Quickstart#

teemi works best in notebooks or Python scripts where design, build, test, and learn steps live together.

Import the package#

import teemi

Explore the main namespaces#

  • teemi.design for sequence design, cloning, and workflow planning helpers.

  • teemi.build for assembly, PCR, and transformation-oriented utilities.

  • teemi.test for genotyping and data wrangling helpers.

  • teemi.learn for analysis and plotting utilities.

  • teemi.lims for sample and sequence tracking integrations.

Example: combinatorial library planning#

One of the quickest ways to get started is to assemble a small combinatorial design workflow from sequence files and inspect the generated primer plan.

from teemi.design.fetch_sequences import read_genbank_files
from teemi.design.combinatorial_design import DesignAssembly
from pydna.dseqrecord import Dseqrecord

path = "../data/genetic_parts/G8H_CYP_CPR_PARTS/"
pCPR_sites = [Dseqrecord(seq) for seq in read_genbank_files(path + "CPR_promoters.gb")]
CPR_sites = [Dseqrecord(seq) for seq in read_genbank_files(path + "CPR_tCYC1.gb")]

library = DesignAssembly(
    [pCPR_sites, CPR_sites],
    pad=[Dseqrecord("TCGGTC")],
    position_of_pads=[1],
    overlap=35,
    target_tm=55,
)

library.primer_list_to_dataframe()

This example is adapted from the repository README and shows the basic flow: load sequence parts, define the assembly configuration, and inspect the resulting primer table.

Example output:

      id anneals to sequence  annealing temperature  length  price(DKK)
0   P001      pMLS1      ...                  56.11      20        36.0
1   P002      pMLS1      ...                  56.18      49        88.2
2    ...        ...      ...                    ...     ...         ...

Continue with examples#

  • Start with the workflow gallery for concise notebook-style examples.

  • Browse Colab notebooks for larger end-to-end case studies.

  • Use the API reference when you want package-level documentation.

  • For a fuller walkthrough, see the combinatorial library example in the repository README.