Preventing Interactive Shells in Production Kubernetes Containers

Introduction

At Ginkgo we ensure that actions taken on software running in production are recorded and auditable. This is generally good practice and there are compliance regimes that require this level of logging and auditability.

We also want to enable our software engineering teams to easily troubleshoot their production applications. When running applications in our Kubernetes (k8s) clusters, we can use core, standard RBAC (Role Based Access Controls) and the cluster audit logs to capture actions taken on cluster resources to ensure adherence to these best practices and policies.

This blog will explain how we used OPA Gatekeeper policies to resolve tension between engineers wanting to execute shell commands in running containers when troubleshooting, while still capturing actions in the K8s cluster audit logs.

The Problem with kubectl exec and Auditability

While we hope to provide all the visibility a software developer could want with our observability tooling, sometimes instrumentation is missing. Developers understandably want the ability to execute commands within running containers when under pressure to quickly resolve a production issue.

Kubernetes provides an exec API , which allows for executing shell commands within a Pod container.

Unfortunately, once an interactive shell session is initiated, any commands issued within the container are no longer captured by the K8s audit logs. The audit logs record who issued an exec on which pod container, and that’s it.

Using standard RBAC resources we can deny any exec command entirely, but developers would feel the loss of that capability. What we really want is to prevent interactive shell sessions, to which the audit logs are blind. Standard RBAC resources are not able to differentiate between interactive and non-interactive exec calls. With non-interactive exec commands, the shell commands are captured in the audit logs. While it may slow developers to have to construct individual exec commands, they can get the troubleshooting capabilities they need while satisfying logging and auditability constraints.

What is OPA Gatekeeper and How Does it Solve the Problem?

Open Policy Agent (OPA) is an open-source policy engine. OPA Gatekeeper is built on top of OPA to provide K8s specific policy enforcement features. The Software Developer Acceleration (SDA) team at Ginkgo is responsible for operating (Elastic Kubernetes Service) EKS clusters. SDA was already considering implementing OPA Gatekeeper for a few cluster policy enforcement use cases.

When concerns about allowing non-interactive exec arose, we thought OPA Gatekeeper might provide a solution. We stumbled upon a Gatekeeper GitHub issue, which described our exact use case. This issue suggested that it should be feasible to implement an OPA Gatekeeper constraint to act on the PodExecOptions which determine whether an exec is interactive or not.

OPA Gatekeeper uses the OPA policy engine to enforce policy in K8s by defining Custom Resource Definitions: ConstraintTemplates and Constraints. Those resources integrate with K8s admission controllers to reject API calls and resources which violate a constraint. K8s admission controls are implemented using validating and mutating webhooks.

OPA Gatekeeper also provides a library of ConstraintTemplates for many common policy use cases. Unfortunately, preventing interactive exec is not one of the already implemented ConstraintTemplates in the community library.

SDA set up the OPA Gatekeeper and then started experimenting and learning how to craft ConstraintTemplates and Constraints based on the examples in the library. OPA policies are expressed in Rego, and this required some learning by members of the SDA team as it’s a Domain-Specific Language (DSL).

Enabling Gatekeeper Webhooks to Validate exec Operations

The first challenge we faced was ensuring that the OPA gatekeeper ValidatingWebhookConfiguration could validate the exec operations. Validating webhook rules match on the following API features:

  • Operations
  • apiGroups
  • apiVersions
  • Resources
  • Scope

To act on exec calls, the webhook must include the pod/exec subresource in the resources, and it must include CONNECT in the operations. We discovered that the released Helm chart for OPA Gatekeeper at the time, only specified the CREATE and UPDATE operations, and had omitted the CONNECT operation. After we modified our OPA Gatekeeper install to add the CONNECT operation our constraints were able to act upon exec calls.

apiVersion: admissionregistration.k8s.io/v1
kind: ValidatingWebhookConfiguration
metadata:
  name: gatekeeper-validating-webhook-configuration
  namespace: gatekeeper-system
webhooks:
  rules:
  - apiGroups:
    - '*'
    apiVersions:
    - '*'
    operations:
    - CREATE
    - UPDATE
    - CONNECT
    resources:
    - '*'
    - pods/ephemeralcontainers
    - pods/exec
    - pods/log
    - pods/eviction
    - pods/portforward
    - pods/proxy
    - pods/attach
    - pods/binding
    - deployments/scale
    - replicasets/scale
    - statefulsets/scale
    - replicationcontrollers/scale
    - services/proxy
    - nodes/proxy
    - services/status

ConstraintTemplates and Constraints

ConstraintTemplates contain policy violation rules, which can then be used by multiple different Constraints.

