Open research

Open research is research conducted in the spirit of free and open-source software. Much like open-source schemes that are built around a source code that is made public, the central theme of open research is to make clear accounts of the methodology freely available via the internet, along with any data or results extracted or derived from them. This permits a massively distributed collaboration, and one in which anyone may participate at any level of the project.

Especially if the research is scientific in nature, it is frequently referred to as open science.[1][2] Open research can also include social sciences, the humanities, mathematics, engineering and medicine.

Open research is concerned with making scientific research more transparent, more collaborative and more efficient. A central aspect to it is to provide open access to scientific information, especially to the research published in scholarly journals and to the underlying data, much of which traditional science tends to hide away. Other aspects are more open forms of collaboration and engagement with a wider audience, including citizen scientists and the public at large.

Types of open projects

Important distinctions exist between different types of open projects.

Projects that provide open data but don't offer open collaboration are referred to as "open access" rather than open research. Providing open data is a necessary but not sufficient condition for open research, because although the data may be used by anyone, there is no requirement for subsequent research to take place openly. For example, though there have been many calls for more open collaborative research in drug discovery[3] and the open deposition of large amounts of data,[4] there are very few active, openly collaborative projects in this area.[5][6][7]

Crowdsourcing projects that recruit large numbers of participants to carry out small tasks which are then assembled into a larger project outcome have delivered significant research outcomes,[8][9] but these projects are distinct from those in which participants are able to influence the overall direction of the research, or in which participants are expected to have creative input into the science behind the project.

Most open research is conducted within existing research groups. Primary research data are posted which can be added to, or interpreted by, anyone who has the necessary expertise and who can therefore join the collaborative effort. Thus the "end product" of the project (which may still be subject to future expansion or modification) arises from many contributions across multiple research groups, rather than the effort of one group or individual. Open research is therefore distinct from open access in that the output of open research is prone to change with time.[10]

Unlike open access, true open research must demonstrate live, online collaboration. Project websites that demonstrate this capability have started to become available.[11][12]

Copyright conventions

Issues with copyright are dealt with by using either standard copyright (where applicable), releasing the content into the Public domain or by releasing the content under licenses such as one of the Creative Commons licenses[11] or one of the GNU General Public Licenses.

Examples

In 2005, several examples arose in the area of the search for new/improved medical treatments of Neglected Diseases.[11][13][14][15][16]

Science and engineering research to support the creation of open-source appropriate technology for sustainable development has long used open research principles.[17][18][19][20][21] Open source research for sustainable development is now becoming formalized with open access for literature reviews, research methods, data, results and summaries for laypeople.[22]

Wiki-based examples include: Appropedia, Wikiversity, Citizendium, Scholarpedia.

While first attempts towards opening research were primarily aimed at opening areas such as scientific data, methodologies, software and publications, now increasingly other artifacts of the scientific workflow are also tackled, such as scientific meta-data[23] and funding ideas.[24]

In 2013, open research became more mainstream with web based platforms such as figshare continuing to grow in terms of users and publicly available outputs.[25]

The Transparency and Openness Promotion (TOP) Committee met in 2014 to address one key element of the incentive systems: journals' procedures and policies for publication. The committee consisted of disciplinary leaders, journal editors, funding agency representatives, and disciplinary experts largely from the social and behavioral sciences. By developing shared standards for open practices across journals, the committee said it hopes to translate scientific norms and values into concrete actions and change the current incentive structures to drive researchers' behavior toward more openness.[26] The committee said it sought to produce guidelines that (a) focus on the commonalities across disciplines, and that (b) define what aspects of the research process should be made available to the community to evaluate, critique, reuse, and extend. The committee added that the guidelines aim to help improve journal policies in order to help transparency, openness, and reproducibility "become more evident in daily practice and ultimately improve the public trust in science, and science itself."[26]

