The vast majority of lateral entrants to biotechnology struggle to understand the problems that biologists face in their work. On the other hand, the vast majority of biologists lack the skills to create and shape policy, build software tools, or create communications and media themselves. Although biotechnology is inherently multidisciplinary, no state or organisation has put forward a plan to fill the skills gap and create a workforce that can bridge the gaps between tech and biotech, policy and biology, and the press and (nutritional) media. An interdisciplinary community is critical to the bio-economy. Lets get started.
Historically, our interest was first to create a BioCoder Training Programme with the explicit goal of training a cadre of software professionals who can rapidly create high quality software tools that biologists need to expedite their work inside and outside of the lab. For the sake of explanation of our mission, we will first deal with the need for developers in biotech, and the challenges they face joining and understanding a biologist.
This proposal will:
create indirect value for individual companies and laboratories who can recruit these professionals;
benefit the greater biotechnology field by fostering the development of tools that expedite the design-build-test cycle, and
help those in the tech industry achieve a fulfilling career in biotechnology.
The plan espouses a long-term mission to cross-pollinate these fields and spark a renaissance in biotech software systems. We finally note a longer-term plan to extend this model to fields other than software development, and highlight our flexibility and desire for others to join us and lead this programme.
The situation today
The UK SynBio roadmap projected that by 2015 there would be a wealth of academic groups and companies creating software tools to facilitate the biotech revolution. This has not yet happened as many in SynBio would like, largely due to the fact that the two disciplines are quite removed from one another – cross-training is difficult due to the lack of common language and rare opportunities for interactions:
Academic biologists have trouble creating modern software tools
While there is a wealth of existing software tools used by biologists, many have been developed by academics with little professional development experience. Historically, scientists developing these tools have been motivated by, and recognized for, the powerful algorithms and predictive models (back-end power) they develop, over and above usability. Little attention may be paid to design thinking, workflow optimisation or making tools “fun” to use (front-end design). This has resulted in the creation of tools that are hard to use and practically impossible for people without appropriate scientific education. Further, as scientists leave labs where they wrote the software, or fail to provide appropriate documentation, many tools lose support and become outdated.
This has led to a saturation of poorly thought-out, ageing, generalist tools that place functionality over form and in many cases act to impede a scientist’s work rather than facilitate it.
Developers have a steep learning curve in biology and on-the-job training is prohibitively expensive
There are high barriers for developers to surmount in order to understand, and therefore participate in, the domain of biology. At Desktop Genetics, a company operating at the intersection of CRISPR gene editing and software development, we have found that developers - while eager to work in the synthetic biology field - have trouble understanding even “the basics”. As such, most developers rarely pick up the knowledge necessary to rapidly translate a biologist’s requirements into working code in desirable times. For academics and small biology companies, it is economically unfeasible to bring in these professionals for one-off projects, as the work to train them in biology may exceed the value of the work product itself.
Some argue that developers do not need to learn biology at all - rather they should be instructed and managed by a biologist, or someone who can translate biology-to-software easily. However, developers are highly sought after by every industry and remain loyal to an employer only when many soft factors are present in a company’s culture - average to good developers that do not see and understand the big picture of their current mission are very likely to leave a company at the next opportunity. Thus, this method can only be used by larger companies, but stifles professional development and the acquisition of biology skills by said developers. Further, this anchors the highly skilled multidisciplinary individual to managing a dev team, and for a business, such individuals are better placed in the field, with customers and end-users.
Bringing the problems together
There is a dearth of useful, intuitive biology software tools that work for the biologist and help them solve problems in a user-friendly and timely manner. For the individual scientist, this means repeated work, wasted time, frustration, and slower research outcomes. This leaves the entire life science domain trapped in step-wise experimentation-optimisation cycles, slow progress at both academic and commercial levels and a reliance on manual work which hampers reproducibility. The latter may be costing the economy >$28 billion, a figure which does not count the time wasted using cumbersome tools. Beyond the financial issues, we can expect that this situation has additional negative impacts on the goals of the research, such as improving human and environmental health.