The PodExecOption which determines whether an exec is interactive is the stdin option. In the following ConstraintTemplate, the Rego rule is reviewing the PodExecOptions object passed to it from the Constraint to determine whether stdin is true or false. If true, the request will violate the Constraint.

apiVersion: templates.gatekeeper.sh/v1
kind: ConstraintTemplate
metadata:
  name: k8sdenyinteractiveexec
  namespace: gatekeeper-system
spec:
  crd:
    spec:
      names:
        kind: K8sDenyInteractiveExec
  targets:
  - rego: |
      package k8sdenyinteractiveexec
      violation[{"msg": msg}] {
        input.review.object.stdin == true
        msg := sprintf("Interactive exec is not permitted in production constrained environments. REVIEW OBJECT: %v", [input.review])
      }
    target: admission.k8s.gatekeeper.sh

The Constraint determines the objects to which the specified ConstraintTemplate should be applied and any enforcement action to take.

SDA provides namespaces for teams operating applications in the EKS clusters. Namespaces containing applications subject to constraints are labeled.

The following Constraint applies the K8sDenyInteractiveExec ConstraintTemplate above to the PodExecOptions object. It also uses a namespaceSelector to only apply the ConstraintTemplate in namespaces bearing the label. The default enforcement action is to deny.

apiVersion: constraints.gatekeeper.sh/v1beta1
kind: K8sDenyInteractiveExec
metadata:
  name: k8sdenyinteractiveexec
  namespace: gatekeeper-system
spec:
  match:
    kinds:
    - apiGroups:
      - ""
      kinds:
      - PodExecOptions
    namespaceSelector:
      matchExpressions:
      - key: <label to constrain the environment goes here>
        operator: In
        values:
        - "true"
    scope: Namespaced

Once this Constraint was in place, we tested by issuing kubectl exec commands against some test Pods in the labeled namespace with and without the stdin option (-i).

% kubectl exec -it test-679bdcc64b-gnjll -- /bin/bash

Error from server (Forbidden): admission webhook "validation.gatekeeper.sh" denied the request: [k8sdenyinteractiveexec] Interactive exec are not permitted in production constrained environment. REVIEW OBJECT: {"dryRun": false, "kind": {"group": "", "kind": "PodExecOptions", "version": "v1"}, "name": "test-679bdcc64b-gnjll", "namespace": "default", "object": {"apiVersion": "v1", "command": ["/bin/bash"], "container": "efs-csi-test-deployment-nginx", "kind": "PodExecOptions", "stdin": true, "stdout": true, "tty": true}, "oldObject": null, "operation": "CONNECT", "options": null, "requestKind": {"group": "", "kind": "PodExecOptions", "version": "v1"}, "requestResource": {"group": "", "resource": "pods", "version": "v1"}, "requestSubResource": "exec", "resource": {"group": "", "resource": "pods", "version": "v1"}, "subResource": "exec"}
% kubectl exec test-679bdcc64b-gnjll -- echo foo 

foo

(Feature photo by Nikola Knezevic on Unsplash)

Optimizing Sourdough Strains for Bakery Products with Il Granaio delle Idee

IGDI will leverage Ginkgo’s Adaptive Laboratory Evolution technology to improve its sourdough starter culture product


We’re so excited to announce our new collaboration with Il Granaio delle Idee (IGDI)!

IGDI has identified a new sourdough bakery strain that can improve the flavor and aroma profile of baked goods via its starter culture product, Pater®. This collaboration will leverage Ginkgo’s Adaptive Laboratory Evolution (ALE) technology to accelerate the growth rate of IGDI’s selected strain.

