Bio-Design Automation hackathon BDAthlon IWBDA 2021

[Jonathan Cline]

---------- Forwarded message ----------

From: Prashant Vaidyanathan via Info <in...@lists.bio-design-automation.org>

Date: Mon, 27 Jul 2020 12:40:59 +0000

Subject: [BDAC-Info] BDAthlon 2020 - A year-long Bio-Design Automation hackathon

 

We are excited to announce that this year, the Bio-Design Automation Consortium<https://www.bio-design-automation.org/> and the NONA Research foundation<https://www.nonasoftware.org/> will be hosting a year-long Bio-Design Automation hackathon - the BDAthlon! This year's BDAthlon is a special programming contest in which teams work to solve specific computational problems identified by members of the synthetic biology. To facilitate this, we will be kicking off the BDAthlon with a Special session at IWBDA 2020 <https://www.iwbdaconf.org/2020/> where participants can brainstorm ideas for projects!

IWBDA 2020 Special Session

We believe that no idea is too big or too small for the BDAthlon! At IWBDA 2020, we'd like to invite the participants to come together and identify open computational problems in the field of synthetic biology and bio-design automation. There will be a 1 hour 45 minute breakout session on Tuesday 4th August 2020, where IWBDA participants can join one of the following 5 tracks:

  1.  Design - Build - Test - Learn Pipelines

  2.  Lab Automation

  3.  Microfluidics

  4.  Circuits & Models

  5.  Open track

The goal of the breakout session is to come up with project ideas for tools, scripts, APIs, frameworks, software that could be potentially useful for the community. Participants of the Special session will get a chance to present their ideas in a 1 hour guided session on Wednesday 5th August 2020. These project ideas will be maintained by Nona in Nona's Github organization<https://github.com/NonaSoftware>.

BDAthlon 2020

The BDAthlon is a great opportunity for the synthetic biology and the open-source community to come together and work on the computational projects identified at IWBDA 2020. There are no restrictions for size of teams, number of participants, or number of projects a participant can work on.

The Nona foundation plans on organizing regular summits throughout the year where participants can:

  1.  Allocate a few focussed days where they can work on their BDAthlon projects.

  2.  Present their progress and reach out to the community if they require any additional resources.

The BDAthlon will end next year at the start of IWBDA 2021, where we would like to encourage participants to submit their progress and milestones as featured abstracts which would be published in the proceedings of IWBDA. The winners of the BDAthlon will be announced at the end of IWBDA 2021.

Additional information can be found here: https://www.iwbdaconf.org/2020/#bdathlon

If you have any questions or suggestions, or would like to volunteer, please reach out here: in...@nonasoftware.org<mailto:in...@nonasoftware.org>

[S James Parsons Jr]

Is it possible to join this BDAathlon without paying for the conference?

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[John Allan]

Yeah I’d be interesting knowing this too

[Jonathan Cline]

Yes, you can always hack. 

SBOL 3 is out, start developing or alpha testing,  https://sbolstandard.org

[Jonathan Cline]

A related challenge:

GP-Write’s Genome Design Software Challenge Jef Boeke and Joel Bader A cash prize for the best software!

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.