The African Open Science Platform (AOSP)

Editor's Notes

• #10: The Sci-GaIA project has developed and deployed a standard-based Open Science Platform that supports federated authentication.Users can access a federated Open Science Platform to reproduce, re-use and publish their research products and link them to their ORCID profile to increase the visibility of both Science and scientists. Read More
• #11: The 2015 edition of Science International has developed an international accord on the values of open data in the emerging scientific culture of big data. The Accord recognises the need for an international framework of principles on “Open Data in a Big Data World” and proposes a comprehensive set of principles. These principles provide a guiding framework for an African data science capacity mobilization initiative spearheaded by ICSU and supported by other Science International partners. The initiative puts forward a comprehensive capacity mobilization plan, to be co-designed and delivered with key partners in Africa. It proposes the establishment of an African Open Data Platform, which will coordinate a series of actions at different levels of national science systems in the region.
• #14: Research Lifecycle enhanced by an "Open Science by Default" Workflow
• #15: Homo naledi has made headlines around the world as one of the most significant fossil discoveries ever made. The unprecedented sample of fossils represents a rich record of an ancient population of human relatives, preserving nearly every part of the skeleton and spanning the lifespan. Many people around the world have been following the compelling story of discovery from the first days of the excavation. Using social media to tell the story As our cavers and scientists worked underground in challenging conditions, we kept the world up to date on Twitter, Facebook and with our Rising Star Expedition blog. Since those first days, the team has worked to build open access into every stage of the project. People can now share not only in the discovery but also in the process of understanding these ancient hominins. After nearly two years of work, on September 10 we published our first scientific papers on this discovery in the journal eLIFE. These original scientific descriptions of these fossils and their geological context are free for anyone in the world to download and share. In the week since we published these papers, the lead paper describing Homo naledi has been viewed more than 170,000 times – an extraordinary figure for any scientific paper. Our team has also moved quickly to make our data available to anyone in the world. Many of our fossils are now represented by research-quality 3D scans on MorphoSource. This online archive of data from skeletal and fossil discoveries, maintained by Duke University, provides a way to share large data sets both for scientific work and teaching. 3D technology used in classrooms Our team has generated virtual reams of scans that enable anyone to visualise these fossils, and even to use 3D printing technology to create their own physical copies. Right now, teachers and researchers all around the world are printing 3D models of the fossils of Homo naledi. Kristina Killgrove, a leader in applying 3D printing technology in her anthropology classroom, wrote: I downloaded the model as an .STL file…and then printed it using my trusty old MakerBot. It took 20 minutes, tops. Then I gave the model to a grad student who was heading in to teach the undergraduate lab in biological anthropology. Bam! Species-announcement-to-teaching-cast in under 12 hours. In the first week after the announcement, more than 1700 copies of these data sets have been downloaded, with makers proudly showing off their printed models on Facebook and Twitter. Find broke boundaries Paleoanthropology has often been caricatured as the lone pursuit of fossils by Indiana-Jones-like characters. But in the 21st century, making new discoveries in paleoanthropology – as in all other areas of science – requires collaboration across many disciplines. This project has involved a team of more than 60 scientists, each bringing their own distinctive expertise and data sets together to help solve the problems posed by these fossils. The project is led from South Africa and stretches across international boundaries to impact the world. At the event announcing Homo naledi at Maropeng, the Vice-Chancellor of the University of the Witwatersrand, Adam Habib, remarked on the importance of open access for building a 21st century science: We often talk about science as having no boundaries, but in our world scientific knowledge has become commodified, and too often, what should be the bequest of the world, the bequest of a common humanity, is locked up under paywalls that postgraduate students and researchers cannot get access to. So what we did when we made this discovery, was we put cameras in the cave, and we streamed it live from day one. We partnered with eLIFE, an open access journal, to make sure that the discovery was available to all of humanity. And what we did in that practice, is create the first elements of a common global academy….We are not simply going to be beneficiaries of open access, but we are going to be contributors to open access, to the knowledge of a common humanity. eLIFE editor Randy Schekman wrote about the benefits of open access publishing in 2013 when he won the Nobel Prize. His article, entitled How to break free from the stifling grip of luxury journals, emphasised that by limiting access to publishing, traditional journals create artificial scarcity to distort the process of scientific communication. Open access makes for better science. Public engagement The open access philosophy has driven our work on Homo naledi from the beginning. Instead of keeping these discoveries veiled behind locked doors, we have tried to bring them to the public in ways that will drive greater curiosity and engagement with science. We are proud to be able to share the original fossils with the public at Maropeng, where they will be on display until October 11. Not only the public benefits from scientific open access; science itself benefits. Showing the process of science in action, we create better tools for educators to equip students with the scientific method. As we train a new generation of scientists, we must give them the tools to build collaborations and work with massive data. By sharing data openly, we build a worldwide community of practice as we attempt to understand this and other future discoveries.
