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What are the design tools that synthetic biology researchers use to create genomes? Is it some sort of EDA environment like Cello or Asimov, or is it done manua
by hsikka 7y ago
What are the design tools that synthetic biology researchers use to create genomes? Is it some sort of EDA environment like Cello or Asimov, or is it done manually?
- daijobu 7y agoMostly its just manipulating text files w/ bash, R, python. The tools used by this particular study: https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/GenomeRecoding https://github.com/TiongSun/iSeq https://github.com/TiongSun/iSeq
- hsikka 7y agoThank you!
- 100ideas 7y agoThat’s a good question! I wouldn’t be surprised if the academic team in this case developed something relatively simple. Let’s try to find out how they dispatched the synthesis orders they made over the two years. Was it excel or csv at the end of the day? If they were an enterprise biotech I would bet the would have a much more elaborate in-house data & design toolchain + Lims. But academic teams rarely have the resources or drive necessary to engineer digital tools approaching that level of sophistication. Other software academics might use - benching - teselagen - maaaaybe antha-lang - ??? Alternatively, perhaps the synthesis vendor supplied their own optimized design and inventory tool. Who did they buy from - gen9?
- udibai 7y agoPlenty of excellent open and closed source tools are available. For example check out clc genomics workbench