October 9th, 2024

[ERIK-KE]

Participants

• Prashant Vaidyanathan
• David Ross
• Georgie Hau Sørensen
• Lukas Buecherl
• Yan Kay
• Gonzalo Vidal
• Carolus Vitalis
• Yehuda Binik
• Chris Myers
• Erik Kubaczka

Prashant gives a brief overview on the topics he wants to talk about today. Topics include the development of the SBOL Converter, the redesign of the website, IWBDA, Bio Design Inovation Week, SBOL Sponsorship, and Server hosting topics.

Erik Kubaczka gave a quick introduction as a new Editor.

• Phd Student in the group of Prof. Koeppl at TU Darmstadt
• New Editor taking over the position of Tom Mitchell
• Research in the area of GDA and Bio Design Automation

Development Efforts

Prashant provides an update on the development efforts.
After Gonzalo stept back of his role as SBOL Editor, he kicked off a joint effort for actively advancing the development efforts for SBOL. At COMBINE, all efforts where focused on the SBOL Converter (SBOL2 to SBOL3). Work on the Converter pointed out, that there are not enough examples for evaluating SBOL2 to SBOL3 conversion. Developers shifted development efforts from converter to create quickstart examples for SBOL2, SBOL3, dnaplotlib, parasbolv, and the other libaries.

Chris Myers confirms, that SBOL2 has many examples which SBOL3 is currently lacking. The simplest approach would be to use the SBOL2 to SBOL3 converter to turn all the SBOL2 examples into SBOL3 examples. A roundtrip back to SBOL2 should produce consistent SBOL2 files again.

Chris points out, that there exist many SBOL2 examples also for the basic objects. They are located at: https://github.com/SynBioDex/SBOLTestSuite.

1. Invalid : SBOL files that incorrectly encode the SBOL validation rules.
2. GenBank : A series of GenBank files
3. RDF : A series of SBOL files encoded using RDF format.
4. SBOL1 : SBOL files which encode the SBOL1 data model.
5. SBOL2 : SBOL files that are compliant, complete, and adhere to best practices.
6. SBOL2_bp : SBOL files that are compliant and complete, but do not follow best practices.
7. SBOL2_ic : SBOL files that are incomplete, but are compliant.
8. SBOL2_nc : SBOL files that are not compliant.

Currently, the notebooks extending with explanations on the example files are targeting SBOL2. They shall be extended to include equivalent SBOL3 examples in the future.

David Ross raises the issue of how to make the transition from GenBank based design information exchange to SBOL based exchanged. This shall be targeted by Notebooks presenting step by step examples of how to represent genetic designs in SBOL and where to add additional information extending on the features possible with GenBank.
In addition, Chris Myers points to a tool developed by Gonzalo Vidal and Carolus Vitalis, which shall automatically annotate sequences to introduce the additional information which can be captured in SBOL3.

SBOL Workshop at IWBDA

The Workshop will be an updated version of the previous SBOL workshops with increased focus on the usage of SBOL. It will include a tutorial on the basis of a Colab Notebook introducing the basics of PySBOL to the participants. This will include wetlab and drylab focused content.

The the workshop shall feature decreased code load and instead include hands-on examples on a selected set of features.

• Brief overview on the capabilities of SBOL
• Hands-on experience for participants
• Presentation of features showing the hands-on examples in action

SBOL Sponsorship

Prashant and Douglas Densmore want to join efforts to approach possible sponsors for BioDesignWeek and SBOL in a joint manner.

Website Redesign

Redesign runs in parallel to converter efforts. The idea is to streamline the access to the content by providing audience oriented routing through the website.

Update on confirmed dates

Harmony in Leuven Belgium: April 13. to April 17. (sunday to thursday)