Peter Murray-Rust

Peter Murray-Rust (born 1941) is a chemist currently working at the University of Cambridge. As well as his work in chemistry, Murray-Rust is also known for his support of open access and open data.

Peter Murray-Rust
Peter Murray-Rust,8083939
at Wikimania 2014
Born1941 (age 77–78)
ResidenceUnited Kingdom
Alma materBalliol College, Oxford
Known for
AwardsHerman Skolnik Award
Scientific career
Fields
Institutions
ThesisA structural investigation of some compounds showing charge-transfer properties (1969)
Websitewww-pmr.ch.cam.ac.uk

Education

He was educated at Bootham School and Balliol College, Oxford. After obtaining a Doctor of Philosophy with a thesis entitled A structural investigation of some compounds showing charge-transfer properties, he became lecturer in chemistry at the (new) University of Stirling and was first warden of Andrew Stewart Hall of Residence. In 1982, he moved to Glaxo Group Research at Greenford to head Molecular Graphics,[1] Computational Chemistry and later protein structure determination. He was Professor of Pharmacy in the University of Nottingham from 1996–2000, setting up the Virtual School of Molecular Sciences. He is now Reader Emeritus in Molecular Informatics at the University of Cambridge and Senior Research Fellow Emeritus of Churchill College, Cambridge.

Research

His research interests have involved the automated analysis of data in scientific publications, creation of virtual communities, e.g. The Virtual School of Natural Sciences in the Globewide Network Academy, and the Semantic Web. With Henry Rzepa, he has extended this to chemistry through the development of markup languages, especially Chemical Markup Language.[2] He campaigns for open data, particularly in science, and is on the advisory board of the Open Knowledge International and a co-author of the Panton Principles for Open scientific data.[3] Together with a few other chemists, he was a founder member of the Blue Obelisk movement in 2005.[4][5][6]

In 2002, Peter Murray-Rust and his colleagues proposed an electronic repository for unpublished chemical data called the World Wide Molecular Matrix (WWMM). In January 2011, a symposium around his career and visions was organized, called Visions of a Semantic Molecular Future.[7][8][9][10] In 2011, he and Henry Rzepa were joint recipients of the Herman Skolnik Award of the American Chemical Society.[11] In 2014, he was awarded a Fellowship by the Shuttleworth Foundation to develop the automated mining of science from the literature.

In 2009 Murray-Rust coined the term "Doctor Who" model for the phenomenon exhibited by the Blue Obelisk project and other Open Science projects, where when a project leader does not have the resources to continue to lead a project (e.g. because he or she has moved to another university with other tasks), someone else will stand up to become the new leader and continue the project.[12][13] This is a reference to the long-running British science fiction television series Doctor Who, in which the main character periodically regenerates into a different form, which is played by a different actor.

As of 2014, Murray-Rust was granted a Fellowship by Shuttleworth Foundation in relation to the ContentMine project which uses machines to liberate 100,000,000 facts from the scientific literature.

Activism

Murray-Rust is also known for his work on making scientific knowledge from literature freely available, and in such taking a stance against publishers that are not fully compliant with the Berlin Declaration on Open Access. In 2014, he actively raised awareness of glitches in the publishing system of Elsevier, where restrictions were imposed by Elsevier on the reuse of papers after the authors had paid Elsevier to make the paper freely available.[14] He has also made statements about predatory journals; he has come under criticism by Jeffrey Beall for his involvement with publisher MDPI and for his account of this involvement.[15][16]

