̽��ֱ�� of Cambridge - open source

Pilot programme encourages researchers to share the code behind their work

sc604 — Fri, 02 Jun 2017 07:30:00 +0000

A new pilot project, designed by a Cambridge researcher and supported by the Nature family of journals, will evaluate the value of sharing the code behind published research.

For years, scientists have discussed whether and how to share data from painstaking research and costly experiments. Some are further along in their efforts toward ‘open science’ than others: fields such as astronomy and oceanography, for example, involve such expensive and large-scale equipment and logistical challenges to data collection that collaboration among institutions has become the norm.

Recently, academic journals, including several Nature journals, are turning their attention to another aspect of the research process: computer programming code. Code is becoming increasingly important in research because scientists are often writing their own computer programs to interpret their data, rather than using commercial software packages. Some journals now include scientific data and code as part of the peer-review process.

Now, in a commentary published in the journal Nature Neuroscience, a group of researchers from the UK, Europe and the United States have argued that the sharing of code should be part of the peer-review process. In a separate editorial, the journal has announced a pilot project to ask future authors to make their code available for review.

Code is an important part of the research process, and often the only definitive account of how data were processed. “Methods are now so complex that they are difficult to describe concisely in the limited ‘methods’ section of a paper,” said Dr Stephen Eglen from Cambridge’s Department of Applied Mathematics and Theoretical Physics, and the paper’s lead author. “And having the code means that others have a better chance of replicating your work, and so should add confidence.”

Making the programs behind the research accessible allows other scientists to test the code and reproduce the computations in an experiment — in other words, to reproduce results and solidify findings. It’s the “how the sausage is made” part of research, said co-author Ben Marwick, from the ̽��ֱ�� of Washington. It also allows the code to be used by other researchers in new studies, making it easier for scientists to build on the work of their colleagues.

“What we’re missing is the convention of sharing code or the tools for turning data into useful discoveries or information,” said Marwick. “Researchers say it’s great to have the data available in a paper — increasingly raw data are available in supplementary files or specialised online repositories — but the code for performing the clever analyses in between the raw data and the published figures and tables are still inaccessible.”

Other Nature Research journals, such as Nature Methods and Nature Biotechnology, provide for code review as part of the article evaluation process. Since 2014, the company has encouraged writers to make their code available upon request.

̽��ֱ��Nature Neuroscience pilot focuses on three elements: whether the code supporting an author’s main claims is publicly accessible; whether the code functions without mistakes; and whether it produces the results cited. At the moment this is a pilot project to which authors can opt in. It may be that in future it becomes mandatory and only when the code has been reviewed will a paper then be accepted.

“This extra step in the peer review process is to encourage ‘replication’ of results, and therefore help reduce the ‘replication crisis’,” said Eglen. “It also means that readers can understand more fully what authors have done.”

An open science approach to sharing code is not without its critics, as well as scientists who raise legal and ethical questions about the repercussions. How do researchers get proper credit for the code they share? How should code be cited in the scholarly literature? How will it count toward tenure and promotion applications? How is sharing code compatible with patents and commercialization of software technology?

“We hope that when people do not share code it might be seen as ‘having something to hide,’ although people may regard the code as ‘theirs’ and their IP, rather than something to be shared,” said Eglen. “Nowadays, we believe the final paper is the ultimate representation of a piece of research, but actually the final paper is just an advert for the scholarship, which here is the computer code to solve a particular task. By sharing the code, we actually get the most useful part of the scholarship, rather than the paper, which is just the author’s ‘gloss’ on the work they have done.”

Adapted from a ̽��ֱ�� of Washington press release.

New project, partly designed by a ̽��ֱ�� of Cambridge researcher, aims to improve transparency in science by sharing ‘how the sausage is made’.

Having the code means that others have a better chance of replicating your work.

Stephen Eglen

Lorenzo Cafaro

Close up code

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Opinion: We need to break science out of its ivory tower – here's one way to do this

Anonymous — Wed, 26 Apr 2017 10:52:33 +0000

Without hardware, there is no science. From Hooke’s microscope to the Hubble telescope, instruments are modern science’s platforms for producing knowledge. But limited access to scientific tools impedes the progress and reach of science by restricting the type of people who can participate in research, favouring those who have access to well-resourced laboratories in industrial or academic institutions.

