Molecular Programming in the Cloud

PI: Niles A. Pierce (BBE and EAS Divisions)
SASE: Cody Newman, Scholar

Over the coming decades, the fields of molecular programming, nucleic acid nanotechnology, and synthetic biology are poised to generate transformative programmable molecular and cellular technologies addressing challenges to science and society ranging from neuroscience and development, to diagnosis and treatment, and from renewable energy to sustainable manufacturing. In a multi-decade effort to support these emerging fields, the Pierce lab developed NUPACK (Nucleic Acid Package), a growing software suite for the analysis and design of nucleic acid structures, devices, and systems. NUPACK algorithms are unique in treating complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these new fields. Launched in 2007, the NUPACK web application ( has grown to have a major impact on nucleic acid analysis and design activities worldwide; in 2019 alone, the NUPACK web application hosted 110,000 user sessions totaling 1,500,000 screen minutes and 2,500,000 page views. NUPACK papers have been cited 2200 times.

Usage has increased to the point where the 240-core NUPACK compute cluster is frequently overwhelmed by the research community. The Schmidt Academy is working with the Pierce lab to re-architect the NUPACK web application to enable the use of a scalable cloud-based computer cluster that can resize dynamically with demand. The new web application will also benefit from a complete rewrite of the NUPACK scientific code base (NUPACK 4.0), introducing expanded secondary structure models and achieving dramatic performance enhancements (e.g., 20-120x speedup for equilibrium test tube analysis). With NUPACK in the cloud, users will be able to perform calculations far beyond current capabilities both in terms of scale and scientific scope.