Lactic acid bacteria helps give sourdough its distinctive taste. IGDI has used its proprietary technology to develop a product, Pater, that keeps lactic acid bacteria dispersed in flour, viable and stable over time. Pater is a shelf stable, dried baking mix that can be used to make sourdough en masse, enabling artisanal and industrial bakers to expand their potential offerings of sourdough-based products. Bakers can use Pater to enhance the flavor, fragrance, structure, and color of bread, improve digestibility, and extend bread freshness. Additionally, Pater can produce natural emulsifiers, and can thus lessen the reliance on chemical additives used widely in the baking industry.

IGDI would like to incorporate a new strain in Pater to further improve the flavor and aroma of baked goods. In order to grow this strain economically, IGDI will leverage Ginkgo’s ALE technology as it seeks to evolve the strain towards a higher growth rate. Ginkgo uses ALE as a fast, powerful strain development tool that can adapt strains to industrially-relevant conditions without gene editing.

“Our collaboration with Ginkgo Bioworks represents a significant milestone in our entrepreneurial journey. We’ve watched Ginkgo excel in the food and nutrition space for years, and we couldn’t be more excited to work with them. Ginkgo’s impressive ALE technology shows promising potential to rapidly improve the growth rate of our strain, and distinguish Pater within the market. Together, we’re enhancing product quality, empowering bakers with innovative solutions that elevate their craft, and preserving the expression of culture and identity in food.”

Federico Allamprese Manes Rossi, founder and CEO of Il Granaio delle Idee

“This collaboration underscores Ginkgo’s commitment to innovation within the food and nutrition industry. We’re thrilled to support Il Granaio delle Idee’s vision by leveraging our strain optimization tools and powerful ALE technology to elevate their sourdough product to advanced levels of quality and efficiency. We welcome opportunities like this to help customers improve their products with Ginkgo’s diverse strain optimization capabilities.”

Simon Trancart, Head of ALE at Ginkgo Bioworks

To learn more about Ginkgo’s ALE technology, read an interview with Ginkgo’s Head of ALE, Simon Trancart (here), and watch Ginkgo’s Foundry Theory video, Fitter Microbes Faster with Automated ALE (here).

Ginkgo Bioworks Announces Acquisition of AgBiome’s Platform Assets

We’re thrilled to announce the acquisition of AgBiome’s platform assets, including over 115,000 fully sequenced and isolated strains, over 500 million unique gene sequences, and relevant functional data and metadata, as well as AgBiome’s development pipeline.

These assets will be integrated into Ginkgo Ag Biologicals Services, established with the acquisition of a Bayer agricultural biologicals R&D facility in 2022, and will expand Ginkgo’s proprietary unified metagenomics database. Combined, this creates one of the deepest and most advanced ag biological discovery and development platforms as well as a rich resource for the development of AI models for biological R&D.

Since its founding in 2012, AgBiome has worked to generate an extensive collection of biological products and technologies – from agricultural products, to bioactive ingredients, to gene editing tools – through its Genesis Discovery Platform. AgBiome has successfully commercialized multiple biological products, including the Howler and Theia product lines, which are not included in the acquisition. AgBiome has developed a massive microbial strain library from over 8,000 geographically diverse environmental samples. These isolates have been fully sequenced, producing a rich library with over 500 million unique gene sequences. Also included in the acquisition is a robust product concept pipeline including a dozen product candidates with greenhouse or field validation – these validated assets create a rich foundation for future partnered programs, as well as a diverse resource of metagenomic data for genomic mining and AI model training.

“We are so excited to bring AgBiome’s incredible strain and metagenomic collection into Ginkgo. This is a world class asset that will significantly expand our capabilities and can directly benefit Ginkgo’s customers in the ag biologicals space. In addition to the platform assets and capabilities, the product concepts pipeline that has been validated by AgBiome to date provides an exciting opportunity to give customers a head-start in their product development efforts.”

Michael Miille, Ginkgo Fellow

“These assets represent a massive, ground-breaking investment into exploring and characterizing microbial diversity for human benefit, and we can’t think of a better home for them than the Ginkgo platform.”