Scientists in developing countries, grassroots community organisations, and citizen scientists can struggle to obtain and maintain the equipment they require to answer their own research questions.

̽��ֱ��result of this exclusion from participation is that scientific research becomes ever more elitist as a small number of people decide what the worthwhile and valid projects are. For example, the relative neglect of many tropical diseases and agricultural research on African subsistence crops demonstrates that local concerns in areas with limited scientific resources are often not sufficiently addressed by global science.

Likewise, public concerns and desire for transparency around technology can also be ignored. Research on fracking has received $137 million from the United States Department of Energy. But despite vocal concerns about water pollution, no affordable technologies have been developed for communities to use to monitor their own air or water, even though access to the relevant data from industry is difficult. Locking science inside ivory and industry towers restricts what it can look like.

Open hardware

̽��ֱ��open science hardware movement challenges these norms with the goal of providing different futures for science, using hardware as a launching point. It argues that plans, protocols and material lists for scientific instruments should be shared, accessible and able to be replicated. ̽��ֱ��fact that a lot of modern scientific equipment is a consumer product that is patented, not supplied with full design information and difficult to repair also blocks creativity and customisation.

For example, open source project Oceanography for Everyone recently crowdfunded an open conductivity, temperature and depth (CTD) instrument out of frustration with the lack of low-cost instrumentation available. CTD instruments are the workhorses of oceanography research, and usually cost thousands of dollars. Oceanography for Everyone’s model achieves comparable data but costs US$300 to build, and the plans are public on GitHub. Think of OpenCTD like a really nice shirt. You could buy one for $40, or if you don’t have enough money but you do have a sewing pattern and some time, you could purchase the fabric for $5 and make it yourself, and even customise it to your needs and tastes.

Lower cost is only one goal of open science hardware. CERN, the European Particle Physics Laboratory in Geneva, pioneered an Open Hardware License to enable large-scale, open collaboration on projects. One of these, White Rabbit, is an electronic controller for precise synchronisation of signals across vast distances. White Rabbit ensures that some of the world’s largest particle accelerators are coordinated. But it’s also freely available to anyone, and has found new uses in designing smart electricity grids.

Members of CLEAR using hand tools to repair an open science hardware trawl (LADI trawl) for monitoring marine plastics. MEOPAR

Equality or equity?

Instruments such as OpenCTD and White Rabbit are built on the premise of equality, the idea that everyone should have access to scientific tools. Yet the ability to access such tools is only half the story: it doesn’t address the acute disparities in who is creating science in the first place. And these are enormous. In 2015, ̽��ֱ��Guardian reported that Africa produces just 1.1% of global scientific knowledge. And recent data from UNESCO indicates that only 28% of researchers globally are women. Women do not represent 50% of scientists in a single country in the world.

Attempting to address this problem, several feminist laboratories create and use open science hardware. For example, the Civic Laboratory for Environmental Action Research (CLEAR) is a feminist marine pollution lab in Newfoundland, Canada. And the GynePunks are a group of bio-hackers at the forefront of DIY gynaecology, based in Barcelona.

These labs are not merely bringing more women and trans scientist-inventors into science-as-usual. They prioritise equity rather than equality, recognising that when people start from fundamentally different social, economic, educational and political positions, treating everyone the same does not overcome those differences. In doing so, they transform science in terms of how research priorities are chosen and articulated, what kinds of knowledge is considered valid, and, of course, how scientific tools are made and distributed.

Equality vs. Equity. Interaction Institute for Social Change. Artist: Angus Maguire. CC BY 2.0

Beyond the lab

Particularly valuable work is being done by groups attempting to move science out of the lab and into places and frameworks where it would not usually occur.

For example, Public Lab is a US-based environmental science community founded by frustrated citizens on the Gulf Coast following the Deepwater Horizon oil disaster in 2010. Getting accurate, timely and public high resolution data about local damage was impossible due to flight restrictions over the spill area and satellites are too far away to provide the same level of detail. So citizen scientists stitched together photos from cheap cameras suspended from helium balloons. ̽��ֱ��tools are open and accessible, and the research is done by and for local people without science degrees.

