://bitsinbio.org/)

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65

Hi everyone, just wanted to chime in here and talk about how we solved in this in PyLabRobot.

We provide a very lightweight, hardware agnostic resource model as a part of the library. The idea here is that the Resource class and its subclasses capture all data and functionality that a resource has in an abstract way. When we added support for the Opentrons, we could immediately use all resources we imported from Hamilton’s VENUS. I talk about this a little bit more in depth in @Stefan’s and mine’s lab meeting, which you watch here (timestamp included).

An example of a resource definition (defined here) (imported from VENUS), that works with both the Opentrons and the Hamiltons:

def Cos_96_EZWash_P(name: str, with_lid: bool = False) -> Plate:
  return Plate(
    name=name,
    size_x=86.0,
    size_y=127.0,
    size_z=14.5,
    one_dot_max=11.3,
    with_lid=with_lid,
    lid_height=10,
    compute_volume_from_height=_compute_volume_from_height_Cos_96_EZWash_P,
    items=create_equally_spaced(Well,
      num_items_x=8,
      num_items_y=12,
      dx=11.5,
      dy=14.0,
      dz=1.0,
      item_size_x=9.0,
      item_size_y=9.0,
    ),
  )

In the future, we hope to host this data online and have the library pull from there. This database will be collaborative, with options for anyone to contribute their resources.

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66

Are you available to join the meeting and discuss the potential use of your solution by the community?

If you’re able to make this available under an open license and open community process quickly, it could simplify the problem we are all facing.

Waiting indefinitely for such a resource or having it “owned” by some group, however, isn’t going to be a good solution for the larger community.

67

It’s already available under the MIT license at GitHub - PyLabRobot/pylabrobot: A hardware agnostic platform for liquid handling, I think that is as open as you should need right?

I think a database that others can post to should be available in a relatively short amount of time as well.

68

Are you available to join the meeting and discuss the potential use of your solution by the community?

Sure! Will DM you my email.

69

Hi there folks,

I wanted to close the loop with some feedback from the every-2-week meetings we’ve been having (mentioned above in this thread)

The notes of the discussions thus far are available here (view-only link):
https://docs.google.com/document/d/1f8EfWB4WLbU1I5EHOeNABkh4JKD6LOgxc6hCV98UAPo/edit?usp=sharing

Our current work item is comparing & contrasting the database models for pyLabRobot and Container Ontology (should probably include the Opentrons Labware Database as well):
https://docs.google.com/spreadsheets/d/1aVB2lm_QnJCXTxtP-PIkyG10IB8RQr348f_JhwmzPMo/edit?usp=sharing

DM me or join the meeting and let us know, if you’d like edit-access to those documents!

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70

How’s the project been progressing @TimFallonUCSD ?

71

Slow and steady! The technical foundation is agreed upon & in development, hashing out all the attributes to potentiall store about labware, is the next step.

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72

I gave a short overview of LabOS’s labware model back in 2022. Today we published the full documentation of our model - https://genielifesciences.com/resources/developers-documents/labware-model/. All labware published in LabOS is of course available via REST API.
Hoping our model will contribute to the overall labware conversation.

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