SynBio Company Tech Stacks

This info was gathered by me by looking at help wanted postings from these companies and other sources. It is a cross cutting view of what the industry as a whole is using, per company.

The technologies listed here are explored in more depth in my blog post biotech libraries and languages.

I’ll be creating this data in table form at some point.

• Ginkgo Bioworks I maintain a blog post about Ginkgo DevOps which is more detailed and has more about the company in general.

  • General Stack: Python, SQL, DNA, Postgres, Snowflake, Airflow, AWS DMS, Spark on EMR
  • Data Eng:
    • Data Pipeline: Airflow, Luigi, etc
    • Big Data tools: Snowflake, Hive, Spark
    • AWS cloud: EC2, EMR, RDS, Redshift, S3
    • Python, Java, Scala, etc
    • Linux
  • Syn Bio Eng: Python, NGS
  • Computational Protein Eng: Python, Rosetta, Schrodinger, molecular simulations (MOE), deep learning
  • Computational Biologist: Python/R, bash, bioinformatics tools (samtools/bwa), snakemake/nextflow, SQL, GraphQL, AWS/Google Cloud distributed computing, Docker, git
  • IT: IAM, AD/LDAP, GPO?, Okta SSO, Centrify?, AWS in general
  • Apps:
    • AWS, Docker, Django, REST, GraphQL, React, MySQL, Postgres, Elastic Search, Airflow
    • Python, Javascript, CI/CD, AWS

• Emerald Cloud Lab. FYI Emerald is building a Cloud Lab at Carnegie Mellon.

  • ECL (Emerald’s Sybolic Lab Language (SLL written in Wolfram))
  • Infrastructure and Tools Eng:
    • ECL, Go, Python, Bash, Wolfram Language
    • Functional Programming: (e.g. Haskell, F#, Elixir)
    • AWS EKS, Lambda, Fargate
    • AWS Postgres RDS
    • Envoy+Contour, Terraform, Prometheus, Grafana, AlertManager, PagerDuty, SendGrid, Auth0,
    • AWS services: EC2, EKS, RDS, ELB/ALB/NLB, IAM, S3, Certificate Manager, CloudWatch, Route 53, ElastiCache, RDS, SQS, VPC, premises-to-cloud VPN, security groups, CloudFront
    • Linux Sys Admin
  • Web Apps and Devops: React, Next.js?, Travis CI
  • Platform Eng: ECL, Go, AWS: Postgres RDS, S3, EC2, SQS, Docker, Kubernetes

• Strateos

  • SCLE (Strateos Common Lab Env)
  • DevOps:
    • OS: Memory Mgr, File Syts
    • OSI networking
    • AWS EC2, VPC, ELB
  • BackEnd:
    • Java, SpringBoot, Scala, EKS
    • Swagger
  • FrontEnd: REST, RabbitMQ (or Kafka), S3, Postgres, Consul?
  • Automated Synth Chemistry
    • Synthetic and anlaysis (LCMS?, NMR?)
    • Automated chemical synthesis platform: ChemSpeed? or Zinsser?

• Synthego

  • LIMS (Lab Info Mgt System) (aka Synthego’s brain)
  • Computational Biologist:
    • Sequencing (Sanger, NGS)
    • BioInformatics: bwa, GATK, Picard, etc.
    • Python, R, MATLAB
  • Data Engineer
    • Python, SQL, Airflow, ETL pipelines, Tableau dashboards
    • AWS ECS, ECR, EC2, SQS. Docker, OLTP/OLAP SQL
    • Python Web apps and ORMs (SQLalchemy, Django ORM)
  • Software Dev (LIMS)
    • Python, Django, React, Redux, gRPC
  • Front End Instrumentation: Mocha, Jest, Linux CLI
    • Python, JS/TS, Node.js, React, Djano, Interest in IOT, Redux
  • Data Eng (other)
    • Python Data (Pandas, Numpy, etc), SQL, AWS
    • Djano REST/ORM, Flask/SQLAlchemy
    • BI tools (Tableau)
    • Workflow mgt: Airflow, Luigi, Prefect

• Riffyn No jobs posted Dec 2021

Bio Lab Automation, Software Focused

• Synthace. Boston and London.
  • Full Stack: React, GraphQL
  • App: TS, Go, Postgres, GCP, Kubernetes, GraphQL.
    • Good in at least 1 lang (Go, Java, etc)
    • HA and distributed
• Radix
  • Eng: Scala, TS (no jobs Dec 2021)

Other Companies

• Mammoth Biosciences
  • BioInformatics: Python, R, SQL, jupyter, pandas, plotting, PCR, qPCR, IVD assay
  • Full Stack:
    • React, Redux, Python, Django, SQL
    • AWS EB, Batch, Lambda, Step funtions, Terraform, Docker
  • Automation Eng:
    • Tecan Freedom Evo or Fluent, Labcyte Echo, SQL
    • MJP/R/SAS, Benchling
• Twist Biosciences
• Benchling Lab automation, config, integration
• Thermo Fischer: Invitogen