Darren PlattView all speakers
Darren Platt heads the Automation and Computing Department at Amyris, which handles computation and robotics from strain design and construction through to high throughput measurement and fermentation. He has worked extensively in the sequencing field beginning with early human genome work at the Sanger Institute. After leading computing at the DOE Joint Genome Institute investigating diverse environmental sequencing including Neanderthal samples, he spent time in the personal genomics field as Director of Research at 23andMe before finally settling on yeast as the preferred sequencing target.
He developed a process for rapid deconvolution of mutagenesis hits in yeast at Amyris using next gen sequencing. More recently he authored the Genotype Specification Language (GSL) which is used in house at Amyris for advanced strain design. His current research interests include higher level design languages for synthetic biology including porting designs across species.
Denovo assembly and annotation of genomes has historically required the resources of large genome centers, custom software pipelines and expensive dedicated compute clusters. Taking advantage of advances in sequencing and software we have built an engineering oriented genome annotation pipeline with an emphasis on identifying standard parts that an engineer needs to rapidly engineer a new chassis. We have substituted a peer to peer architecture and cloud computing for traditional, IT-intensive compute clusters. The annotation process focuses on finding core canonical gene sets, flagging any species specific irregularities in those systems rather than characterizing the eccentricities of a specific organism. Our goal is to generate a set of standard promoters, loci, pathway parts and codon usage patterns from raw next generation sequencing data within hours of DNA sequencing. The output formats are tailored to work directly with our Genotype Specification Language (GSL). Coupled with a pathway design of interest we envisage a novice using GSL to translate a general pathway design into species specific parts within a day of sequencing a candidate microbial chassis