See also

References

  1. ^ For an overview, see "Reinventing Discovery" by Michael Nielsen, Princeton University Press (21 October 2011), ISBN 0-691-14890-2
  2. ^ Woelfle, Michael; Olliaro, Piero; Todd, Matthew H. (23 September 2011). "Open science is a research accelerator". Nature Chemistry. 3 (10): 745–748. doi:10.1038/nchem.1149. PMID 21941234. Retrieved 16 October 2013.
  3. ^ Hopkins, Andrew L.; Witty, Michael J.; Nwaka, Solomon (13 September 2007). "Neglected Diseases Mission possible". Nature. 449 (7159): 166–169. doi:10.1038/449166a. PMID 17851512. Retrieved 16 October 2013.
  4. ^ F. -J. Gamo, et al. Thousands of chemical starting points for antimalarial lead identification. Nature 2010, 465, 305–310
  5. ^ Open Source Drug Discovery wiki
  6. ^ Indian Open Source Drug Discovery portal
  7. ^ Mendeley Group on Open Source Drug Discovery
  8. ^ S. Cooper, et al. Predicting protein structures with a multiplayer online game. Nature 2010 466, 756–760
  9. ^ K. Land et al. Galaxy Zoo: the large-scale spin statistics of spiral galaxies in the Sloan Digital Sky Survey, Mon. Not. R. Astron. Soc. 2008, 388, 1686–1692
  10. ^ Todd, Matthew H. (1 January 2007). "Open access and open source in chemistry". Chemistry Central Journal. 1 (1): 3. doi:10.1186/1752-153X-1-3. PMC 1975827. PMID 17939849. Retrieved 16 October 2013.
  11. ^ a b c The Synaptic Leap
  12. ^ MIAWiki for Open Research and Collaboration
  13. ^ Usefulchem
  14. ^ Article in the American Chemical Society's magazine C&E News on Open Research
  15. ^ Kepler, Thomas B.; Marti-Renom, Marc A.; Maurer, Stephen M.; Rai, Arti K.; Taylor, Ginger; Todd, Matthew H. (1 January 2006). "Open Source Research – the Power of Us". Australian Journal of Chemistry. 59 (5): 291. doi:10.1071/CH06095. Retrieved 16 October 2013.
  16. ^ Butler, Declan (4 February 2010). "Open-source science takes on neglected disease". Nature. doi:10.1038/news.2010.50. Retrieved 16 October 2013.
  17. ^ Kapczynski, Amy; et al. (2005). "Addressing Global Health Inequities: An Open Licensing Approach for University Innovations". Berkley Technology Law Journal. 20: 1031–1114.
  18. ^ Maurer, Stephen M.; Rai, Arti; Sali, Andrej (2004). "Finding Cures for Tropical Diseases: Is Open Source an Answer?". PLoS Medicine. 1 (3): 183–186. doi:10.1371/journal.pmed.0010056. PMC 539047. PMID 15630466.
  19. ^ Pearce, Joshua M. (2012). "The Case for Open Source Appropriate Technology". Environment, Development and Sustainability. 14 (3): 425–431. doi:10.1007/s10668-012-9337-9.
  20. ^ A. J. Buitenhuis, I. Zelenika and J. M. Pearce, "Open Design-Based Strategies to Enhance Appropriate Technology Development", Proceedings of the 14th Annual National Collegiate Inventors and Innovators Alliance Conference: Open, 25–27 March 2010, pp. 1–12.
  21. ^ Grue, Amanda J. An investigation into and recommendations for appropriate technology education. MIT. 2011. open access
  22. ^ Pearce, Joshua M. (2012). "Open Source Research in Sustainability". Sustainability: The Journal of Record. 5 (4): 238–243. doi:10.1089/sus.2012.9944.
  23. ^ Main Page – OpenResearch.org
  24. ^ Auer, S.; Braun-Thürmann, H.: Towards Bottom-Up, Stakeholder-Driven Research Funding – Open Source Funding, Open Peer Review. In Peer Review Reviewed: The International Career of a Quality-control Instrument and New Challenges 24–25 April 2008, Social Science Research Center Berlin (WZB), Berlin.
  25. ^ Boyd, S: Tools for sharing open research materials Gizmodo, 27 December 2013
  26. ^ a b B. A. Nosek*, G. Alter, G. C. Banks, D. Borsboom, S. D. Bowman, S. J. Breckler, S. Buck, C. D. Chambers, G. Chin, G. Christensen, M. Contestabile, A. Dafoe, E. Eich, J. Freese, R. Glennerster, D. Goroff, D. P. Green, B. Hesse, M. Humphreys, J. Ishiyama, D. Karlan, A. Kraut, A. Lupia, P. Mabry, T. A. Madon, N. Malhotra, E. Mayo-Wilson, M. McNutt, E. Miguel, E. Levy Paluck, U. Simonsohn, C. Soderberg, B. A. Spellman, J. Turitto, G. VandenBos, S. Vazire, E. J. Wagenmakers, R. Wilson, T. Yarkoni. Promoting an open research culture (26 June 2015), Science, vol. 348 no. 6242 pp. 1422–1425, DOI: 10.1126/science.aab2374(subscription required)
Bergens Tidende