References

  1. ^ Murray-Rust, P.; Glusker, J. P. (1984). "Directional hydrogen bonding to sp2- and sp3-hybridized oxygen atoms and its relevance to ligand-macromolecule interactions". Journal of the American Chemical Society. 106 (4): 1018–1025. doi:10.1021/ja00316a034.
  2. ^ Murray-Rust, P.; Rzepa, H. S. (1999). "Chemical Markup, XML, and the Worldwide Web. 1. Basic Principles". Journal of Chemical Information and Modeling. 39 (6): 928–942. CiteSeerX 10.1.1.40.8275. doi:10.1021/ci990052b.
  3. ^ http://pantonprinciples.org/ Panton Principles for Open data in science
  4. ^ Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. (2006). "The Blue Obelisk - Interoperability in Chemical Informatics". Journal of Chemical Information and Modeling. 46 (3): 991–998. doi:10.1021/ci050400b. PMC 4878861. PMID 16711717.
  5. ^ O'Boyle, N. M.; Guha, R.; Willighagen, E. L.; Adams, S. E.; Alvarsson, J.; Bradley, J. C.; Filippov, I. V.; Hanson, R. M.; Hanwell, M. D.; Hutchison, G. R.; James, C. A.; Jeliazkova, N.; Lang, A. S. D.; Langner, K. M.; Lonie, D. C.; Lowe, D. M.; Pansanel, J. R. M.; Pavlov, D.; Spjuth, O.; Steinbeck, C.; Tenderholt, A. L.; Theisen, K. J.; Murray-Rust, P. (2011). "Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on". Journal of Cheminformatics. 3 (1): 37. doi:10.1186/1758-2946-3-37. PMC 3205042. PMID 21999342.
  6. ^ The Blue Obelisk, CDK News, 2005, 2, 43–46
  7. ^ Jones, R.; MacGillivray, M.; Murray-Rust, P.; Pitman, J.; Sefton, P.; O'Steen, B.; Waites, W. (2011). "Open Bibliography for Science, Technology, and Medicine". Journal of Cheminformatics. 3: 47. doi:10.1186/1758-2946-3-47. PMC 3206455. PMID 21999661.
  8. ^ CCL Archives, 2010, http://ccl.net/chemistry/resources/messages/2010/11/12.005-dir/
  9. ^ Meeting Archives and publications, 2011, http://www.dspace.cam.ac.uk/handle/1810/238409
  10. ^ Murray-Rust, P. (2011). "Semantic science and its communication - a personal view". Journal of Cheminformatics. 3: 48. doi:10.1186/1758-2946-3-48. PMC 3206456. PMID 21999715.
  11. ^ CCL Archives, 2011, http://www.ccl.net/cgi-bin/ccl/message-new?2011+09+26+014
  12. ^ Glyn Moody, The Doctor Who Model of Open Source, 2009, http://opendotdotdot.blogspot.nl/2009/06/doctor-who-model-of-open-source.html
  13. ^ P. Murray-Rust, The Doctor Who Model of Open Source, 2009, http://blogs.ch.cam.ac.uk/pmr/2009/06/06/the-doctor-who-model-of-open-source/
  14. ^ Paul Jump, Elsevier: bumps on road to open access, Times Higher Education, 2014, http://www.timeshighereducation.co.uk/news/elsevier-bumps-on-road-to-open-access/2012238.article
  15. ^ "Beall's criticism of MDPI lacks evidence and is irresponsible". cam.ac.uk.
  16. ^ "MDPI and Beall - further comments from a "brainwashed Brit"". cam.ac.uk.

External links

1941 in science

The year 1941 in science and technology involved some significant events, listed below.

Blue Obelisk

Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obelisk, among which, in alphabetical order, Avogadro, Bioclipse, cclib, Chemistry Development Kit, GaussSum, JChemPaint, JOELib, Kalzium, Openbabel, OpenSMILES, and UsefulChem.

The project has handed out personal awards for achievements in promoting Open Data, Open Source and Open Standards. Among those who received a Blue Obelisk Award are:

Christoph Steinbeck (2006)

Geoff Hutchinson (2006)

Bob Hanson (2006),

Egon Willighagen (2007)

Jean-Claude Bradley (2007)

Ola Spjuth (2007)

Noel O'Boyle (2010)

Rajarshi Guha (2010)

Cameron Neylon (2010)

Alex Wade (2010)

Nina Jeliazkova (2010)

Henry Rzepa (2011)

Dan Zaharevitz (2011)

Sam Adams (2011)

Jens Thomas (2011)

Marcus Hanwell (2011)

Roger Sayle (2011)

the Environmental Molecular Sciences Laboratory (2012)

Saulius Gražulis (2014)

Antony Williams (2014)

Daniel Lowe (2014)

Andrew Lang (2014)

Matthew Todd (2014)

WikiChemists (2014)

Greg Landrum (2016)

Mark Forster (2016)

John Mayfield (2017)

Churchill College, Cambridge

Churchill College is a constituent college of the University of Cambridge, England. It has a primary focus on science, engineering and technology, but still retains a strong interest in the arts and humanities.

In 1958, a trust was established with Sir Winston Churchill as its chairman of trustees, to build and endow a college for 60 fellows and 540 students as a national and Commonwealth memorial to Winston Churchill; its Royal Charter and Statutes were approved by the Queen, in August 1960. It is situated on the outskirts of Cambridge, away from the traditional centre of the city, but close to the University's main new development zone (which now houses the Centre for Mathematical Sciences), which some would argue is the new city centre. Its 16 hectares (40 acres) of grounds make it physically the largest of all the colleges.

Churchill was the first all-male college to decide to admit women, and was among three men's colleges to admit its first women students in 1972. Within 15 years all others had followed suit. The college has a reputation for relative informality compared with other Cambridge colleges, and traditionally admits a larger proportion of its undergraduates from state schools.

The college motto is "Forward". It was taken from the final phrase of Winston Churchill's first speech to the House of Commons as Prime Minister – his famous "Blood, Toil, Tears and Sweat" speech – in which he said "Come, then, let us go forward together".

