Antha is the first high level language designed to enable robust, reproducible and composible work in the
biosciences. Antha is designed to take away much of the detail of experimental planning, allowing biologists to
focus on what they want to do, not how to do it. This allows researchers to think about the biology of their
system, and successfully carry out ever more complex and illuminating
A high level language enables ease of design, better reproducibility and scalability. Lack of reproducibility is still a major barrier to progress in the biosciences (an article from Amgen reports that they could reproduce findings in only 11% of 53 published papers).
Compared to other industries our
The will to improve reproducibility is not new. In recent years efforts have been made to abstract the layers of biological complexity and to standardize by breaking down biological components into repositories of well-characterised standardized parts which can be combined to form more complex devices. The biobrick registry at iGEM is a good example of this. This is a move in the right direction but the problem is far from fully solved since biology is not that simple and often it’s not straightforward standardise parts.
The idea of abstraction and standardization are very welcome but unfortunately we don’t yet fully understand how even the simplest and most well-studied bacteria such as E.coli function… We know that the genome is 5.7million letters long and that about 4-5000 genes are produced but only around 66% of these genes have been experimentally verified. So how can we use a standardized parts based approach to building new microbes when we don’t fully understand how the operating system works? The answer may be to standardize the experimental format in which these parts are characterized, and capture all of the subtle artisanal details of a procedure not usually captured in a material and methods section of a research article.
Antha allows you to do this and critically, the hard work will largely be performed behind the scenes so quality standards can be met but without the normal effort overhead. With Antha we can embrace the fact that we don’t fully understand the complexity of the biology and perform our characterizations reproducibly in a way in which new parts and devices are tested for robustness in the full genetic, biological and environmental context and to do so in a way where we design this approach to be performed by a liquid handling robot in which the characterisation process then becomes a software algorithm rather than a written material and methods section in a scientific journal, which has been the case up until now. This approach would be a far more reproducible, scalable and robust way of standardization; not so dependent on a lab technician’s green fingers!
None of these are high-level languages capable of incorporating genetic design, experimental design, physical experimental execution and data processing.
Antha is currently in “community preview.” Many of the pieces that are being integrated into Antha have been in production use at Synthace and other organisations for years. However, the full integration into is new and will inevitably uncover bugs in the component pieces it has brought together.
Antha uses Chromium’s continuous build infrastructure to test the entire system and each polyfill, individually.
Go is an open source language designed and built by Google to make building fast, simple and scalable software. Go is capable of concurrency and communicating directly with devices. Learn Go here.
Absolutely, whether you’re a programmer, bioinformatician or scientist we welcome contributions to both the
language itself and the building of
Antha translates the proprietary formats of the various devices accessed as part of the process of
experiment execution into open JSON based data. The original proprietary format
The low level details are taken care of by Antha and its associated scheduler and device drivers. Details such as analysis of raw data are often dealt with in Antha scripts, so someone that writes Antha can go in and edit them, while “users” can take advantage of what is scripted without having to worry about the details. Another example of a low level issue is physically where samples are placed in a multiwell plate by a liquid handler, and how the liquid handler is instructed to do the necessary actions. These issues are dealt with by the scheduler and liquid handler driver respectively.
Not yet. But eventually, yes, via the network protocol.