Posts Tagged ‘computing’
Wednesday, May 16th, 2018
Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on how ten years of progress in technology has required changes and the challenge of how any necessary changes might be kept “under the hood” of this blog.
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Tags:Ajax, Computer programming, computing, Cross-platform software, HTML, Interesting chemistry, Java, Java applet, Java technology, JavaScript, JavaScript libraries, jmol, JQuery, NPAPI, Scientific Journal, Software engineering, Technology/Internet, web browser behaviour, web browsers, Web-page security
Posted in Uncategorised | 6 Comments »
Thursday, December 7th, 2017
FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi- or even fully processed/interpreted data. Here I illustrate a new example of how both kinds of data can be made to co-exist.
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Tags:Chemical IT, computing, Context, data, Data management, Information, Knowledge, Raw data, software simulations, Technology/Internet
Posted in crystal_structure_mining | No Comments »
Tuesday, November 14th, 2017
PIDapalooza is a new forum concerned with discussing all things persistent, hence PID. You might wonder what possible interest a chemist might have in such an apparently arcane subject, but think of it in terms of how to find the proverbial needle in a haystack in a time when needles might look all very similar. Even needles need descriptions, they are not all alike and PIDs are a way of providing high quality information (metadata) about a digital object.
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Tags:Chemical IT, chemist, computing, Information, Information science, Knowledge representation, librarian, Needle, PID
Posted in Uncategorised | No Comments »
Saturday, June 10th, 2017
In an earlier post, I lamented the modern difficulties in running old instances of Jmol, an example of an application program written in the Java programming language. When I wrote that, I had quite forgotten a treasure trove of links to old Java that I had collected in 1996-7 and then abandoned. Here I browse through a few of the things I found.
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Tags:Alan Tongue, City: London, City: Paris, Company: Sun Microsystems, computing, Computing platforms, Country: Poland, Darek Bogdal, Guillaume Cottenceau, Historical, Java, Java platform, jmol, Person Travel, Roman law, Wyn Locke
Posted in Uncategorised | 5 Comments »
Monday, May 29th, 2017
As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]
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References
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H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Phys. Chem. Chem. Phys., vol. 11, pp. 1340-1345, 2009. http://dx.doi.org/10.1039/b810301a
Tags:Applet, Chemical IT, compression algorithm, computing, Cross-platform software, HTML, HTML element, Internet Journal, Java, Java applet, Java platform, jmol, Markup languages, Open formats, publishers site, publishers systems, technology moves, Technology/Internet, the Internet Journal, Web browser, web technologies, Web-components age, XML, XSLT
Posted in Uncategorised | 8 Comments »
Thursday, May 25th, 2017
It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.‡
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Tags:animation, Chemical IT, chemical reactions, City: Cupertino, Company: Cupertino Elec, Company: Firefox Communic, Computer Hardware - NEC, computing, detective, Digital media, Drip, Electronic documents, Electronic publishing, Email, HTML, Imperial College, Linux, operating system, Password, Person Location, Steven Kirk, Technology/Internet, XML
Posted in Uncategorised | No Comments »
Tuesday, October 4th, 2016
Tags:Analytical chemistry, chemical information, chemical insight, Cheminformatics, Chemistry, Chemometrics, Clyde Fare, Company: GitHub, computation chemical research projects, computational chemistry, computing, Cross-platform software, driver, GitHub, Jan Szopinski, machine learning, open sourcing software development, opensource healthchecker software, Peter Murray-Rust, public web sites, Python, quantum chemical calculation, quantum chemical codes, quantum chemical data, quantum chemical research, Quotation, Server & Database Software, simulation, Software, supervisor, sustainable software conference prize, Technology/Internet
Posted in Bradley-Mason Prize for Open Chemistry | No Comments »
Wednesday, June 5th, 2013
In a time of change, we often do not notice that Δ = ∫δ. Here I am thinking of network bandwidth, and my personal experience of it over a 46 year period.
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Tags:acoustic coupler, Addison-Wesley, Austin Texas, BT, building I, California, Cambridge, computing, electronics, ethernet, Global Intelligence, Google, Historical, Imperial College, Leeds, London, New York, operating system, quantum chemical calculations, Samuel Butler, United Kingdom, University College London
Posted in Uncategorised | 4 Comments »
Saturday, January 1st, 2011
When Watson and Crick (WC) constructed their famous 3D model for DNA, they had to decide whether to make the double helix left or right handed. They chose a right-handed turn, on the grounds that their attempts at left-handed models all “violated permissible van der Waals contacts“. No details of what these might have been were given in their original full article (or the particular base-pairs which led to the observation). This follow-up to my earlier post explores this aspect, using a computer model.
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Tags:B-DNA, computing, conformational analysis, dispersion energy, DNA duplex, interaction energy, Interesting chemistry, optical rotation, van der Waals, Z-DNA
Posted in Uncategorised | 7 Comments »