lattice-automation / synbio Goto Github PK

• Gibson
• RestrictionDigest
• Gateway

Right now both Gibson and GoldenGate create a setup plate. But if only a few fragments/inserts are being mixed, it'd be better to just use tubes and skip the reagent layout step.

• add default switch on number of containers, below which tubes are used

Right now there is a default for MoClo:

• 2.0uL DNA per sample per assembly
• 4.0uL Assembly Mix per assembly
• fill to 20.0 uL with water

That should be a custom parameter

see: https://www.thermofisher.com/us/en/home/life-science/cloning/gateway-cloning/protocols.html

Make a list of requirements for ordering. Example for Gibson:

• primers
• pipette tips
• plates
• reagents (ex gibson mix)

• add a method to Primers for checking, against a template sequence, whether the binding is specific. like def specific(template: str) -> bool
  • check last bp of the primer against their count in the template sequence
• add the ability to add restriction sites up and downstream of the template sequence during Primers.pcr()

finish the opentrons picklist MVP

it's failing consistently on data/gibson/BBa_K1649003.fa

Add functionality for oligo design for multiplex automated genome engineering (MAGE).

Existing tools:

• MODEST (web): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086063/
  • RBS tuning with RBS calculator
  • list of operations lie mutation, substitution, upregulate, knockdown, etc
• MERLIN (Java): https://www.ncbi.nlm.nih.gov/pubmed/27054880
  • free energy calculation for binding efficiency on primers
  • BLAST to avoid off-target primers
• OptMAGE (Perl): https://github.com/churchlab/optmage

I have used the example goldengate_plasmid.py without any modifications and have received the following error:

    154             filename = self._filename() + ".fasta"
    155 
--> 156         self._check_output()
    157         return SeqIO.write(self.output, filename, "fasta")
    158 

...\synbio\protocol.py in _check_output(self)
    346         """
    347         if not self.containers:
--> 348             self.run()
    349 
    350             if not self.output:

...\synbio\protocols\goldengate.py in run(self)
     75         # get all the unique contents and set them up in their own wells
     76         mixed_wells = self._create_mixed_wells()
---> 77 
     78         for step in [
     79             Setup(

...\synbio\protocols\goldengate.py in _create_mixed_wells(self)
    125         if not mixed_wells:
    126             raise RuntimeError(f"Failed to create any GoldenGate assemblies")
--> 127 
    128         return sorted(mixed_wells)

RuntimeError: Failed to create any GoldenGate assemblies

Gibson assembly examples work perfectly for me, but none of the GoldenGate examples do.

Thank you!

Edit: The examples work if linear = False is specified in the design.

wells should leave some volume unused