Getting the complexity score from SBOL files to streamline DNA synthesis using standards

[Gonza10V]

Background

Synthetic biologists use the Design, Build, Test, Learn (DBTL) cycle to engineer biological systems. The Synthetic Biology Open Language (SBOL) was developed by the community as a standard to represent biological designs and covers the whole DBTL cycle. Although this standard is used and agreed by the community it is mostly used in its visual format and the data format has not been widely adopted, being PDF the primary format to share DNA sequences [1]. The adoption of SBOL [2] by the community can increase the reproducibility of experiments, facilitating building upon previous knowledge.
To streamline the DBTL cycle and increase the adoption of SBOL we propose the development of a function in SBOL-utilities that allow researchers to easily check synthesizability by different synthesis providers.

[1] Mante, J., Myers, C.J. Advancing reuse of genetic parts: progress and remaining challenges. Nat Commun 14, 2953 (2023). https://doi.org/10.1038/s41467-023-38791-0
[2]Buecherl, Lukas, Mitchell, Thomas, Scott-Brown, James, Vaidyanathan, Prashant, Vidal, Gonzalo, Baig, Hasan, Bartley, Bryan, Beal, Jacob, Crowther, Matthew, Fontanarrosa, Pedro, Gorochowski, Thomas, Grünberg, Raik, Kulkarni, Vishwesh, McLaughlin, James, Mısırlı, Göksel, Oberortner, Ernst, Wipat, Anil and Myers, Chris. "Synthetic biology open language (SBOL) version 3.1.0" Journal of Integrative Bioinformatics, vol. 20, no. 1, 2023, pp. 20220058. https://doi.org/10.1515/jib-2022-0058

Goal

To build a function to assess the complexity score of DNA sequences in SBOL using Twist API. Develop a function that integrates the previous function with the existing IDT complexity score function to get relevant synthesizability information.

Specific Goals:
A function that uses a SBOL file as input, interfaces the TWIST API, and outputs the complexity score.
Contribute that function to sbol-utilities by adding propper format and tests.
Develop a mediator to encapsulate functions to get complexity score for different providers (TWIST, IDT).
Document the mediator and how to add complexity score calculation for other providers.

Difficulty Level: Medium

This project involves the understanding of an API, the development of Python functions and integrating them using unittest in the CI/CD workflow of sbol-utilities.

Size and Length of Project

• medium: 175 hours
• 16 weeks

Skills

Essential skills: Python
Nice to have skills: API calls, Git, DevOps

Public Repository

https://github.com/SynBioDex/SBOL-utilities

Potential Mentors

Gonzalo Vidal (Gonzalo.vidalpena@colorado.edu)
Jake Beal

[vinayakjeet]

Hello Mentors @Gonza10V and @jake Beal,

I'm an undergraduate student at BITS Pilani with a strong foundation in biology, genetics, and a keen interest in biochemistry. I'm drawn to the SBOL project due to its significant role in advancing DNA synthesis.
With solid skills in Python and DevOps, I'm eager to contribute effectively and expand my understanding of SBOL utilities.
I'm quickly familiarizing myself with SBOL utilities and am excited to apply this knowledge to contribute to the project. I would greatly appreciate any advice on how best to contribute and any specific areas where you think my involvement could be most beneficial.

[vinayakjeet]

I would like to work on this project
Thanks

[Gonza10V]

Hi @vinayakjeet thanks for your interest in the project. For now please get yourself familiar with the GitHub actions in this repository. Let me know if you have any question about the actual workflow and the project specific goals.

[khanspers]

@vinayakjeet : All proposals for GSoC must be submitted via the GSoC interface before the deadline (April 2, 18:00 UTC); we cannot consider proposals sent to us by other means. You can update a draft proposal in the GSoC interface up until the deadline.

[sriramsowmithri9807]

Hello Mentors @Gonza10V and @jake Beal,

I hope this message finds you well!

I’m an AIML undergraduate student at JNTUH, with a strong foundation in biology, genetics, and an ever-growing curiosity about biochemistry. The SBOL project excites me because of its transformative impact on advancing DNA synthesis and standardization in synthetic biology.

Beyond my academic background, I bring solid skills in Python and DevOps, which I’m eager to apply to meaningful contributions within the SBOL ecosystem. Over the past weeks, I’ve been diving into SBOL utilities to quickly get up to speed, and I’m thrilled at the prospect of combining my technical expertise with my passion for biology in this project.

I’d love to hear your thoughts on where my skills might add the most value to the SBOL project.

[RATED-R-SUNDRAM]

Hi Everyone , I'm shivam sundram , I've working experience and domain knowledge about data science and python also having my majors in computational biology, I'm new to open source contributing and I looking to make a contribution in this organization/project, please provide any suggestions on any prerequisites for this project

[jakebeal]

@Gonza10V is expected to be the lead supervisor for this and other SBOL projects this year; I will be the secondary, supporting him.