The Open Source Ethos | A Growing Culture

“The internet now provides a free platform for sharing knowledge. How is it possible—or even socially just—that so many of us can’t get access to scholarly research? Isn’t society propelled forward by access to the science, literature, and art of the world’s scholars? What if that research is publicly funded? These are the primary concerns that drive the open access movement.

What would these concerns look like if we removed them from the scholarly communications circle and applied them to realms beyond the ivory tower like nature, society, technology, and ultimately the intersection of those things—agriculture. How does resource sharing affect biodiversity? How does knowledge exchange drive community resilience? How is information access—delivered via technologies—an equalizer among the underrepresented, marginalized, and oppressed? How does our ability to feed a growing planet depend on a culture of openness? Let me work my way back.”

Tanzania workshop on Access to Global Online Research in Agriculture (AGORA) | Agricultural Information Management Standards (AIMS)

The Food and Agriculture Organization of the United Nations (FAO of the UN) in conjunction with several partners organized a series of training workshops in 2016 and 2017 across Asia, Africa and Latin America focused on access to research in agriculture and fisheries. Earlier, workshops were held in NamibiaMyanmarTanzaniaZimbabwe, Laos PDR, Honduras and Guatemala.

The workshops are aimed at drawing attention to the scope of free online agricultural information available on Access to Global Online Research in Agriculture (AGORA) and International System for Agricultural Science and Technology (AGRIS) and in effectively using these resources. Alongside this core focus, the workshops raise awareness of key trends in scientific publishing in agriculture, fisheries and forestry, with a look at the further range of resources available to researchers in agricultural research, and on Research4Life

The most recent workshop was held at Tanzania Commission for Science and Technology (COSTECH), 26-27 July 2017. In the United Republic of Tanzania, 115 national institutions are registered for free access to scientific journals and e-books through AGORA and Research4Life.”

Open risk assessment: methods and expertise – Verloo – 2016 – EFSA Journal – Wiley Online Library

Abstract:  Risk analysis and risk governance face a decline in social trust at both the scientific and policy levels. The involvement of society in the process has been proposed as an approach to increasing trust and engagement by making better use of available data and knowledge. In this session, EFSA explored the challenges in building trust and engagement and the latest thinking and methodologies for increasing openness that can help the organisation to move beyond traditional dialogue and towards a more sustainable stakeholder and society interaction. The discussion centred on the needs of EFSA and of target audiences throughout the process, from risk assessment initiation through societal decision-making and communication. The main focus of the session was on methodologies and approaches that would enable EFSA to increase its scientific rigour and build trust from additional inputs gained by opening up its risk assessments at the level of data gathering, data analysis, expertise and innovation. This will require an approach that moves beyond traditional risk assessment practices that rely on a long chain of static information and knowledge such as scientific articles, reviews, expert groups and committees.

Open risk assessment: data – Gilsenan – 2016 – EFSA Journal – Wiley Online Library

Abstract:  Since its foundation, EFSA and the Member States have made significant progress in the area of data collection for risk assessment and monitoring. In partnership with competent authorities and research organisations in the Member States, EFSA has become a central hub of the European data on food consumption, chemical occurrence and foodborne outbreaks. Beyond EFSA’s use of these data and sharing of contaminants and food consumption data with the World Health Organization and the Food and Agriculture Organization to support international risk assessment, they remain largely unexploited. In addition, for some of its risk assessments, EFSA also relies on published information, as well as on scientific studies sponsored and submitted by industry. The environment in which the Authority operates has significantly evolved since its foundation. The growth of digital technology has granted scientists and consumers alike faster and more efficient access to data and information. The open data movement, which has entered the sphere of the European Union institutions, is unleashing the potential for reuse of data. In parallel, the work of EFSA is increasingly subject to demands for more openness and transparency across its spectrum of stakeholders. EFSA aims to enhance the quality and transparency of its outputs by giving access to data and promoting the development of collaborative platforms in Europe and internationally. EFSA also plans to work with data providers and organisations funding research to adopt open data concepts and standards; gaining better access to, and making better use of, data from a wider evidence base. During the breakout session on ‘Open Risk Assessment: Data’ at the EFSA 2nd Scientific Conference ‘Shaping the Future of Food Safety, Together’ (Milan, Italy, 14–16 October 2015) opportunities and challenges associated with open data, data interoperability and data quality were discussed by sharing experiences from various sectors within and outside EFSA’s remit. This paper provides an overview of the presentations and discussions during the breakout session.

Kenya leads the way for African countries to shift to more open, accessible and data-driven national agricultural policies | Diana Szpotowicz | Pulse | LinkedIn

“The event had a simple mission: to spur greater investment in agriculture and food nutrition data, especially in the G77 countries – a mission shared by the United Nations and the African Union this year.