Bergens Tidende is Norway's fifth-largest newspaper, and the country's largest newspaper outside Oslo.

Bergens Tidende is owned by the public company Schibsted ASA. Norwegian owners held a mere 42% of the shares in Schibsted at the end of 2015. Bergens Tidende is thus foreign-owned.

Bruce Perens

Bruce Perens (born around 1958) is an American computer programmer and advocate in the free software movement. He created The Open Source Definition and published the first formal announcement and manifesto of open source. He co-founded the Open Source Initiative (OSI) with Eric S. Raymond.In 2005, Perens represented Open Source at the United Nations World Summit on the Information Society, at the invitation of the United Nations Development Programme. He has appeared before national legislatures and is often quoted in the press, advocating for open source and the reform of national and international technology policy.

Perens is also an amateur radio operator, with call sign K6BP. He promotes open radio communications standards and open-source hardware.In 2016 Perens, along with Boalt Hall (Berkeley Law) professor Lothar Determann, co-authored "Open Cars" which appeared in the Berkeley Technology Law Journal.

In 2018 Perens founded the Open Research Institute (ORI), a non-profit research and development organization to address technologies involving Open Source, Open Hardware, Open Standards, Open Content, and Open Access to Research. ORI facilitate worldwide collaboration in the development of technology that would otherwise be restricted under national laws like ITAR and EAR.

Computational science

Computational science (also scientific computing or scientific computation (SC)) is a rapidly growing multidisciplinary field that uses advanced computing capabilities to understand and solve complex problems. It is an area of science which spans many disciplines, but at its core it involves the development of models and simulations to understand natural systems.

Algorithms (numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve science (e.g., biological, physical, and social), engineering, and humanities problems

Computer and information science that develops and optimizes the advanced system hardware, software, networking, and data management components needed to solve computationally demanding problems

The computing infrastructure that supports both the science and engineering problem solving and the developmental computer and information scienceIn practical use, it is typically the application of computer simulation and other forms of computation from numerical analysis and theoretical computer science to solve problems in various scientific disciplines. The field is different from theory and laboratory experiment which are the traditional forms of science and engineering. The scientific computing approach is to gain understanding, mainly through the analysis of mathematical models implemented on computers. Scientists and engineers develop computer programs, application software, that model systems being studied and run these programs with various sets of input parameters. The essence of computational science is the application of numerical algorithms and/or computational mathematics. In some cases, these models require massive amounts of calculations (usually floating-point) and are often executed on supercomputers or distributed computing platforms.

Digital image processing

In computer science, digital image processing is the use of computer algorithms to perform image processing on digital images. As a subcategory or field of digital signal processing, digital image processing has many advantages over analog image processing. It allows a much wider range of algorithms to be applied to the input data and can avoid problems such as the build-up of noise and signal distortion during processing. Since images are defined over two dimensions (perhaps more) digital image processing may be modeled in the form of multidimensional systems.

Faculty of 1000

Faculty of 1000 (abbreviated F1000) is a publisher of services for life scientists and clinical researchers.

Image

An image (from Latin: imago) is an artifact that depicts visual perception, such as a photograph or other two-dimensional picture, that resembles a subject—usually a physical object—and thus provides a depiction of it. In the context of signal processing, an image is a distributed amplitude of color(s).

LabKey Server

LabKey Server is a software suite available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources. Specific scientific applications and workflows can be added on top of the basic platform and leverage a data processing pipeline.

