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Phytoform Labs processes plant genomes 100x faster with AWS HealthOmics
Phytoform Labs is a biotechnology company pioneering AI-driven genetic engineering to address one of agriculture’s most pressing challenges: developing crops that can withstand increasingly unpredictable weather patterns caused by climate change.
History shows that crop genetic advancements have improved human well-being through increased food security, improved nutrition, and reduced pesticide exposure. The innovative CRE.AI.TIVE™ platform of Phytoform uses artificial intelligence to accelerate crop evolution. It identifies precise genomic modifications that regulate plant gene expression and strengthen resilience. This is a process that would naturally take decades to develop through conventional breeding.
To achieve this at the speed and scale required to meet current agricultural needs, Phytoform uses AWS HealthOmics, a HIPAA-eligible service that provides fully managed bioinformatics workflow infrastructure, to process thousands of plant genomic datasets.
We will show how Phytoform leveraged HealthOmics to achieve 100x faster genomic processing, deploy custom bioinformatics pipelines at scale, and significantly improve their AI model’s performance to develop climate-resilient crops.
Challenge: racing to meet global food supply needs
Climate change is fundamentally disrupting global agriculture through increasingly frequent and severe weather events. Droughts, flooding, and extreme temperatures are devastating crop yields worldwide, with tangible consequences already visible. In 2023, UK cereal production fell below its five-year average due to unseasonably poor weather. These outcomes are not only costly but pose a direct threat to food security, with no sign of improvement if agriculture development continues with business-as-usual approaches.
While clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 technology offers promise for improving crop resilience by rapidly targeting and editing resilience-associated genetic regions, the formidable challenge lies in determining exactly which edits to make. The CRE.AI.TIVE platform’s sequence-to-function AI model requires learning patterns from vast quantities of multiomics data that need to be collected, quality controlled, and processed uniformly.
“Climate change isn’t giving agriculture the luxury of time,” explains Dr. Nicolas Kral, CTO and Co-founder of Phytoform. “While we could develop resilient traits through conventional breeding, it might take decades we don’t have. The computational challenge is equally daunting—we need to process thousands of multimodal omics experiments to train our AI models, something that would have been impossible with our on-premises infrastructure.”
Solution: powering AI-driven crop evolution
Phytoform implemented HealthOmics to build a scalable bioinformatics data processing infrastructure capable of handling the massive computational demands of their CRE.AI.TIVE platform. For Phytoform, HealthOmics addresses the critical need to efficiently processing vast amounts of plant genomic data at scale. HealthOmics workflows eliminates the need to configure and manage separate underlying services, such as AWS Lambda and AWS Batch.
“AWS HealthOmics transformed how we approach bioinformatics at scale,” notes Dr. Kral. “We can deploy our customized nf-core pipelines across thousands of datasets while the service handles all the resource scaling and parallelization automatically. This means our scientists focus on improving crop resilience rather than managing compute infrastructure.”
The platform’s approach is both innovative and practical. CRE.AI.TIVE accelerates evolution by finding genomic changes that could have been developed through conventional breeding methods but compressed from decades into manageable timelines. To confirm results translate to the field, all the AI predictions of Phytoform are validated in their in-house wet lab, ensuring only viable solutions are delivered. The platform’s scalability allows application to different plants and traits—from improving drought tolerance in tomatoes to increasing disease resistance in maize.
Outcome: transforming agricultural research through cloud-scale genomics
With HealthOmics powering their computational infrastructure, Phytoform has achieved remarkable results that directly impact their ability to combat climate change through agricultural innovation. “With AWS HealthOmics, we’ve achieved a 100-fold improvement in processing speed compared to our previous on-premises stack,” emphasizes Dr. Kral. “This isn’t just about computational efficiency—it directly translates to how quickly we can improve our AI model’s ability to design sustainable, climate change-resilient crops.”
This acceleration in processing capability has led to significant improvements in the performance of their CRE.AI.TIVE AI model, which directly translates to designing crops that are more sustainable and resilient to climate change. By eliminating the need to manage complex infrastructure, the scientists of Phytoform can focus entirely on their mission of improving sustainability in agriculture. The automated scaling and parallelization provided by HealthOmics has transformed what would have been impossible within their required timeframes into an achievable reality.
Looking ahead: scaling climate solutions across the globe
Phytoform Labs continues to expand their AWS HealthOmics-powered platform to address an even broader range of climate challenges. Their enhanced computational capabilities provides them a way to tackle more complex traits across various crop species, from improving water-use efficiency in cereals to increasing heat tolerance in vegetables.
The scalability of HealthOmics means that as their data requirements grow, the infrastructure seamlessly scales to match. The company’s work represents a critical advancement in agricultural biotechnology, demonstrating how modern computational tools can compress decades of selective breeding into practical development timelines.
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