Laura Potter, AgBiome CSO

Leverage Ginkgo’s R&D services and validated assets to get a headstart in ag biologicals. Visit our website at https://www.ginkgobioworks.com/offerings/ag-biologicals-discovery-development.

Ginkgo Bioworks Previews Today’s Annual Ferment Conference, Announces “Lab Data as a Service”

Today we’re thrilled to be hosting our 5th annual Ferment conference!

The conference brings together stakeholders from across the synthetic biology community, including R&D leaders, Ginkgo Technology Network partners, experts from across academia, journalists, and many more. Because the event has reached its in-person capacity limits, a livestream will be available on Ginkgo’s YouTube page and Ginkgo’s Investor Relations page.

Lab Data as a Service

Ferment will begin with a keynote address from Ginkgo co-founder and CEO, Jason Kelly, who will discuss the value that customers across industries can create on Ginkgo’s platform, whether they’re engaging in end-to-end cell engineering programs or are leveraging Ginkgo’s new Lab Data as a Service product. His keynote will describe Ginkgo’s progress in building out the Foundry, Codebase, and AI assets which comprise its powerful horizontal platform, and which can help customers unleash the full power of their R&D teams using Ginkgo’s services.

“AI is rapidly changing how all of us think about biological research. The ingredient that’s missing is high-quality data, and we’re so excited to make the data factory we’ve built, and are continuing to scale, available to scientists across the industry. Our scientists already have access to these best-in-class services, and now we’re opening them up to you, so you can get better data, better models, and better bioengineering.” 

Jason Kelly, CEO and co-founder, Ginkgo Bioworks

Platform Presentations

Ginkgo’s technical experts will share more details about platform developments and services throughout the day at Ferment.

Ginkgo’s General Manager of Biosecurity, Matt McKnight, will introduce Ginkgo Biosecurity, the evolution of Concentric by Ginkgo, which is building and deploying the next-generation biosecurity infrastructure and technologies that global leaders need to predict, detect, and respond to a wide variety of biological threats.

“I’m so excited to share our keystone products with the world today. Biological risk, whether natural or manmade, is increasing across the board, but we have the power to change the calculus. Ginkgo Canopy, our radar for biological anomalies, tracks the emergence and evolution of biological threats for early warning and deep insight. It’s always-on, pervasive, and can be tuned to detect a large and growing set of pathogen targets, to help leaders worldwide understand the biological risks that are closest to home. And with Ginkgo Horizon, we can generate actionable biological intelligence that integrates insights from the global network of Canopy biomonitoring with our digital open-source intelligence and AI-powered modeling tools to help those leaders get the decision support they need. All of these capabilities will come together in CUBE-D, our first flagship biosecurity facility in Doha.”

Matt McKnight, General Manager of Biosecurity, Ginkgo Bioworks

Ginkgo’s co-founder and CTO, Barry Canton, will take the stage for a technical keynote featuring technical leaders from across Ginkgo’s platform, including Will Serber (Head of Automation), Emily Wrenbeck (Head of Protein Engineering), Uri Laserson (Senior Director of AI Research), and Shawdee Eshghi (Senior Director of Mammalian Engineering) to discuss Ginkgo’s strides in data generation and model training for AI across a range of applications.

“Data is the limiting reagent for AI. When it comes to biology, data is the key ingredient for standing up foundation models and making use of fine-tuned models. You need enormous data sets for the former, and rapid access to high-quality, lab-in-the-loop data generation for the latter. We’re very excited to share our progress in making both of these offerings available to our customers so they can make the most of this revolution in biological R&D.”

Barry Canton, CTO and co-founder, Ginkgo Bioworks

Lightning Talks

Hear from developers using the Ginkgo platform to build new applications, including:

Ginkgo’s customers will speak to the strides they have made by leveraging Ginkgo’s platform to supercharge their biological R&D and accelerate everything from the design to development to commercialization of their products. This newly announced progress includes the achievement of a major milestone, ahead of schedule, in a previously announced program on nitrogen fixation between Ginkgo and Bayer.