Mobile cloud computing

Mobile Cloud Computing (MCC) is the combination of cloud computing, mobile computing and wireless networks to bring rich computational resources to mobile users, network operators, as well as cloud computing providers. The ultimate goal of MCC is to enable execution of rich mobile applications on a plethora of mobile devices, with a rich user experience. MCC provides business opportunities for mobile network operators as well as cloud providers. More comprehensively, MCC can be defined as "a rich mobile computing technology that leverages unified elastic resources of varied clouds and network technologies toward unrestricted functionality, storage, and mobility to serve a multitude of mobile devices anywhere, anytime through the channel of Ethernet or Internet regardless of heterogeneous environments and platforms based on the pay-as-you-use principle."

National Center for Computational Sciences

The National Center for Computational Sciences (NCCS) is a United States Department of Energy Leadership Computing Facility. The NCCS provides resources for calculation and simulation in fields including astrophysics, materials, and climate research. This research is intended to enhance American competitiveness in industry.

The NCCS, founded in 1992 and located at Oak Ridge National Laboratory (ORNL), currently manages a 2.33-petaflop (theoretical peak) Cray XT5 supercomputer named Jaguar for use in open research by academic and corporate researchers. Jaguar was named the world's fastest computer at SC09, a position it held until October 2010.

Founded in 1992, the NCCS is a managed activity of the Advanced Scientific Computing Research program of the Department of Energy Office of Science (DOE-SC).

Nature Reviews Disease Primers

Nature Reviews Disease Primers is a peer-reviewed medical journal publishing broad review articles about disease areas, offering a global overview of the field and outlining "key open research questions". Each "Primer" is accompanied by a "PrimeView" summary poster containing accessible artwork and highlighting key points from the review.The journal is abstracted and indexed in Index Medicus/MEDLINE/PubMed.

Open-access mandate

An open-access mandate is a policy adopted by a research institution, research funder, or government which requires researchers—usually university faculty or research staff and/or research grant recipients—to make their published, peer-reviewed journal articles and conference papers open access (1) by self-archiving their final, peer-reviewed drafts in a freely accessible institutional repository or disciplinary repository ("Green OA") or (2) by publishing them in an open-access journal ("Gold OA") or both.

OpenWetWare

OpenWetWare is a wiki whose mission is "to support open research, education, publication, and discussion in biological sciences and engineering."

OpenWetWare was created by graduate students at MIT on April 20, 2005. Initially, it served as a private lab wiki for the labs of Drew Endy and Tom Knight at MIT. The site was opened up to allow any lab to join on June 22, 2005. As of April 6, 2007 the site hosted 100 research laboratories from over 40 institutions, including Boston University, Brown University, Caltech, Cambridge Research Institute, CNRS, Duke University, and many others.

In addition to laboratories, a number of scientific communities are based on the site, including synthetic biology, Mimulus, and the BioBricks Foundation. One scientific community is the iGEM community with over 60 different teams represented on June 28, 2013 including the | NRP-UEA-Norwich team and the | Groningen team.

OpenWetWare runs on MediaWiki software on Linux servers. All content is available under free content licenses, specifically the GNU free documentation license (GFDL) and the Creative Commons Attribution ShareAlike license.

Open science

Open science is the movement to make scientific research (including publications, data, physical samples, and software) and its dissemination accessible to all levels of an inquiring society, amateur or professional. Open science is transparent and accessible knowledge that is shared and developed through collaborative networks. It encompasses practices such as publishing open research, campaigning for open access, encouraging scientists to practice open notebook science, and generally making it easier to publish and communicate scientific knowledge.

Open Science can be seen as a continuation of, rather than a revolution in, practices begun in the 17th century with the advent of the academic journal, when the societal demand for access to scientific knowledge reached a point at which it became necessary for groups of scientists to share resources with each other so that they could collectively do their work. In modern times there is debate about the extent to which scientific information should be shared. The conflict that led to the Open Science movement is between the desire of scientists to have access to shared resources versus the desire of individual entities to profit when other entities partake of their resources. Additionally, the status of open access and resources that are available for its promotion are likely to differ from one field of academic inquiry to another.

Open science data

Open science data is a type of open data focused on publishing observations and results of scientific activities available for anyone to analyze and reuse. A major purpose of the drive for open data is to allow the verification of scientific claims, by allowing others to look at the reproducibility of results, and to allow data from many sources to be integrated to give new knowledge. While the idea of open science data has been actively promoted since the 1950s, the rise of the Internet has significantly lowered the cost and time required to publish or obtain data.

