Benchling SBOL3 App

[jakebeal]

Background

Benchling is a popular DNA design tool, but currently supports only SBOL 1 and poorly at that. Benchling also offers a Python SDK for accessing their API and the ability to add apps to extend the capabilities of Benchling. It should thus be possible provide SBOL import and export capabilities in a Benchling app using pySBOL3 and Benchling SDK.

Goal

This project will produce a Benchling app that can import and export files in SBOL3 format. Correctness will be validated by round-tripping (import, then export) at least the Component and Sequence objects in SBOL3 files from the SBOL test suite and by checking that imported materials can be sensibly viewed and edited in Benchling.

Difficulty Level: Medium

While the overall project is relatively straightforward, it will require figuring out how to use Benchling's SDK and app interfaces.

Size and Length of Project

• 175 hours
• Timeline: flexible, length 12 weeks

Skills

Essential skills: Python Will be learned if not known: SBOL

Public Repository

This project will produce a new app in a new open-source repository on GitHub.

Potential Mentors

Vishwesh V Kulkarni vvk215@gmail.com, tom.mitchell@raytheon.com

[ArchitJain1201]

Hello @khanspers @jakebeal; I am Archit Jain looking forward to contributing to this project for GSOC 2022, any suggestions from where to begin and what to learn before contributing to it. Here is my Github Profile GitHub

[jakebeal]

@ArchitJain1201 Glad to hear of your interest; please get in touch with potential mentors who are listed.

[tcmitchell]

@jakebeal I corresponded with @ArchitJain1201 about this project and I was unable to provide guidance on Benchling. @ArchitJain1201 did not receive any reply from Vishwesh V Kulkarni. Are there other resources for information on Benchling? @ArchitJain1201 has also expressed interest in Conversion between GenBank and SBOL3 #183

[jakebeal]

@ArchitJain1201 If you are interested in learning more in advance, I would suggest either 1) familiarizing yourself with the Benchling interface by following their "build your first app" tutorial, and/or 2) familiarizing yourself with SBOL via the tutorials.

[khanspers]

NRNB has officially been accepted as a mentoring organization for GSoC 2022! Here are some useful links:

• Project proposal template
• GSoC contributor guide
• Program timeline

[tcmitchell]

Here are some links from the GSoC Mentors mailing list that might be generally helpful to all who are interested in this project:

• Naman Gera's Quora post
• Sayak Paul's blog post

[khanspers]

A reminder that the application period opens on Monday April 4. Proposals to NRNB must be submitted on the official GSoC Site (https://summerofcode.withgoogle.com/) before April 19, 18:00 UTC to be considered, and contributors are encouraged to submit proposals in draft format early, so that mentors can give feedback directly at the GSoC site.

[khanspers]

Closing in preparation for GSoC 2023.

[jakebeal]

Project is still valid and needed: reopening for 2023

[HarshRathi2511]

@tcmitchell @jakebeal @VishweshGitHub Hello there, I'm Harsh Rathi writing to express my interest in contributing to the SBOL project as a part of the Google Summer of Code program. I have worked decently in Python and I am excited to work on this project and learn more about it. Could you provide me with the resources and necessary theory for getting familiar with the codebase of SBOL, so that I can start contributing . Here is my Github profile .

[jakebeal]

I would suggest starting by familiarizing yourself with pySBOL3 and SBOL-utilities. There is a good tutorial that you can use as a starting point at: https://github.com/SynBioDex/Community-Media/tree/master/2022/IWBDA22/sbol3-workshop

The other side of this will be connecting with Benchling's API, As a student, you should be able to get access to Benchling with a free academic license.

[khanspers]

@HarshRathi2511 : Please note that we (NRNB) are still in the process of applying as a mentoring organization; mentoring organizations will be announced on Feb 22. Check back after that date for more information.

[HarshRathi2511]

@khanspers Noted. @jakebeal Thanks a lot . I'll have a look at this .

[khanspers]

NRNB has been accepted as a mentoring organization for GSoC 2023! Contributor applications open on March 20. Here are some useful links:

GSoC contributor guide NRNB project proposal template Eligibility requirements Full program timeline

[HarshRathi2511]

Hey @jakebeal @tcmitchell @khanspers @VishweshGitHub ,I had a look at the tutorial on SBOL. I have been looking at benchling for the past few days ,while I went through the documentation of it ,I couldn't follow along since the section of API Key is not available for me as shown in the image attached below. I went through their docs but couldn't find something useful . Also for technical queries like this ,what is the appropriate medium to reach out to you guys ,Email or Github discussions ?

[HarshRathi2511]

Also @jakebeal @tcmitchell @VishweshGitHub can you suggest me some good issues to work that'll help me understand the product better.

[jakebeal]

@HarshRathi2511 Apologies for the slow reply - this is the right way to connect with us, but @tcmitchell and I have both been unavailable for a few days.

With regards to the Benchling API key: that is indeed mysterious. I've gotten in touch with their customer support, and will see about getting an answer. One way or another, I think we should be able to obtain you an API key.

In the mean time, to familiarize yourself with the SBOL side of the code base, I would suggest picking 1-2 issues from the "good first issues" tags on pySBOL3 or SBOL-utilities and trying to make a patch to fix them. That will help familiarize you with the code you'll be using, how to test the software, and how we review contributions coming into the project.

[jakebeal]

@HarshRathi2511 : Unfortunately, Benchling has told me that your problem is deliberate. Apparently, they are not allowing academics to use their API. Unfortunately, I think this means that this is no longer appropriate as an open source project: even though the SDK has an Apache license, one cannot actually use the library without a cost license. I am thus going to close this issue as a non-viable GSoC project.

Would you be interested in one of the other SBOL-related projects? Projects #187 and #215 are also format conversion projects, but work directly with files rather than depending on a closed API.

[HarshRathi2511]

@jakebeal Thanks for letting me know. I'm interested in the Snap Gene /SBOL3 integration