• #21: William Edwards Deming (October 14, 1900 – December 20, 1993) was an American engineer, statistician, professor, author, lecturer, and management consultant. Educated initially as an electrical engineer and later specializing in mathematical physics, he helped develop the sampling techniques still used by the U.S. Department of the Census and the Bureau of Labor Statistics. In his book The New Economics for Industry, Government, and Education,[1] Deming championed the work of Walter Shewhart, including statistical process control, operational definitions, and what Deming called the "Shewhart Cycle"[2] which had evolved into PDSA (Plan-Do-Study-Act). This was in response to the growing popularity of PDSA, which Deming viewed as tampering with the meaning of Shewhart's original work.[3] Deming is best known for his work in Japan after WWII, particularly his work with the leaders of Japanese industry. That work began in August 1950 at the Hakone Convention Center in Tokyo when Deming delivered a speech on what he called "Statistical Product Quality Administration". Many in Japan credit Deming as one of the inspirations for what has become known as the Japanese post-war economic miracle of 1950 to 1960, when Japan rose from the ashes of war on the road to becoming the second largest economy in the world through processes partially influenced by the ideas Deming taught:[4] Better design of products to improve service Higher level of uniform product quality Improvement of product testing in the workplace and in research centers Greater sales through side [global] markets Deming is best known in the United States for his 14 Points (Out of the Crisis, by W. Edwards Deming, preface) and his system of thought he called the "System of Profound Knowledge". The system includes four components or "lenses" through which to view the world simultaneously: Appreciating a system Understanding variation Psychology Epistemology, the theory of knowledge[5] Deming made a significant contribution to Japan's reputation for innovative, high-quality products, and for its economic power. He is regarded as having had more impact on Japanese manufacturing and business than any other individual not of Japanese heritage. Despite being honored in Japan in 1951 with the establishment of the Deming Prize, he was only just beginning to win widespread recognition in the U.S. at the time of his death in 1993.[6] President Ronald Reagan awarded him the National Medal of Technology in 1987. The following year, the National Academy of Sciences gave Deming the Distinguished Career in Science award.
• #23: Last April, five months into the largest Ebola outbreak in history, an international group of researchers sequenced three viral genomes, sampled from patients in Guinea1. The data were made public that same month. Two months later, our group at the Broad Institute in Cambridge, Massachusetts, sequenced 99 more Ebola genomes, from patients at the Kenema Government Hospital in Sierra Leone. Uncertainties over whether the information belongs to local governments or data collectors present further barriers to sharing. So, too, does the absence of patient consent, common for data collected in emergencies — especially given the vulnerability of patients and their families to stigmatization and exploitation during outbreaks. Ebola survivors, for instance, risk being shunned because of fears that they will infect others. Related stories Tensions linger over discovery of coronavirus Dreams of flu data Nature special: Ebola outbreak More related stories We immediately uploaded the data to the public database GenBank (see go.nature.com/aotpbk). Our priority was to help curb the outbreak. Colleagues who had worked with us for a decade were at the front lines and in immediate danger; some later died. We were amazed by the surge of collaboration that followed. Numerous experts from diverse disciplines, including drug and vaccine developers, contacted us. We also formed unexpected alliances — for instance, with a leading evolutionary virologist, who helped us to investigate when the strain of virus causing the current outbreak arose. The genomic data confirmed that the virus had spread from Guinea to Sierra Leone, and indicated that the outbreak was being sustained by human-to-human transmission, not contact with bats or some other carrier. They also suggested new probable routes of infection and, importantly, revealed where and how fast mutations were occurring2. This information is crucial to designing effective diagnostics, vaccines and antibody-based therapies. What followed was three months of stasis, during which no new virus sequence information was made public (see 'Gaps in the data'). Some genomes are known to have been generated during this time from patients treated in the United States3. The number is likely to have been much larger: thousands of samples were transferred to researchers' freezers across the world. Sources: Sequences, NCBI/virological.org; Ebola cases, WHO Expand In an increasingly connected world, rapid sequencing, combined with new ways to collect clinical and epidemiological data, could transform our response to outbreaks. But the power of these potentially massive data sets to combat epidemics will be realized only if the data are shared as widely and as quickly as possible. Currently, no good guidelines exist to ensure that this happens. Speed is everything Researchers working on outbreaks — from Ebola to West Nile virus — must agree on standards and practices that promote and reward cooperation. If these protocols are endorsed internationally, the global research community will be able to share crucial information immediately wherever and whenever an outbreak occurs. The rapid dissemination of results during outbreaks is sporadic at best. In the case of influenza, an international consortium of researchers called GISAID established a framework for good practice in 2006. Largely thanks to this, during the 2009 H1N1 influenza outbreak, the US National Center for Biotechnology Information created a public repository that became a go-to place for the community to deposit and locate H1N1 sequence information4. By contrast, the publishing of sequence information in the early stages of the 2012 Middle East respiratory syndrome (MERS) outbreak in Saudi Arabia highlighted uncertainties about intellectual-property rights, and the resulting disputes hampered subsequent access to samples. Hasan Jamali/AP Pilgrims in Saudi Arabia try to protect themselves from Middle East respiratory syndrome (MERS) virus. Sharing data is especially important and especially difficult during an outbreak. Researchers are racing against the clock. Every outbreak can mobilize a different mixture of people — depending on