Station B

Station B

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Overview

“The ability to program biology could enable fundamental breakthroughs across a broad range of industries, including medicine, agriculture, food, construction, textiles, materials and chemicals. It could also lay the foundation for a future bioeconomy based on sustainable technology. Despite this potential, programming biology today is still done largely by trial-and-error. To tackle this challenge, the field of synthetic biology is working collectively to develop methods and technology for programming biology more systematically. Station B is part of this broader effort, with a focus on developing an integrated platform for programming biology, to enable selected partners to improve productivity within their own organisations, in line with Microsoft’s core mission. The name Station B is inspired by Station Q, which launched Microsoft’s efforts in quantum computing, where Station B focuses instead on biological computing. The Station B platform is being developed at Microsoft Research in Cambridge, UK, which houses Microsoft’s first molecular biology laboratory. The platform aims to improve all phases of the Design-Build-Test-Learn workflow typically used for programming biology. Station B is a collaborative effort being carried out with selected technology, academic and commercial partners.

We are currently focusing on two main abstractions: programming genetic circuits that function in living cells and programming nucleic acid circuits that perform information processing.

Abstractions

Genetically modified cell illustration

Genetic Engineering of Living Cells

We are developing a programming language for designing genetic circuits, together with methods for modelling, simulating and analysing these circuits within living cells.”

DNA illustration

Programming DNA Circuits

We are developing a programming language for designing information processing circuits made of DNA, together with methods for understanding and predicting interactions between DNA molecules.

 

Partners

Station B is a collaborative effort being carried out with selected technology, academic and commercial partners.
Person in Oxford Biomedica lab

Photo by Jonathan Banks.

Oxford Biomedica

Oxford Biomedica are the first commercial partners for Station B and are a leading cell and gene therapy company. They secured a deal with Novartis to produce the first treatment approved in the U.S. and the E.U. that reprograms a patient’s own immune cells to recognize and kill cancer cells in patients with leukemia and lymphoma. The drug must be specially made for each individual and costs nearly half a million dollars to treat a child with acute lymphoblastic leukemia. Before the treatment, those children typically had weeks or months to live. After receiving the cell therapy, 81 percent of the children in clinical trials went into remission. The initial goal of the partnership will be to apply the modeling and machine learning expertise developed at Station B to improve both the production yield and quality of therapies, in order to reduce overall costs and facilitate the future production of new therapies.

 

Bonnie Bassler poses in a laboratory at Princeton

Photo by Denise Applewhite, copyright Princeton University.

Princeton University

Princeton University are the first academic partners for Station B. The focus of the partnership will be to develop and apply the Station B platform to understand the formation of biofilms – surface associated colonies of bacteria that kill as many people as cancer and play a key role in antibiotic resistance, recognised by the world health organisation as a global crisis. The partnership will involve a collaboration with Prof. Bonnie Bassler, a world-leading microbiologist and chair of Princeton’s Department of Molecular Biology. The Princeton team also includes Bassler’s longtime collaborator Prof. Ned Wingreen, a physicist in Princeton’s Lewis-Sigler Institute for Integrative Genomics. The Station B platform will be deployed in the Bassler lab to construct and test different versions of proteins that are key to biofilm formation, and to build on their extensive inventory of genetic components, models and experimental data collected over many years of studying bacterial biofilms.

People in the Synthace lab

Photo by Jonathan Banks.

Synthace

Technology partner Synthace provides a key abstraction layer for the digital encoding of biological experiments. Their Antha software allows the same digitally encoded experiment to be executed by a range of lab automation devices made by different manufacturers, much like printer drivers allow the same PDF to be printed by any make or model of printer. This ability to run experiments in the same way each time gives users higher confidence in their results. Antha aims to tackle the reproducibility crisis in biological experiments by digitally encoding all aspects of the experiment in a systematic fashion. It also allows substantial scaling up of experiments. This automated generation of reproducible experimental data at scale is a key requirement for machine learning, allowing users to pose and learn from much more sophisticated lines of inquiry.

Archive

illustration of t-cells

Modelling Immune System Processes

Immunodominance lies at the heart of the immune system’s ability to distinguish self from non-self. Understanding and possibly controlling the mechanisms that govern immunodominance will have profound consequences for the fight against several classes of diseases, including viral infections and cancer. We have been attempting to understand the computation performed by the immune system that gives rise to immunodominance, using techniques from computer science, applied mathematics and Bayesian statistics.

Decision-Making in Stem Cells

Decision-Making in Stem Cells

Development proceeds via a sequence of decisions that cells have to make about whether to divide, to differentiate, or to migrate. Differentiation is the process by which a cell changes from one type to another, which enables the expansion of the different lineages and growth of the different structures of the adult.

RE:IN interface in use

Reasoning Engine for Interaction Networks (RE:IN)

The Reasoning Engine for Interaction Networks (RE:IN) is a tool that runs online in your web browser, which is designed for the synthesis and analysis of biological programs.

Stochastic Pi Machine screenshot

Stochastic Pi Machine

The Stochastic Pi Machine (SPiM) is a programming language for designing and simulating computer models of biological processes.

People