“We have our eyes set on realizing a bigger future for biologicals by leveraging open innovation through partners like Ginkgo, who are using the power of synthetic biology to change agriculture for the better. Whether it’s crop protection, nitrogen optimization, or carbon sequestration, the potential for these innovations for growers and communities worldwide is massive. The important scientific progress we have seen coming out of our nitrogen fixation program enables that better future, and will help us deliver the next generation of biologicals.”

Benoit Hartmann, Head of Biologics at Bayer Crop Sciences

“It’s always such a thrill to see so many of our partners and colleagues under one roof at Ferment. The ingenuity and drive they bring to product innovation and commercialization has always been the inspiration for what we do. Like so many of us across the team, I know what it’s like to be in their shoes and to be sitting across the table from R&D vendors and need a solution that just doesn’t exist. That’s the gap we’re closing with our service offerings at Ginkgo, and we’re just getting started.”

Jennifer Wipf, Chief Commercial Officer, Ginkgo Bioworks

The day’s programming will also include a series of panels and discussions:

Beyond Bits and Bases: AI’s Path to Unlocking the Mysteries of Biology

  • Moderator: Christina Agapakis, PhD (Senior Vice President of Creative & Marketing, Ginkgo Bioworks)
  • Panelists:
    • Kristina Buožytė (Director, Vesper, and CEO, Natrix Natrix)
    • Alexis Perrin (Producer, Vesper & founder, Rumble Fish Productions)
    • Bruno Samper (Director, Vesper & co-founder and CEO, Nedd)

Global Biosecurity in Practice

  • Moderator: Alison Snyder (Managing Editor, Axios)
  • Panelists:
    • Cindy Friedman, MD (Founding Director, CDC’s Traveler-Based Genomic Surveillance Program)
    • Wilmot James, PhD (Professor of Practice in Health Policy Services and Practice & Senior Advisor for Pandemics and Global Health Security at the School of Public Health, Brown University)
    • Nikki Romanik (Special Assistant to the President, Deputy Director and Chief of Staff for the Office of Pandemic Preparedness and Response Policy)

Productivity Redefined: Paving the Way to Sustainable Pharma Innovation

  • Marcus Schindler, PhD (Executive Vice President & Chief Scientific Officer, Novo Nordisk)
  • Jennifer Wipf (Chief Commercial Officer, Ginkgo Bioworks)

Fireside Chat with Renee Wegrzyn and Jon Terrett

  • Moderator: Michael Specter (Staff Writer, The New Yorker & Visiting Scholar, MIT Media Lab)
  • Panelists:
    • Jon Terrett, PhD (Head of Research, CRISPR Therapeutics)
    • Renee Wegrzyn, PhD (Director, Advanced Research Projects Agency for Health)

Building Biological Worlds: A Conversation About the Future with the Creators of “Vesper”

  • Moderator: Christina Agapakis, PhD (Senior Vice President of Creative & Marketing, Ginkgo Bioworks)
  • Panelists:
    • Kristina Buožytė (Director, Vesper, and CEO, Natrix Natrix)
    • Alexis Perrin (Producer, Vesper & founder, Rumble Fish Productions)
    • Bruno Samper (Director, Vesper & co-founder and CEO, Nedd)

The full event schedule can be found at https://www.ginkgoferment.com. A video livestream of the event will also be made available to the public, including on the company’s investor relations website at https://investors.ginkgobioworks.com/events.

Ginkgo Bioworks and Novo Nordisk Expand Alliance to Collaborate Across R&D Value Chain

We’re excited to announce the expansion of our strategic partnership with global healthcare leader Novo Nordisk under a framework agreement that initially is contemplated to run over five years.

Novo Nordisk and Ginkgo have created a flexible and scalable new model for their R&D partnership. Together, we aim to improve the manufacturing of Novo Nordisk’s medicines for serious chronic diseases, including diabetes and obesity medications. We also plan to collaborate on several early pipeline projects, further technology exploration, and engineering of scalable manufacturing solutions across Novo Nordisk’s portfolio.

“We have been very pleased with the progress made in our initial work with Ginkgo focused on exploring strategies for a more effective future production process. We look forward to leveraging Ginkgo’s synthetic biology platform across our R&D pipeline, from discovery through new ways of manufacturing, in this broader strategic partnership. Moreover, we are eager to explore more flexible models for external partnerships and this agreement allows Novo Nordisk to start more projects with Ginkgo in a faster and more agile manner.”