Operator product expansion

In quantum field theory, the operator product expansion (OPE) is used as an axiom to define the product of fields as a sum over the same fields. As an axiom, it offers a non-perturbative approach to quantum field theory. One example is the vertex operator algebra, which has been used to construct two-dimensional conformal field theories. Whether this result can be extended to QFT in general, thus resolving many of the difficulties of a perturbative approach, remains an open research question.

In practical calculations, such as those needed for scattering amplitudes in various collider experiments, the operator product expansion is used in QCD sum rules to combine results from both perturbative and non-perturbative (condensate) calculations.

University College Cork

University College Cork – National University of Ireland, Cork (UCC) (Irish: Coláiste na hOllscoile Corcaigh) is a constituent university of the National University of Ireland, and located in Cork.

The university was founded in 1845 as one of three Queen’s Colleges located in Belfast, Cork, and Galway. It became University College, Cork, under the Irish Universities Act of 1908. The Universities Act 1997 renamed the university as National University of Ireland, Cork, and a Ministerial Order of 1998 renamed the university as University College Cork – National University of Ireland, Cork, though it continues to be almost universally known as University College Cork.

Amongst other rankings and awards, the university was named Irish University of the Year by the Sunday Times on five occasions; most recently in 2017. In 2015, UCC was also named as top performing university by the European Commission funded U-Multirank system, based on obtaining the highest number of "A" scores (21 out of 28 metrics) among a field of 1200 partaking universities. UCC also became the first university to achieve the ISO 50001 standard in energy management in 2011.

University of Exeter

The University of Exeter is a public research university in Exeter, Devon, South West England, United Kingdom. It was founded and received its Royal Charter in 1955, although its predecessor institutions, St Luke's College, Exeter School of Science, Exeter School of Art, and the Camborne School of Mines were established in 1838, 1855, 1863, and 1888 respectively. In post-nominals, the University of Exeter is abbreviated as Exon. (from the Latin Exoniensis), and is the suffix given to honorary and academic degrees from the university.

The university has four campuses: Streatham and St Luke's (both of which are in Exeter); and Truro and Penryn (both of which are in Cornwall). The university is primarily located in the city of Exeter, Devon, where it is the principal higher education institution. Streatham is the largest campus containing many of the university's administrative buildings, and is regarded as the most beautiful in the country. The Penryn campus is maintained in conjunction with Falmouth University under the Combined Universities in Cornwall (CUC) initiative. The Exeter Streatham Campus Library holds more than 1.2 million physical library resources, including historical journals and special collections.Exeter was named the Sunday Times University of the Year in 2013 and was the Times Higher Education University of the Year in 2007. It has maintained a top ten position in the National Student Survey since the survey was launched in 2005. The annual income of the institution for 2017–18 was £415.5 million of which £76.1 million was from research grants and contracts, with an expenditure of £414.2 million.Exeter is a member of the Russell Group of leading research-intensive UK universities and is also a member of Universities UK, the European University Association, and the Association of Commonwealth Universities and an accredited institution of the Association of MBAs (AMBA).

Verdens Gang

Verdens Gang ("The course of the world"), generally known under the abbreviation VG, is a Norwegian tabloid newspaper. In 2016, circulation numbers stood at 93,883, having declined from a peak circulation of 390,510 in 2002. VG is nevertheless the most read online newspaper in Norway, with about 2 million daily readers.Verdens Gang AS is a private company wholly owned by the public company Schibsted ASA. Somewhere between 30% and 60% of Schibsted is owned by international institutional investors such as Goldman Sachs and Northern Trust. Norwegian owners held a mere 42% of the shares in Schibsted at the end of 2015; VG is thus foreign-owned.

Wellcome Trust

The Wellcome Trust is a biomedical research charity based in London, United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Sir Henry Wellcome to fund research to improve human and animal health. The aim of the Trust is to "achieve extraordinary improvements in health by supporting the brightest minds", and in addition to funding biomedical research it supports the public understanding of science. It has an endowment of £25.9 billion (2018) making it the third wealthiest charitable foundation in the world, after the Bill & Melinda Gates Foundation and the INGKA Foundation.The Trust has been described by the Financial Times as the United Kingdom's largest provider of non-governmental funding for scientific research and one of the largest providers in the world.

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