Open Source Biotechnology



Real-life experiments in open source biotechnology

Although open source biotechnology is at an early stage of development, several past and present biotechnology initiatives have adopted one or more aspects of the open source model.

General Public Licence for Plant Germplasm

Proposed by plant scientist Tom Michaels in 1999, the General Public Licence for Plant Germplasm is a fairly straightforward adaptation of the archetypal share-alike software licence, the GPL, to germplasm (the indispensable raw material of plant breeding). 

Public Sector Human Genome Project

Another proposal for open source-style licensing of biological information was privately floated in the context of the race between public and private sector scientists to complete a draft sequence of the human genome.

Public sector researchers at the UK’s Sanger Institute were concerned that their commitment to publish their own sequence data with no strings attached gave their competitors an opportunity to free ride on their efforts. 

In 1999, the researchers explored the possibility of licensing the data on share-alike terms and went so far as to commission a draft licence before ultimately deciding that any constraint on data use, even constraints intended to promote public access, would likely be unacceptable to their collaborators. 

HapMap Data Access Agreement

The International HapMap Project was a private–public collaboration established to create a haplotype map of the human genome.

Before December 2004, researchers wishing to access the Project’s online database had to agree to set of “click-wrap” conditions designed to discourage database users from filing patent applications that would block other users’ access to the data. According to a notice on the site, the software GPL directly inspired the terms of the click wrap agreement. 

Implementation was problematic, however, and the requirement was withdrawn before the Project was completed.

Tropical Disease Initiative and The Synaptic Leap

The Tropical Disease Initiative (TDI) is an open source-style drug discovery scheme proposed in 2004 by lawyers Stephen Maurer and Arti Rai and computational biologist Andrej Sali.

Key to implementation of the TDI scheme is its partnership with the Synaptic Leap (TSL), a non-profit organisation founded in 2005 by a former commercial software industry executive. TSL’s goal is to extend the range of scientific collaborations beyond researchers’ personal networks by establishing a usable online open information and communications infrastructure.

Recognising that the provision of a “seed” or “kernel” of usable technology is an important ingredient in successful open source collaborations, researchers associated with TDI/TSL have recently published results identifying potential drug targets in ten organisms that cause tropical disease. 

Biobricks Foundation

The BioBricks Foundation (BBF) is a non-profit organisation dedicated to promoting and coordinating the production of standardized modules or “biobricks” that can be assembled into functional synthetic biological systems.

Some of the earliest writings on open source biology were triggered by synthetic biologists’ desire to ensure the viability of the enormous collaborative effort needed to realize their engineering goals.  As of 2009, efforts are underway to develop a set of open source-style guidelines to encourage resource and data sharing in this growing field. 

Private companies

A number of for-profit biotechnology companies have been inspired by the success of open source software enterprises to pursue business models that differ from the more conventional monopoly-based approach. 

One example is Diversity Arrays Technology (DArT), a privately held Australian company established in 2001 to commercialize a patented molecular marker technology invented by its founder and director, Andrzej Kilian. The company’s non-proprietary, service-based business model has been inspired by that of Red Hat, the successful Linux distribution company whose initial public offering made Wall Street history in August 1999.

DArT offers a concrete illustration of the distinctive commercial logic underpinning open source biotechnology. Instead of relying on injections of funds from capital markets supplemented by licensing revenue, the company’s business model is designed to exploit the synergy between service provision and ongoing technology development.

Biological Innovation for Open Society

Biological Innovation for Open Society (“BIOS”) was an initiative of CAMBIA (Center for Application of Molecular Biology in International Agriculture), an independent non-profit research institute formerly based in Canberra, Australia.

The BIOS initiative, launched in 2005, incorporated:

  1. the “Patent Lens,” a searchable patent database containing ancillary information and tutorials;

  2. “BioForge,” a portal modelled on the open source software collaboration site; and

  3. Biological Open Source” (“BiOS”) licensing of some elements of CAMBIA’s own patent portfolio.

Under the BiOS licences, products derived from the licensed technology could be patented and commercialized subject to a number of constraints.  These included a requirement that a broadly defined class of improvements be non-exclusively granted back to CAMBIA.

CAMBIA’s BiOS licenses explicitly invoked the language of open source, and for a time the initiative was widely regarded as the world’s first working prototype of open source biotechnology R&D. 

However, CAMBIA’s own website cautioned against treating open source as anything more than a metaphor in this case - and in fact, the terms of the BiOS licences diverged in key respects from the institutional logic of open source. 

In particular, they gave CAMBIA much more control over the actions of follow-on innovators than would have been compatible with established standards for open source software licensing.  These standards are designed, in part, to protect contributors to an open source collaboration from exploitation by the project leader (in this case, CAMBIA).  Perhaps for this reason, BiOS licences do not appear to have enjoyed significant uptake.

As of early 2009, CAMBIA is relocating to the Queensland Institute of Technology.

Network for Open Scientific Innovation

The Network for Open Scientific Innovation (NOSI) seeks to bring together experts from multiple disciplines to develop and analyse licences that comply with open source and other sharing principles for use in the life sciences.

Equitable Access and Neglected Disease Licensing

“Equitable Access” and “Neglected Disease” licensing are twin elements of an open source-inspired proposal for improving access to essential medicines, put forward by Amy Kapczynski and colleagues at Yale University.

These licensing models explicitly envisage universities as licensors but could be adopted, for example, by other researchers and institutions operating within the TDI framework described above. 

Equitable Access licensing aims to improve access to biomedical innovations in low-and middle-income countries. Neglected Disease licensing aims to facilitate research on orphan or neglected diseases.

Free and open source software programs for use in biotechnology settings

In the post-genomic age, software programs have become key research tools in biotechnology and related industries.  Some of the most powerful and widely used software tools for handling the large and complex data sets produced by molecular biologists are open source in the software sense. 

Why is the open source approach particularly suitable for bioinformatics software? The reason is that bioinformatics applications generally incorporate similar fundamental features, but often require extensive customisation before they can be applied to specific data sets. Unlike proprietary programs, open source bioinformatics tools can be re-used in other contexts but also freely modified to suit unique use environments.

In the long term, open source bioinformatics may turn out to be significant as a non-proprietary wedge driven into the culture of an industry that has historically been strongly committed to proprietary strategies.  If biotechnology industry participants are already willing to embrace non-proprietary tools in specific contexts, that willingness may gradually extend to other contexts. 

This is especially true as biotechnology research and development comes to rely more and more heavily on computer modelling and data analysis and the industry continues to experience an influx of researchers with “hard” science backgrounds who are familiar with open source.

Open Source Drug Discovery initiative

Open Source Drug Discovery (OSDD) is an initiative led by the Council of Scientific and Industrial Research (CSIR) of India. 

The goal of the initiative is to “provide affordable healthcare to the developing world by providing a global platform where the best minds can collaborate” to develop new therapies for diseases that disproportionately affect poorer countries.

OSDD is supported by the Indian government, which has committed US$38 million to the project.  It seeks to raise an equivalent amount of funding from international agencies and private philanthropies. 

The first phase of the initiative entails promoting Internet-mediated sharing of data and techniques among independent biologists working on developing drugs against tuberculosis.

Janet Hope, Australian National University, 2009-