2021/2022 PAML pilot project
Friendzymes is producing the first practical demonstration of a new lab automation standard, Protocol Activity Markup/Modeling Language (PAML), applied to a real, multi-lab task. We are aiming to use all of the Friendzymes network's OT-2s as part of this work. The wetlab task itself has been chosen for simplicity, since the initial focus is simply on using PAML to do it. It is a basic Golden Gate protocol. Friendzymes is collaborating with CRI Paris and London Biofoundry on this pilot. The publication target for initial outcomes is the COMBINE organization's spring event, HARMONY 2022. This event is typically held mid-March. Other PAML working groups are targeting this date as well.
- Information about the COMBINE standards organization
- Information about the Bioprotocols organization
- The repository where work will be deposited
| Task | Progress | Remarks |
|---|---|---|
| OT2 Specialization - Implement well range locations | 80% | - |
| Multi-execution enviroment implementation | Debugging | Finding a way to split code into different scripts |
| Golden Gate Implementation - Implement sample collection library | 30% | Interim solution for now- need to ask head devs re. standards |
| Golden Gate Implementation - Implement Seal and Spin Markdown | - | - |
| Golden Gate Implementation - Implement Incubate Markdown | - | - |
| Golden Gate Implementation - Implement Incubate Ot2 Module | - | - |
| OT2 Specialization - !!!Refactor!!! | - | Lotsa unused code |
| OT2 Specialization - Add Github upload | - | Use Multi execution |
| OT2 Specialization - Create OT2 Python Template | - | Ask help from expert |
| OT2 Specialization - Implement smart pipetting | - | - |
| OT2 Specialization - Implement relative locations | - | - |
| OT2 Specialization - Implement smart deck assignment | - | - |
| OT2 Specialization - Implement OT2 Upload | - | Decide between HTTP,SCP, or SSH |