Marcus Schindler, Novo Nordisk EVP and CSO

Novo Nordisk has played an important role in shaping the landscape for pharmaceutical products in the 21st century. We’re so excited to expand our partnership to help them achieve their ambitious and global goals. With this deal structure, Novo Nordisk can easily access the entire expanse of Ginkgo’s pharma services from discovery through manufacturing. Our teams share a deep passion for discovering, developing, and manufacturing innovative therapeutics for serious chronic diseases that affect billions of people around the world. We are honored to work shoulder-to-shoulder with the brilliant scientists, engineers, and developers at Novo Nordisk to help change disease outcomes for patients around the world.

To learn more about Ginkgo’s offering, visit our webpage or email us at [email protected].

Ginkgo Bioworks Awarded Grant for AI-enabled Forecasting of Measles Outbreaks

Ginkgo epidemiological modeling experts and Northeastern University researchers awarded new grant from the Bill & Melinda Gates Foundation


Today we’re thrilled to announce that we’ve been awarded a grant from the Bill & Melinda Gates Foundation to build an open-access, AI-enabled measles forecasting model to empower proactive public health measures, such as immunization campaigns, in partnership with Northeastern University researchers Alessandro Vespignani and Sam Scarpino.

Measles is a highly contagious and often severe disease that most commonly affects children.

While the widespread availability of measles vaccines has dramatically reduced the disease burden over the past several decades, cases are on the rise in the U.S. this year, and global outbreaks continue to cause significant illness and mortality, particularly in low- and middle-income countries. These consequences are largely preventable through early interventions, but getting ahead of major outbreaks is difficult when access to data is limited.

With support from the Gates Foundation, expert epidemiologists and modelers from Ginkgo Bioworks and Northeastern University will develop a measles forecasting model to assess the risk of outbreaks and inform decision-making for timely interventions. Because measles reporting is often sparse, especially in low-resource settings, the model will draw upon traditional and non-traditional data, including public health reports, travel patterns, economic activity, and other factors, and utilize AI approaches such as machine learning and deep learning to structure and analyze a multitude of data sources to produce actionable insights.

“With support from the Gates Foundation, our project with Ginkgo Bioworks sets a new standard for what can be achieved when academia, industry, and philanthropy come together to develop global health solutions. By bringing together the expertise of multiple sectors and modern AI capabilities, we can create powerful, innovative tools that will provide critical information for safeguarding communities worldwide against the threat of measles.”

Alessandro Vespignani, Director of the Network Science Institute and Sternberg Family Distinguished Professor at Northeastern University

The forecasting model will be available open-access to help the global health community understand how likely it is that measles will emerge and spread within a given area, with the intent of enabling them to better allocate scarce resources and reduce the global burden of measles.

If we wait until large pockets of measles show up in hospital systems to launch public health responses, we are missing a critical window to act and slow the spread of this debilitating and highly contagious disease. Modern data and AI tools can shift the biosecurity and public health paradigm from reactive to proactive by helping global health leaders make more timely, effective decisions to prevent outbreaks from happening in the first place.

We believe the technologies we’re developing will give us the ability to get ahead of the curve for measles and other biological threats.

Ginkgo Bioworks to Host 5th Annual Ferment Conference

We’re hosting our annual conference, Ferment, on Thursday, April 11, 2024 in Boston, MA!

The conference brings together stakeholders from across the synthetic biology ecosystem and the Ginkgo community — from shareholders and customers to suppliers, academics, and many more.

Because we have reached in-person capacity, a video livestream of the event will be made available to the public, including on Ginkgo’s YouTube channel and on the company’s investor relations website at https://investors.ginkgobioworks.com/events.

Next-Gen Enzyme Development for Sustainable API Manufacturing with Prozomix

We’re so excited to announce our new partnership with Prozomix, a UK-based biotech company focused on novel biocatalyst discovery and manufacturing!

