Posts Tagged ‘opendata’
Sunday, September 15th, 2013
I do go on rather a lot about enabling or hyper-activating[1] data. So do others[2]. Why is sharing data important?
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References
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O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, "Hyperactive molecules and the World-Wide-Web information system", Journal of the Chemical Society, Perkin Transactions 2, pp. 7, 1995. http://dx.doi.org/10.1039/P29950000007
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R. Van Noorden, "Data-sharing: Everything on display", Nature, vol. 500, pp. 243-245, 2013. http://dx.doi.org/10.1038/nj7461-243a
Tags:chemical tagger, data mining, datument, David Scheschkewitz, e-notebook, Google, opendata, Peter Murray-Rust, pre-processor, researcher, scientific tool, supervisor, United Kingdom
Posted in Chemical IT, Interesting chemistry | 9 Comments »
Friday, July 5th, 2013
The title of this post summarises the contents of a new molecular database: www.molecularspace.org[1] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “The Harvard Clean Energy Project: Large-scale computational screening and design of organic photovoltaics on the world community grid“. It reminds of a 2005 project by Peter Murray-Rust et al at the same sort of concept[2] (the World-Wide-Molecular-Matrix, or WWMM[3]), although the new scale is certainly impressive. Here I report my initial experiences looking through molecularspace.org
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References
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J. Hachmann, R. Olivares-Amaya, S. Atahan-Evrenk, C. Amador-Bedolla, R.S. Sánchez-Carrera, A. Gold-Parker, L. Vogt, A.M. Brockway, and A. Aspuru-Guzik, "The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid", The Journal of Physical Chemistry Letters, vol. 2, pp. 2241-2251, 2011. http://dx.doi.org/10.1021/jz200866s
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P. Murray-Rust, H.S. Rzepa, J.J.P. Stewart, and Y. Zhang, "A global resource for computational chemistry", Journal of Molecular Modeling, vol. 11, pp. 532-541, 2005. http://dx.doi.org/10.1007/s00894-005-0278-1
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P. Murray-Rust, S.E. Adams, J. Downing, J.A. Townsend, and Y. Zhang, "The semantic architecture of the World-Wide Molecular Matrix (WWMM)", Journal of Cheminformatics, vol. 3, 2011. http://dx.doi.org/10.1186/1758-2946-3-42
Tags:energy gap, energy levels, Google, Harvard, Jan Jensen, molecularspace site, opendata, Peter Murray-Rust, software agent acting, www.compchemhighlights.org, www.molecularspace.org
Posted in Chemical IT | 7 Comments »
Monday, June 24th, 2013
The blog post by Rich Apodaca entitled “The Horrifying Future of Scientific Communication” is very thought provoking and well worth reading. He takes us through disruptive innovation, and how it might impact upon how scientists communicate their knowledge. One solution floated for us to ponder is that “supporting Information, combined with data mining tools, could eliminate most of the need for manuscripts in the first place“. I am going to juxtapose that suggestion on something else I recently discovered.
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Tags:data mining, data mining tools, Google, opendata, researcher
Posted in Chemical IT | 2 Comments »
Monday, June 24th, 2013
The blog post by Rich Apodaca entitled “The Horrifying Future of Scientific Communication” is very thought provoking and well worth reading. He takes us through disruptive innovation, and how it might impact upon how scientists communicate their knowledge. One solution floated for us to ponder is that “supporting Information, combined with data mining tools, could eliminate most of the need for manuscripts in the first place“. I am going to juxtapose that suggestion on something else I recently discovered.
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Tags:data mining, data mining tools, Google, opendata, researcher
Posted in Chemical IT | 2 Comments »
Sunday, June 2nd, 2013
A few years ago, we published an article which drew a formal analogy between chemistry and iTunes (sic)[1]. iTunes was the first really large commercial digital music library, and a feature under-the-skin was the use of meta-data to aid discoverability of any of the 10 million (26M in 2013) or so individual items in the store.‡ The analogy to digital chemistry and discoverability of the 70 or so million known molecules is, we argued, a good one.
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References
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O. Casher, and H.S. Rzepa, "SemanticEye: A Semantic Web Application to Rationalize and Enhance Chemical Electronic Publishing", Journal of Chemical Information and Modeling, vol. 46, pp. 2396-2411, 2006. http://dx.doi.org/10.1021/ci060139e
Tags:Apple, BBC, digital photography, engineer, Google, Historical, HTML, metadata, opendata, RDF, search term, Steve Bachrach, United Kingdom
Posted in Chemical IT | No Comments »
Sunday, January 20th, 2013
With metrics in science publishing controversial to say the least, I pondered whether to write about the impact/influence a science-based blog might have (never mind whether it constitutes any measure of esteem). These are all terms that feature large when an (academic) organisation undertakes a survey of its researchers’ effectiveness.‡ WordPress (the organisation that provides the software used for this blog) recently enhanced the stats it offers for its users, and one of these caught my eye.
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Tags:manager, opendata
Posted in General | 3 Comments »
Saturday, July 21st, 2012
I blogged about this two years ago and thought a brief update might be in order now. To support the discussions here, I often perform calculations, and most of these are then deposited into a DSpace digital repository, along with metadata. Anyone wishing to have the full details of any calculation can retrieve these from the repository. Now in 2012, such repositories are more important than ever.
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Tags:API, Chemspider, computational chemistry, Digital respository, Imperial College, InChI Key, Mark Hahnel, Matt Harvey, opendata, pubchem, QRCode, Skolnik, United Kingdom, wikipedia
Posted in Chemical IT | 1 Comment »
Monday, October 24th, 2011
I have for perhaps the last 25 years been urging publishers to recognise how science publishing could and should change. My latest thoughts are published in an article entitled “The past, present and future of Scientific discourse” (DOI: 10.1186/1758-2946-3-46). Here I take two articles, one published 58 years ago and one published last year, and attempt to reinvent some aspects. You can see the result for yourself (since this journal is laudably open access, and you will not need a subscription). The article is part of a special issue, arising from a one day symposium held in January 2011 entitled “Visions of a Semantic Molecular Future” in celebration of Peter Murray-Rust’s contributions over that period (go read all 15 articles on that theme in fact!).
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Tags:Acrobat, Amazon, Android, chemical structure drawing packages, e-books, HTML, HTML5, iPad, iPads, Java, KF8, Kindle, mobile devices, opendata, Peter Murray-Rust, printing costs, SVG, Vector Graphics
Posted in Chemical IT, General | 3 Comments »