Opportunities and challenges
A workforce that is literate in both biology and modern software engineering practices would be a great asset to all segments of the life sciences. Software engineers bring fresh perspectives to biology and the tools that biologists use. They think computationally, break apart problems, and simplify complex workflows in a unique way. When applied to the challenges of SynBio, their thinking could substantially improve biology researchers’ ability to get work done.
For example, software engineers trained in biology have become tremendously useful personnel for Desktop Genetics, its competitors and our customers. Bio-literate software engineers (let’s call them BioCoders) can move through the problem space of two fields very fluidly by: directly interacting with a biologist (no need for “translation” staff/time); understanding the context of the technical problem(s); empathising with user experience issues; working quickly to design a solution; testing proposed solutions with the user; coding the solution itself and ultimately testing and delivering a useful product. Whilst bioinformaticians and computational biologists bridge some aspects of tech-biotech, they are distinct professions that focus on data analysis and virtualizing experiments, rather than creating products.
The power of a biocoding revolution
Software condenses the knowledge and work-processes of experts into a black box that can be used by a non-expert, at will, anywhere in the world. To achieve the dream of engineering living solutions to mankind’s problems, the requirement to simplify “programming life” will continue increase, and deeper expertise will need to be made available easily.
Biocoders are few in number today, and they are often snapped up by major companies, resulting in a brain drain from the academic labs and the innovative startups that need them. As more biocoders are trained, not only will we see a new wave of tools that can speed up work in the lab, we will also create a new generation of biologists who can program computers and life, work with startups, and create new companies and laboratories to develop these technologies even further.
Our plan to put tech in biotech
The tech community is inspired by biology and is hungry to get involved in the “next digital revolution”. Most devs simply have no time or resources to do a Postdoc in Biological Engineering. Moreover, training developers in biology and expecting them to hold on to that information in the long-term is unlikely to yield the results we are after.
Instead, developers learn new programming languages best when they are:
able to practice them either on the job or in a project;
have suitable materials and documentations to foster self-learning, and;
My plan has four steps aimed at creating strong ties between the biology and tech communities, teaching new skills, creating a cadre of bio-literate software professionals, and creating an institute that can continue this work in perpetuity:
Generate a wealth of open source teaching materials that provide budding BioCoders with the bare minimum needed to understand what a biologist is talking about. This includes teaching the language biologists speak in order to understand the basics of genetics and then the concepts of engineering cells.
Trial a series of hackathon-style events that bring real biologists together with budding BioCoders in order to create open source software tools (or code libraries) that solve real problems the biologists have, and in doing so, provide BioCoders with more experience.
Formally settle on a event style that can be run by any interested party (akin to TedX) in order to grow the BioCoder programme globally.
Bring together the teaching materials, biologists, and emerging (or emerged) BioCoder community together under the banner of the BioCoder Academy – a non-profit that is part university, part think-tank and part business incubator.
The Individual Pieces – details & status
SynBio.info – a wiki and community devoted to understanding SynBio together
Already live with 250 content pages, 50+ active users, 19,000+ facebook followers, SynBio.info provides accessible and easy to understand descriptions of key concepts in synthetic biology to lateral entrants with non-biotech backgrounds – the initial focus is on developers, and makes use of CS-centric explanations, but will be extended to mechanical engineers, designers, businesspeople etc.
SynBio.info was initiatlly started by Jérôme Lutz, a software and mechanical engineer who quit his startup job mid 2014 to get involved in SynBio. One core mantra of software engineers is to never repeat yourself, so instead of repetitively telling others about SynBio, we both decided to put our knowledge together and store it on SynBio.info so others can easily repeat our learning process. Additionally, we assume that only a collectively-created wiki will be able to stay up to date with the ever-accelerating progress of SynBio in a structured way.
Inspired by our own learning process, SynBio.info takes the following approach to education:
- New entrants to biology must learn the language of biologists quickly. In addition to wiki articles, this browser extension supports constant learning by highlightng key biological terms on every website, and providing definitions, videos and other learning tools
- The Basics of Genetics provides a general introduction to core molecular biology principles
- Additional sections (in progress) introduce biotechnology, cell line engineering, and important applications of the technologies
- Soon, we will provide guided tours through the wiki and help the user assemble a curriculum and track the learning progress. Funds are being donated and are currently being used to recruit additional content writers and promote the site. Once it is incorporated as a non-profit, we will set up a business model that sells the software we develop to pursuit this mission for companies that can use it for their internal knowledge management. The generated revenues will be 100% redirected into fulfilling the mission and sustain a healthy and ongoing improvement.