Together, we aim to build out the production of next generation enzyme plates for active pharmaceutical ingredient (API) manufacturing. This collaboration aims to leverage Ginkgo’s Enzyme Services and industry-leading AI/ML models along with Prozomix’s existing enzyme libraries and deep experience manufacturing enzyme plates.

This agreement also marks Prozomix’s entry into the Ginkgo Technology Network!

Ginkgo’s Technology Network brings together a diverse array of partners, spanning AI, genetic medicines, biologics, and manufacturing, with the aim of integrating their capabilities to provide customers with robust end-to-end solutions for successful R&D outcomes. With Prozomix now in the Technology Network, Ginkgo customers will have access to Prozomix’s scalable contract manufacturing services, including enzyme samples from mg to kg scale.

For several decades, demands for both improved supply chain sustainability and reduction of costs of goods sold has driven the pharma industry towards the adoption of biocatalysts in commercial API manufacturing. Existing enzyme plates offer users an opportunity to rapidly screen potential candidates early in development to identify and de-risk the use of biocatalysts capable of supporting specific reactions in API manufacturing routes. As such, biocatalyst adoption largely depends on the diversity and performance of the enzymes available in these plates.

Prozomix and Ginkgo are partnering to usher in a new generation of biocatalysts built off of sequences and activity data from previous enzyme libraries.

Ginkgo will build class-specific AI models informed by enzyme sequences and data from its own massive metagenomic database as well as Prozomix’s enzyme libraries and associated screening data. These models can then be used to discover novel functional enzyme sequences. Prozomix intends to then use next-gen enzyme libraries, designed by these models, to manufacture novel enzyme plates.

Together, we expect these next-gen enzyme plates to have a diversity and performance that traditional plates lack, potentially unlocking biocatalytic opportunities where previous plates have failed. These plates will be freely available to all pharma process chemistry groups, provided that screening data is shared back with Ginkgo to drive further refinement of the Ginkgo AI/ML models.

“With a global reputation for de-risking early stage biocatalytic processes, we believe the Ginkgo partnership will keep Prozomix at the forefront of best in class biocatalyst provision throughout the AI revolution, enabling our customers to continue saving and improving more lives.”

Simon J. Charnock, CEO of Prozomix

API manufacturing is poised to greatly benefit from the latest in enzyme engineering and AI/ML enzyme models.

We are so excited to partner with Prozomix to get enzymes into as many API routes as possible and help partners meet both their COGs savings and sustainability goals.

To learn more about Ginkgo’s Enzyme Services, please visit https://www.ginkgobioworks.com/offerings/biopharma-enzyme-services/

Acquiring Modulus Therapeutics’ Cell Therapy Assets to Strengthen Next-Gen CAR Designs

Today we’re excited to announce our acquisition of Modulus Therapeutics’ cell therapy platform assets, including their chimeric antigen receptor (CAR) and switch receptor libraries.

Modulus Therapeutics is a cell engineering company focused on the design of next-generation cell therapies for autoimmune diseases. In contrast to legacy cell therapy design, the company uses a combinatorial approach to build and screen cell therapy components that work in concert with one another to yield novel cell behaviors.

Modulus has used its platform to develop and screen libraries of novel NK-specific and T-cell specific CAR and switch receptor designs, which enable improved control and performance of immune cell-based therapies. This technology has the potential to improve the safety and efficacy of cell therapies by allowing for more precise control over activation and targeting. Modulus’ CAR-NK and CAR-T components are designed to enhance proliferation and cytotoxicity, even in inhospitable cellular environments, providing a deeper and more durable response against target cells.

Modulus’ assets complement Ginkgo’s extensive cell therapy capabilities.

With this addition, Ginkgo looks forward to supporting its customers who are improving the performance of T-cell and NK-cell based CAR therapies to treat solid tumors, autoimmune, and other diseases.

Modulus Therapeutics has built an array of incredible cell therapy assets that we are excited to add into the significant cell therapy capabilities Ginkgo has developed to date. Modulus’ CAR and switch receptor designs and libraries seamlessly integrate into our existing infrastructure and offerings. We are excited to put these new assets to work for our customers and contribute to the transformative advancements in CAR and cell therapies.