Public Lab volunteers mapping the Deep Horizon oil spill using a low-cost weather balloon setup that is openly documented on the Public Lab wiki. Jeff Warren/Flickr

Likewise, the work of Lifepatch, an Indonesian citizen initiative in art, science, and technology which uses low-cost methods and open tools such as webcam microscopes, is deeply rooted in Indonesian collective culture. ̽��ֱ��questions of basic, daily life and everyday needs have driven projects with local communities on river water quality, bio-recovery of soils altered by volcanic eruptions and safe fermentation practices in collaboration with local academics.

All of these projects demonstrate the value of science grounded in specific places, complex local traditions, ethics, contexts and research questions, rather than a universal science that works the same everywhere for everyone. We need to push science towards communal, bottom-up, and collaborative practices; away from territorial, proprietary, institutional, Western-dominated and individualistic practices.

This has significant implications for where science happens, who is involved, and as a result, the types of knowledge that can be produced. Open science hardware is about creating new futures for science.

Max Liboiron, Professor of Geography and Environmental Science, Memorial ̽��ֱ�� of Newfoundland and Jenny Molloy, Coordinator, Synthetic Biology Strategic Research Initiative, ̽��ֱ�� of Cambridge

This article was originally published on ̽��ֱ��Conversation. Read the original article.

Science doesn't work the same for everyone everywhere - there are huge disparities in access to scientific hardware, and in gender and minority representation in labs. In this piece from ̽��ֱ��Conversation, Jenny Molloy (Department of Earth Sciences) and Max Liboiron (Memorial ̽��ֱ�� of Newfoundland) look at some of the initiatives around the world which are attempting to level the playing field for scientists.

US Food and Drug Administration

Stem Cell Research

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From foundry to factory: building synthetic plants

lw355 — Fri, 20 Jun 2014 09:32:42 +0000

Humans have been modifying plants for millennia, domesticating wild species and creating a bewildering array of crops. Modern agriculture allows global cultivation of plants at extremely low cost, with production on the gigatonne scale of a wide range of biostuffs – from fibres, wood, oils and sugar, to fine chemicals, drugs and food.

But, in the 21st century, we face both ever-increasing demand and the need to shift towards more sustainable production systems. Can we build new plants that make better materials, act as miniature ‘factories’ for food and fuel, and minimise the human impact on the environment?

With this in mind, synthetic biologists are beginning to build new organisms – or at least reprogramme existing organisms – by turning the biology lab into an engineering foundry.

Synthetic biologists choose a ‘chassis’ and then bolt on standard parts – such as genes, the promoters that activate them and the systems they drive – to build something that’s tailor-made. And, like open-source software programmers, they have been looking to open-access and the sharing of code – in this case the DNA that codes for each part – as a practical means of speeding up innovation.

“Providing free access to an inventory of molecular parts for use in the construction of diverse plant-based systems promotes their creative use by others, just as the open-source feature has driven innovation in the computer software industry,” explained Professor Sir David Baulcombe from Cambridge’s Department of Plant Sciences.

Earlier this year, the ̽��ֱ�� of Cambridge and the John Innes Centre in Norwich received £12 million in funding for a new UK synthetic biology centre – OpenPlant – to focus on the development of open technologies in plant synthetic biology and their application in engineering new crop traits. ̽��ֱ��effort is being led by Baulcombe and Dr Jim Haseloff in Cambridge, and by Professors Dale Sanders and Anne Osbourn in Norwich.

It’s one of three new UK centres for synthetic biology that, over the next five years, will receive more than £40 million in funding from the Biotechnology and Biological Sciences Research Council and the Engineering and Physical Sciences Research Council.

OpenPlant aims to establish the first UK open-source DNA registry for sharing specific plant parts. It will also support fundamental science: “Construction of these parts will allow us to test our understanding of natural plant systems in which assemblages of parts create a greater whole,” Baulcombe explained.

Researchers like Baulcombe and Haseloff, who also leads a new Strategic Research Initiative to advance cross-disciplinary research in synthetic biology in Cambridge, believe that the investment in the three new centres will help the UK stay at the leading edge of plant synthetic biology.

“Any large-scale reprogramming of living systems requires access to a large number of components and, as the number of these parts balloons, the cost of building a portfolio of patents, or licensing parts from patent owners, could strangle the industry and restrict innovation,” explained Haseloff.

“While US researchers lead in the synthetic biology of microbes, the UK has the edge in plants. ̽��ֱ��field needs a new two-tier system for intellectual property so that new tools including DNA components are freely shared, while investment in applications can be protected.”