Hackathons and SynBio Events – community-building and problem-solving
We have elicited a number of “bane of existence software problems” that real biologists face in the lab. We will bring these biologists together with developers (recruiting is ongoing since soft launch in summer), and create small projects focused on solving these very specific biology/software problems. These events are aimed at teaching developers enough biology to communicate with a scientist about that subject, and inspire them to learn more biology and work on more projects. Prior to each event, developers will be sent key articles from SynBio.info, which they will be expected to learn.
It has been noted that hackathons are good for producing proofs-of-concept products and little more. As such, the focus may instead be on creating open source code libraries which are more useful. New event formats will need to be tested to see what produces the most favourable results for all involved. The overall vision would be to create a TEDx style programme, where any interested party could advertise for biologists and developers to get together, solve problems, learn new skills, and build out their professional networks in fields that each party is rarely exposed to. The primary focus is on community-building, which will assist the stated aim of cross-pollinating the two fields and seeding more BioCoding hubs.
Status: pitched, planned, slowly coming together. Planning to make this happen in 2016.
SynBio Academy – a non-profit providing bio-literacy courses for everyone
The emerging bio-economy needs more than just developers-turned-biocoders. BioCoders are simply the group that we need first, so we can speed up our progress in the lab. In the same way that new professions have emerged to meet the fusion of “tech” with “everything else”, I predict that a similar situation will evolve vis-à-vis biotech within the next few decades. Mechanical engineers, data scientists, investors, politicians and others will all have reason to gain a deep understanding of synthetic biology, a technology predicted to dominate our society. Each professional requires unique course materials, training sessions and other resources. The SynBio Academy will be a bricks-and-mortar institute that brings together all of the lessons learned from SynBio.info and the events described this plan. It will be devoted to creating these materials and communities, and will support these professionals in acquiring domain knowledge that can help humanity take advantage of their expertise within a new biological paradigm.
Status: five years away, domain www.synbio.academy ordered, Let’s get started!
Imperial College London – academic interest in proposing problems for hackathons
University College London – academic interest in proposing problems for hackathons
SynbiCite –interest in funding hackathons and funneling promising teams into startup funding
Google [X] – have been supportive in advertising this project internally and making connects
Desktop Genetics - for validating the commercial need for this plan
Synthace – for validating the commercial need for this plan
O’Reilly Media – interest in helping develop “bio-for-devs” curricula and publishing my plan in the BioCoder journal
iGEM – put their faith in me to steer the iGEM software track to align with this plan
Singularity University – for connecting me with wonderful, enthusiastic people who can help make this happen
HM Government, Department of Business Innovation & Skills – ongoing discussions for making the development of BioCoders a six month “grand challenge” programme with political support
SynBio.info – huge thanks to everyone who has helped build this, especially Jérôme Lutz
unternehmertum.de - for providing organizational support in constructing these non-profits and free office space
seakademie.de - for providing a fantastic social entrepreneurship education and network
The plan to put tech in biotech, develop a BioCoder training programme, and to create a road towards a SynBio Academy is audacious, but necessary. We will continue to recruit content writers for SynBio.info, raise funds to run hackathons and events, and bring software professionals into the fantastic world of the life sciences. More importantly, We are looking to find others who can help me lead this program over the next decade – and longer.
Edward Perello is the founder of Desktop Genetics, a company at the forefront of CRISPR genome editing technology. His team is working to provide researchers with access to state of the art genome engineering capabilities from their computers and create an AI that can predict optimal genome editing solutions in any organism. Edward is a SynBio LEAP fellow working to get more non-biologists into the field.
Edward Perello is the founder of Desktop Genetics, a company at the forefront of CRISPR genome editing technology. His team is working to provide researchers with access to state of the art genome engineering capabilities from their computers and create an AI that can predict optimal genome editing solutions in any organism.
Edward is a SynBio LEAP fellow working to get more non-biologists into the field.