July 2nd, 2025

[ERIK-KE]

Participants

Prashant Vaidyanathan
David Ross
Goksel Misirli
Chris Myers
Yan Kay Ho
Georgie Hau Sørensen
Carolus Vitalis
Erik Kubaczka

Topics

• Update on the paper
• Discuss current efforts of the converter
• How to welcome new members and what to consider for collaborations
• Chris provides an update on SEED
• Goksel informs about the plans for the SBOL workshop

Paper

SBOLvisual 10 paper is submitted and thanks to all the contributors. Prashant will reach out to the ACS editors to inform them that we will upload the preprint to arXiv instead of bioRxiv.

SEED Poster Feedback

SBOLvisual is widely used in SBOL posters and presentations.

Chris reached an influential audience while presenting the Poster. This includes people from Twist Bioscience as well as the ACS SynBio Managing Editor.

The ACS ICE (?) repository, which basically stores GenBank files, will be shutdown. We can get in touch with ACS to discuss possible transfer of data to SynBioHub or to provide SynBioHub as alternative service.

The ACS authors center will change, which could bring the potential to introduce a checkmark that highlights work with sequences uploaded to some repository.

Days after SEED, the Nona Works Hackathon was in Boulder. Asimov people where interested in the beneficial use cases of the SBOL data model.

Leading questions arising for us from this are:
How to most easily allow people to store their data, models, designs in SBOL, if they only want to publish some data and designs in a journal like ACS SynBio.
A solution could be to support authors during the revision phase to ask them to upload their models/designs/data to offer some help or conversion service to make it.

Benchling only offers a broken SBOL1 export. However, we potentially could get access to some Benchlich Service through Douglas Densmore to create a plugin for Benchling allowing for a Benchling export to SBOL3. This could help for sequence related information but is likely to not work for more complex information. Nevertheless, this could be a good starting point.

It would be possible to talk to other companies (SnapGene etc.) as well.

Chris and Prashant plan to contact the Managing Editor of ACS to pitch the idea of some SBOL verification/approval or stamp for published papers.

Onboarding new People

How to do the onboarding of people interested in joining the SBOL devs group properly.

The current idea is to invite them to one of the SBOL Editor meetings in a month to talk to them and identify opportunities for collaborations.

Yehuda has joined a company in New York which focuses on broadening people's scope for the SynBio application. Yehuda did get in touch with us regarding whether and how we can support their mission. Prashant outlines that there is a continuous scale with two extremes. The first is how to make SBOL more accessible, while the other is how to develop the SBOL ecosystem (like SynBioHub). Inbetween, are efforts like the converters etc..

Chris highlights that asynchronous courses are helpful to onboard new people and to advertise SBOL in general as they allow this at any time of the year. In person workshops often have a limited outreach as participants leave conferences for several reasons.

Prashant and Chris converge that it would be best of both worlds to provide (virtual) workshops to onboard people when a critical mass of new interests is reached (i.e. 6 to 12 people).

At IWBDA, the schedule prevents the people participating at the NONA Works Hackathon to join the SBOL Workshop which is in the main schedule of IWBDA. A solution could be to move the SBOL workshop into the NONA Works Hackathon as this could increase the outreach of SBOL at IWBDA.

Yan Kay highlights that we don't have a central FAQ or similar on Slack. Also there could be an up to date list presenting the current tasks SBOL devs are working on, including some lead devs to get in touch with to discuss how one can help with the particular tasks. Yan Kay wants to support such efforts.

The steep learn curve of SBOL can be an obstacle for new developers to join SBOL dev as well as for people interested in SBOL. Suitable onboarding events with workshops can help to jump this gap.

Converter

Goksel reported that the efforts with his converter are going on well and are close to finalization.

Goksel's SBOL Workshop

Goksel plans on doing two SBOL workshops with his funding. The first should be hosted in Keele while the second could be at another venue.

The biological engineering students of the Bristol University could be a good target audience as well.

IGEM

Igem is planning a revamp of their registry but will be done in roughly one month. Georgie is in the loop for any synchronization with SBOL.