[DIYbio] Re: Bio-Design Automation hackathon BDAthlon IWBDA 2021

Software for genome design is research-ready but not production-ready. The BioStudio platform, for example, was designed with yeast in mind but has limitations that prevent ready use for mammalian-scale genomes.   A challenge for the global GP-Write community to develop robust open source software for designing entire chromosomes and genomes across well-annotated genomes.    Require command-line tools for sophisticated users implementing batch edits (recoding, watermarking), a GUI for fine editing and visualization, and mechanisms for converting a genome design into a DNA order sheet.  

The finalists will be given identical hard drives containing a genome of interest and associated annotation files (e.g. gff3 for input/output) and a specific task or set of global genome wide editing tasks to be accomplished (e.g. convert all TAG stop codons to TAA and insert a loxPsym sequence 3 bp downstream of each stop codon). Each will be given a chance to show off the user interface and speak about capabilities in a special session.

The runtime and precision of the output will be measured, ideally in a real-time live meeting session. The software packages will be assessed based on a combination of adherence to requirements, accuracy, memory footprint, run time performance, command line functionality and GUI ease-of-use, and additional features.