Department of Chemistry, University of Cambridge

The Department of Chemistry at the University of Cambridge is the chemistry department of the University of Cambridge. It was formed from a merger in the early 1980s of two separate departments that had moved into the Lensfield Road building decades earlier: the Department of Physical Chemistry (originally led by Professor Ronald Norrish FRS, Nobel Laureate; the department was previously located near the Old Cavendish in Free School Lane - see photo) and the Department of Chemistry (that included theoretical chemistry and which was led by Lord Alexander R. Todd FRS, Nobel Laureate) respectively. Research interests in the department cover a broad of chemistry ranging from molecular biology to geophysics. The department is located on the Lensfield Road, next to the Panton Arms on the South side of Cambridge. As of 2015 the department is home to around 200 postdoctoral research staff, over 250 postgraduate students, around sixty academic staff.

Do-it-yourself biology

Do-it-yourself biology (DIY biology, DIY bio) is a growing biotechnological social movement in which individuals, communities, and small organizations study biology and life science using the same methods as traditional research institutions. DIY biology is primarily undertaken by individuals with extensive research training from academia or corporations, who then mentor and oversee other DIY biologists with little or no formal training. This may be done as a hobby, as a not-for-profit endeavour for community learning and open-science innovation, or for profit, to start a business.

Herman Skolnik Award

The Herman Skolnik Award is awarded annually by the Division of Chemical Information of the American Chemical Society, "to recognize outstanding contributions to and achievements in the theory and practice of chemical information science". As of 2011 the award is of 3,000 US dollars.It is named for Herman Skolnik (1914-1994), who was a co-founder of the then ACS Division of Chemical Literature in 1948 and a key figure in the Division. The first award was made to him.

JOELib

JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other operating systems supporting the programming language Java. It is free and open-source software distributed under the GNU General Public License (GPL) 2.0.

Murray (surname)

Murray (listen ) is both a Scottish and an Irish surname with two distinct respective etymologies. The Scottish version is a common variation of the word Moray, an anglicisation of the Medieval Gaelic word Muireb (or Moreb); the b here was pronounced as v, hence the Latinization to Moravia. These names denote the district on the south shore of the Moray Firth, in Scotland. Murray is a direct transliteration of how Scottish people pronounce the word Moray. The Murray spelling is not used for the geographical area, which is Moray, but it became the commonest form of the surname, especially among Scottish emigrants, to the extent that the surname Murray is now much more common than the original surname Moray. See also Clan Murray.

The Irish version derives from Ó Muireadhaigh. However, there were many Scottish Murray immigrants into Ireland during the Middle Ages and so a Murray of Irish heritage today could be descended from either source of the name.

Open-door academic policy

An open-door academic policy, or open-door policy, is a policy if a university accepting to enroll students without asking for evidence of previous education, experience, or references. Usually, payment of the academic fees (or financial support) is all that is required to enroll.

Universities may not employ the open-door policy for all their courses, and those that have a universal open-door policy where all courses have no entry requirements are called open universities. The policy is seen to be a part of the educational revolution. From the dictionary meaning of the open-door policy, which is the idea of granting access to those who want access to the country freely, a similar idea can be drawn in terms of education.According to Deepa Rao, the open-door academic policy is one of the main ways in which adult learners become a part of university/college life. The recognized demand for post-secondary education made many institutions commit strongly to the policy, but many concealed limitations in the policy can prevent some from securing a degree.

Open-notebook science

Open-notebook science is the practice of making the entire primary record of a research project publicly available online as it is recorded. This involves placing the personal, or laboratory, notebook of the researcher online along with all raw and processed data, and any associated material, as this material is generated. The approach may be summed up by the slogan 'no insider information'. It is the logical extreme of transparent approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'. The practice of open notebook science, although not the norm in the academic community, has gained significant recent attention in the research and general media as part of a general trend towards more open approaches in research practice and publishing. Open notebook science can therefore be described as part of a wider open science movement that includes the advocacy and adoption of open access publication, open data, crowdsourcing data, and citizen science. It is inspired in part by the success of open-source software and draws on many of its ideas.

Open Knowledge International

Open Knowledge International (OKI), known as the Open Knowledge Foundation (OKF) until April 2014 and then Open Knowledge until May 2016, is a global, non-profit network that promotes and shares information at no charge, including both content and data. It was founded by Rufus Pollock on 24 May 2004 in Cambridge, UK.Its slogan is, "Sonnets to statistics, genes to geodata ..."

Open admissions

Open admissions, or open enrollment, is a type of unselective and noncompetitive college admissions process in the United States in which the only criterion for entrance is a high school diploma or a certificate of attendance or General Educational Development (GED) certificate.