“At Modulus, we have always been motivated by enhancing access to cutting-edge cell therapy innovation. We’re very pleased that Ginkgo Bioworks shares this commitment and can leverage our technology to help transform oncology and autoimmune cell therapies. We are thrilled to contribute our innovative designs to the Ginkgo ecosystem, and look forward to seeing these tools deployed across a range of Ginkgo-partnered programs.”

Max Darnell, CEO and co-founder of Modulus Therapeutics

Ginkgo’s platform works to enable its partners to sample CAR domains with a variety of functional roles and structural positions, sourced from diverse immune cell types.

This approach to cell therapy discovery allows partners to thoroughly sample the breadth of therapeutic activities a CAR can produce.

Last year, Ginkgo entered a partnership with the Wisconsin Alumni Research Foundation (WARF) to discover and develop next-generation CAR-T cell therapies.

Ginkgo also presented new data on its high throughput pooled screening method to discover novel CAR-T designs for solid tumors at the 37th Annual Meeting of the Society for Immunotherapy of Cancer (SITC) in 2022, as well as data on its high-throughput screening platform for chimeric antigen receptor (CAR) libraries at the 26th American Society of Gene & Cell Therapy (ASGCT) Annual Meeting in 2023. The poster highlighted Ginkgo’s Foundry-enabled methods for large-scale, combinatorial library design and screening of CAR domains for improved persistence.

We expect Modulus’ cell therapy assets to help us continue to strengthen our CAR-T research & development offerings!

Learn more about Ginkgo Cell Therapy Services here.

Producing Novel Proteins to Control Ice in Extreme Cold Weather Environments with DARPA

Ginkgo has been awarded a contract for up to $6 million from the Defense Advanced Research Projects Agency (DARPA) to achieve DARPA’s objectives under its new Ice Control for cold Environments (ICE) program.

DARPA’s ICE program aims to develop new materials that control the physical properties of ice crystals to facilitate operations in extreme cold weather environments, which can pose a variety of risks to both personnel health and critical equipment. To meet this goal, Ginkgo, in collaboration with Netrias, Cambium, and consultant Dr. Ran Drori, aims to develop novel biologically-sourced and inspired materials that leverage biological adaptations to cold environments.

The Ginkgo team will work to enable the sustainable production of novel de-icing proteins with ice-modulating behaviors to improve operational efficacy in extreme cold weather environments.

These materials will be designed with the goal of meeting U.S. Department of Defense specifications and could potentially be used in solutions with broad commercial applications. One such application could be a lens coating to prevent frost formation for a range of optics applications from satellites and high altitude imaging instruments to security and wildlife cameras. The aviation and automobile industries could also benefit from de-icing products that facilitate safe operations in icy conditions. Furthermore, a topical frostbite prevention product could be developed for outdoor enthusiasts. If successful, these solutions could impact high value and consumer markets and facilitate replacement of current environmentally harmful de-icing agents.

The team plans to leverage Ginkgo Protein Services to design, screen, and optimize a library of novel proteins that demonstrate ice-modulating behaviors.

Ginkgo will design a library of proteins using metagenomic discovery and de novo computational design to source known, naturally occurring ice-modulating behavior proteins. During the discovery phase, predictive models will be used to iterate Design–Build–Test–Optimize loops, maximizing discovery of proteins with ice inhibition, induction, and low-adhesion properties. Throughout the process, Ginkgo will selectively screen promising proteins with further high-performance, application-specific characterization to inform the final down selection.

We are honored to be selected by DARPA to work on this program to facilitate sustained cold weather operations.

Building high-throughput libraries of candidate proteins is possible thanks to Ginkgo’s unique and differentiated data assets. Biology offers us a myriad of ways to adapt to our environment, and synthetic biology allows us to tap into nature’s capabilities and apply them to our own needs. We look forward to the products that the ICE program generates, which may enable enhanced safety and proficiency across various use cases.

To learn more about Ginkgo Protein Services, please visit https://www.ginkgobioworks.com/offerings/protein-services/.

If you are interested in working with Ginkgo for the public sector, check out our Offerings for Governments page.

Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Defense Advanced Research Projects Agency.