As well as new DNA components, Haseloff and colleagues have been focusing on a new plant chassis. Rather like the frame of a car, the chassis is the body of the cell that houses the rest of the desired parts. And for this they have turned to liverworts, relics of the first land plants to evolve around 500 million years ago.

̽��ֱ��Marchantia polymorpha liverwort is small, grows rapidly, has a simple genetic architecture and is proving such a useful test-bed for developing new DNA circuits that Haseloff has launched a web-based resource (www.marchantia.org) for a growing international community to exchange ideas. ̽��ֱ��hub characterises one of the wider aims of OpenPlant in promoting interdisciplinary exchange between fundamental and applied sciences, and is one of a series of collaborative projects, such as OpenLabTools (see panel), which are promoting open technology, innovation and exchange between engineers and physical, biological and social scientists across the ̽��ֱ��.

In parallel with the development of standardised parts, the Centre will support around 20 researchers and their teams in Cambridge and Norwich who are engineering new plant traits. For instance, scientists at the John Innes Centre are investigating new systems for producing useful compounds like vaccines. In Cambridge, researchers are creating systems with altered photosynthetic capabilities and leaf structure to boost conversion of the sun’s energy into food, as well as developing plant-based photovoltaics for fuel.

Another of OpenPlant’s aims is to foster debate on the wider implications of the technology at local and global scales. As Baulcombe described, “ ̽��ֱ��open source feature may allow straightforward discussion about the applications of synthetic biology in plants. Societal discussion about other strands of biotechnology has been greatly hampered by the complications following from intellectual property restrictions.”

“We think that biological technologies are the underpinning of the 21st-century’s industrial processes,” added Haseloff. “Plants are cheap and inherently sustainable, and have a major role to play in our future.

In order to implement ideas and shift towards more rational design principles to support advances, we need to have the ability to exploit synthetic biology technologies in a responsive way, and that’s where we see OpenPlant contributing in the years to come.”

Inset images: Marchantia - a primitive plant form used as the 'chassis' for designing new plants. Credit: Jim Haseloff.

A movement is under way that will fast-forward the design of new plant traits. It takes inspiration from engineering and the software industry, and is being underpinned in Cambridge and Norwich by an initiative called OpenPlant.

Plants are cheap and inherently sustainable, and have a major role to play in our future

Jim Haseloff

Marchantia - a primitive plant form used as the 'chassis' for designing new plants

OpenLabTools

OpenPlant is part of a wider move towards ‘sharing’ in Cambridge that now includes scientific tools of the trade.

Resourcing laboratories with scientific tools is a costly business. An automated microscope, for instance, could cost upwards of £75,000, and yet be a key tool in materials and biological laboratories.

Now, an initiative coordinated by Dr Alexandre Kabla, from the Department of Engineering, is rethinking how scientists can access the tools that they need at a less-prohibitive cost.

He recognised that a wealth of instrument-building know-how exists across the ̽��ֱ�� – expertise that could be drawn on to develop a suite of low-cost open-access scientific tools.

Raspberry Pi, for example, was conceived and incubated in the Computer Laboratory to encourage children to learn programming for themselves: this credit-card-sized computer is now available for only $25.

̽��ֱ��OpenLabTools initiative has set itself the task of creating high-end tools such as microscopes, 3D printers, rigs for automation and sensors, with an emphasis on undergraduate and graduate teaching and research. It was created with funding from the ̽��ֱ�� and the Raspberry Pi Foundation, and is supported by an academic team of engineers, physicists, materials scientists, plant biologists and computer scientists.

“Current projects primarily focus on the development of core components, thanks to the contributions of a team of physics and engineering students. However, we have already made significant progress towards the development of imaging systems and mechanical testing devices,” said Kabla, whose own expertise lies in the physics and mechanics of biological systems. “We anticipate that these will be rolled out in undergraduate laboratories sometime next year.”

To encourage open access, ‘How To’ manuals and designs are being published on the OpenLabTools website.

“It’s an exciting prospect,” said Kabla. “When you consider that consumer-grade low-cost microscopes are essentially a digital camera with a high magnification objective, not only can we build this but we can also provide a means to automate the microscopy, dramatically reducing the cost of the tool. ̽��ֱ��blueprints and tutorials we make available will be useful for undergraduate and research projects, as well as school activities and small-scale industrial applications running on a tight budget.”

www.openlabtools.org

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