Open collaboration

Open collaboration is "any system of innovation or production that relies on goal-oriented yet loosely coordinated participants who interact to create a product (or service) of economic value, which they make available to contributors and noncontributors alike." It is prominently observed in open source software, but can also be found in many other instances, such as in Internet forums, mailing lists and online communities. Open collaboration is also thought to be the operating principle underlining a gamut of diverse ventures, including bitcoin, TEDx, and Wikipedia.Open collaboration is the principle underlying peer production, mass collaboration, and wikinomics. It was observed initially in open source software, but can also be found in many other instances, such as in Internet forums, mailing lists, Internet communities, and many instances of open content, such as creative commons. It also explains some instances of crowdsourcing, collaborative consumption, and open innovation.Riehle et al. define open collaboration as collaboration based on three principles of egalitarianism, meritocracy, and self-organization. Levine and Prietula define open collaboration as "any system of innovation or production that relies on goal-oriented yet loosely coordinated participants who interact to create a product (or service) of economic value, which they make available to contributors and noncontributors alike." This definition captures multiple instances, all joined by similar principles. For example, all of the elements — goods of economic value, open access to contribute and consume, interaction and exchange, purposeful yet loosely coordinated work — are present in an open source software project, in Wikipedia, or in a user forum or community. They can also be present in a commercial website that is based on user-generated content. In all of these instances of open collaboration, anyone can contribute and anyone can freely partake in the fruits of sharing, which are produced by interacting participants who are loosely coordinated.

An annual conference dedicated to the research and practice of open collaboration is the International Symposium on Wikis and Open Collaboration (OpenSym, formerly WikiSym). As per its website, the group defines open collaboration as "collaboration that is egalitarian (everyone can join, no principled or artificial barriers to participation exist), meritocratic (decisions and status are merit-based rather than imposed) and self-organizing (processes adapt to people rather than people adapt to pre-defined processes)."

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.

Open university

An open university is a university with an open-door academic policy, with minimal or no entry requirements. Open universities may employ specific teaching methods, such as open supported learning or distance education. However, not all open universities focus on distance education, nor do distance-education universities necessarily have open admission policies.

P2P Foundation

P2P Foundation: The Foundation for Peer to Peer Alternatives is an organization with the aim of studying the impact of peer to peer technology and thought on society. It was founded by Michel Bauwens, James Burke and Brice Le Blévennec.The P2P Foundation is a registered institute founded in Amsterdam, Netherlands. Its local registered name is: Stichting Peer to Peer Alternatives, dossier nr: 34264847.

Panton Principles

The Panton Principles are a set of principles which were written to promote open science. They were first drafted in July 2009 at the Panton Arms pub in Cambridge.

Peter Murray

Peter Murray may refer to:

Peter Murray (architectural writer) (born 1944), British architectural journalist

Peter Murray (art historian) (1920–1992), professor of history of art

Peter Murray (Harvard Law School), lecturer at Harvard Law School

Pete Murray (born 1969), Australian singer-songwriter

Pete Murray (DJ) (born 1925), British radio and television presenter

Pete Murray (American musician), American musician and singer-songwriter

Peter Murray (Yorkshire Sculpture Park), founding director of Yorkshire Sculpture Park

Peter J. Murray (born 1951), retired mathematics teacher and children's author

Peter Marshall Murray (1888–1969), president of the National Medical Association, 1932–1933

Peter Murray (rugby union) (1884–1968), New Zealand rugby union player and politician

World Wide Molecular Matrix

The World Wide Molecular Matrix (WWMM) was a proposed electronic repository for unpublished chemical data. First introduced in 2002 by Peter Murray-Rust and his colleagues in the chemistry department at the University of Cambridge in the United Kingdom, WWMM provided a free, easily searchable database for information about thousands of complicated molecules, data that would otherwise remain inaccessible to scientists.

Murray-Rust, a chemical informatics specialist, has estimated that 80% of the results produced by chemists around the world is never published in scientific journals. Most of this data is not ground-breaking, yet it could conceivably be of use to scientists doing related projects—if they could access it. The WWMM was proposed as a solution to this problem. It would house the results of experiments on over 100,000 molecules in physical chemistry, organic chemistry, biochemistry and medicinal chemistry.

In other scientific fields, the need for a similar depository to house inaccessible information could be more acute. In a presentation at the "CERN Workshop on Innovations in Scholarly Communications (OAI4)", Murray-Rust said that chemistry actually leads other fields in published data. He estimated that the majority of the data in some scientific fields never reaches publication.Although scientific in nature, the WWMM was part of the broader open archives and open source movements, pushes to make more and more information freely available to any user via the Internet or World Wide Web. In his CERN presentation, Murray-Rust stated that the WWMM was a "response to the expense of [scientific] journals", and he asked the rhetorical question, "Can we win the war to make data open, or will it be absorbed into the publishing and pseudo-publishing world?" Murray-Rust and his colleagues are also responsible for the development of the Chemical Mark-up Language (CML), a variant of XML intended for chemists.

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