the microbe and location involved — bringing together communities with different norms, in wildly different places. Uncertainties over whether the information belongs to local governments or data collectors present further barriers to sharing. So, too, does the absence of patient consent, common for data collected in emergencies — especially given the vulnerability of patients and their families to stigmatization and exploitation during outbreaks. Ebola survivors, for instance, risk being shunned because of fears that they will infect others. Nature special: Ebola outbreak Fortunately, useful models for responsible data sharing have been developed by the broader genomics community. In 1996, at a summit held in Bermuda, the heads of the major labs involved in the Human Genome Project agreed to submit DNA sequence assemblies of 1,000 bases or more to GenBank within 24 hours of producing them5, 6. In exchange, the sequencing centres retained the right to be the first to publish findings based on their own complete data sets, by laying out their plans for analyses in 'marker' papers. This rapid release of genomic data served the field well. New information on 30 disease genes, for instance, was published before the release of the complete human genome sequence. Since 1996, the Bermuda principles have been extended to other types of sequence data and to other fields that generate large data sets, such as metabolite research. Guidelines for sharing More-recent policies on data release similarly seek to align the interests of different parties, including funding agencies, data producers, data users and analysts, and scientific publishers. Since January, for example, the US National Institutes of Health has required grantees to make large-scale genomics data public by the time of publication at the latest, with earlier deadlines for some kinds of data7. We urge those at the forefront of outbreak research to forge similar agreements, taking into account the unique circumstances of an outbreak. First, incentives and safeguards should be created to encourage people to release their data quickly into the public domain. One possibility is to request that data users (and publishers) honour the publication intentions of data producers — the questions and analyses that they want to pursue themselves — for, say, six months. These intentions could be broadcast through several channels, including citable marker papers, disclaimer notices on data repositories such as GenBank, and online forums, such as virological.org and the EpiFlu database. Alternatively, data producers could publish an announcement about their data and their intentions on online forums as a resource that can be used by others as long as they cite the original source. “We urge researchers working on outbreaks to embrace a culture of openness.” Second, ethical, rigorous and standardized protocols for the collection of samples and data from patients should be established to facilitate the generation and sharing of that information. A global consortium involving the leading health and research agencies and the ministries of health of engaged nations should work together towards establishing these. Ethicists should be involved to safeguard subjects' privacy and dignity. Biosecurity experts will also be needed to address potential dual-use research and other safety concerns. A helpful analogue is the approach used by the Human Heredity and Health in Africa (H3Africa) Initiative, which aims to apply genomics to improving the health of African populations. Since August 2013, H3Africa has used standard consent-form guidelines8 for collecting DNA samples from subjects for genomic studies, regardless of their country of origin. Toshifumi Kitamura/AFP/Getty Quarantine officers rush to test passengers at Tokyo's Narita airport amid the 2009 swine-flu outbreak. Lastly, any preparation for future outbreaks should include provisions for rapidly building new bridges and establishing community norms. Successful collaborations in genomics and historical data-sharing agreements have tended to involve a fairly stable group of individuals and organizations, making norms of behaviour relatively easy to establish and sustain. By contrast, outbreaks can involve a new cast of characters each time, and cases in which the pathogen is new to science call for whole new fields of research. The Kenema way As a first step, we call on health agencies such as the World Health Organization, the US Centers for Disease Control and Prevention and Médecins Sans Frontières, as well as genome-sequencing centres and other research institutions, to convene a meeting this year — similar to that held in Bermuda in 1996. Attendees must include scientists, funders, ethicists, biosecurity experts, social scientists and journal editors. We urge researchers working on outbreaks to embrace a culture of openness. For our part, we have released all our sequence data as soon as it has been generated, including that from several hundred more Ebola samples we recently received from Kenema. We have listed the research questions that we are pursuing at virological.org and through GenBank, and we plan to present our results at virological.org as we generate them, for others to weigh in on. We invite people either to join our publication, or to prepare their own while openly laying out their intentions online. We have also made clinical data for 100 patients publicly available and have incorporated these into a user-friendly data-visualization tool, Mirador, to allow others to explore the data and uncover new insights. Kenema means 'translucent, clear like a river stream' or 'open to the public gaze'9. To honour the memory of our colleagues who died at the forefront of the Ebola outbreak, and to ensure that no future epidemic is as devastating, let's work openly in outbreaks. Nature 518, 477–479 (26 February 2015) doi:10.1038/518477a
• #30: Whilst most researchers appreciate the benefits of sharing research data, on an individual basis they may be reluctant to share their own data. The "Showing the Seed" study, commissioned by Knowledge Exchange, has gathered evidence, examples and opinions on current and future incentives for research data sharing from the researcher’s point of view, in order to provide recommendations for policy and practice development on how best to incentivise data access and reuse. This study is based on qualitative interviews with 22 selected researchers of five research teams that have established data sharing cultures, in the partner countries of Knowledge Exchange: Denmark, Finland, Germany, the Netherlands and the United Kingdom.The five case studies span various academic disciplines: arts and humanities, social sciences, biomedicine, chemistry and biology.