The conference was co-convened by the Government of Kenya, the G77 Secretariat, African Union (NEPAD) and the Platform of African Farmers’ Organizations (PAFO).”

African countries to combat food crisis with open data

“The Global Open Data for Agriculture & Nutrition (GODAN) initiative together with the Government of Kenya and 15 African Ministers including from South Africa, Congo, Sudan, Kenya, Uganda, Sierra Leone, Rwanda and Ghana, have agreed to a declaration for comprehensive open data collaboration in the nutrition and agriculture sectors, to combat the global food security crisis. The declaration is historic in that it presents the first time a ministerial level network, focusing on open data for agriculture and nutrition, has been formed. Coincidentally the Conference takes place in Africa, the continent with the largest untapped agriculture potential, proving a major milestone towards achieving global food security worldwide. …”

Supporting the Changing Research Practices of Agriculture Scholars | Ithaka S+R

“The issue of cost also factors into interviewees’ approach to making their peer-reviewed publications available via open access. When asked about whether their publications are available via open access, many interviewees focused on the cost of gold open-access models.[15] These interviewees highlighted that while they are generally supportive of open access, the cost of making their articles open access through the journals they publish in is prohibitively high, especially since they are expected to publish multiple articles per project and per year. A typical response by an interviewee: “I am all for the open access. That’s good but I have mixed feelings because you have to pay to get your paper published… That’s a lot of money and my lab can publish around twenty papers a year. I tell my students to please find a free journal. If it is open access where is my money?” Some had built those costs into their grants or had qualified for funds made available for that purpose by their institution, but others noted that money is already such a concern that they didn’t perceive it as prudent to allot costs towards open access or that institutional funds were not available. As the same interviewee highlighted, “Yes you can use grants to get it published, but you have to make the cuts somewhere else to make it work. …When I first came the department would pay for publication but now the department cannot afford it.”

 

Interviewees rarely reported deliberately seeking out green open access peer-reviewed publications, which reflects that other considerations such as reputation and scope are generally more important. Interviewees also reported low participation in their institutional repositories as a mechanism for making their publications open access, with some being unaware of such programs or perceiving the participation as too onerous. Some recognize that they may be required in the future to deposit their publications in an appropriately designated repository as a condition of receiving government funding, but the majority had not yet experienced such a requirement. Those who have reported that they deposited did so because non-agriculture-specific agencies, such as the National Institute of Health, required it. Others conflated open access and institutional repositories with academic social networking sites (discussed in further detail below)….”

Open source lessons for synthetic biology – O’Reilly Radar

“So, that’s software. How does open source work in biology? Examples lie on a spectrum ranging from “garage” to “academic lab.”

 

Biohackers, for one, in many ways resemble the original “two nerds in a garage” origins of the computer movement. Biohackers use open source protocols and designs for equipment, such as PCR to set up personal laboratories that would normally be beyond the scope of casual tinkerers. This is assisted by recent attempts to standardize genetic elements, as seen, for example, in the BioBrick movement (which curates various DNA sequences designed to easily clone together into a biological circuit) or the OpenPlant collaborative initiative (which promotes an open source approach to plant synthetic biology). Supported by a surprising number of open, collaborative labs around the world, these groups aim to bring about the same sort of changes as were seen with the start of the PC era.

 

At the other end, we have institutions such as CambiaLabs and the BiOS Initiative, which aim to support open source IP initiatives for biological systems via collaborative licensing agreements. A good example of their work would be the Transbacter project, an attempt to perform an end-run around the multitude of Agrobacteria-mediated plant engineering techniques patents by identifying other vectors — which were then released to the community.

 

Both of these are attempts to democratize biological research and development, and tie into a general increase in popular interest over biotechnology — as can be seen by the success of the crowdfunded “Glowing Plants” synthetic biology project….”

OpenPlant

“OpenPlant is a joint initiative between the University of Cambridge, John Innes Centre and the Earlham Institute, funded by the BBSRC and EPSRC as part of the UK Synthetic Biology for Growth programme. 

Synthetic Biology offers the prospect of reprogrammed biological systems for improved and sustainable bioproduction. While early efforts in the field have been directed at microbes, the engineering of plant systems offers even greater potential benefits. Plants are already cultivated globally at low cost, harvested on the giga-tonne scale, and routinely used to produce the widest range of biostuffs, from fibres, wood, oils, sugar, fine chemicals, drugs to food.

There is urgent need to improve our ability to reprogram crop metabolism and plant architecture in the face of global threats from new pathogens, climate change, soil degradation, restricted land use, salinity and drought. The next generation of DNA  tools for “smart” breeding of crop systems should be shared – to promote global innovation and equitable access to sustainable bioeconomies….”