Archive for the ‘Chemical IT’ Category
Friday, July 21st, 2017
There is much focus at the moment on how to ensure experimental replicability in e.g. the molecular sciences. An important aspect of that is having access to FAIR data; data which is findable, accessible, inter-operable and re-usable. One of the “gold standards” in chemistry is the data associated with crystal structures. Here I take an inside peek into the standard file-type for carrying crystal structure data, the CIF file (the Crystallographic Information File).
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Posted in Chemical IT | 7 Comments »
Thursday, June 8th, 2017
As data repositories start to flourish, it is reasonable to ask questions such as what sort of chemistry can be found there and how can I find it? Here I give an updated[cite]10.1515/ci-2016-3-408[/cite] worked example of a digital repository search for chemical content and also pose an important issue for the chemistry domain.
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Tags:chemical content, chemical/x- media type, chemical/x-gaussian, Company: DataCite, Company: Google, digital repository search, domain-specific chemical content, media type, media:chemical/x-mnpub, media:chemical\/x\-gaussian*, Question, search definition, search engines, search string, search syntax, subject search
Posted in Chemical IT | 1 Comment »
Friday, June 2nd, 2017
In 2016, the world heard that gravitational waves had been detected and now a third instance is reported.‡ Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.
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Tags:Astronomy, Binary stars, Black holes, famous chemical controversy, General relativity, Gravitational wave, Gravity, Physics, search procedures, Technology/Internet, Wave
Posted in Chemical IT | 1 Comment »
Thursday, June 1st, 2017
Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir).[cite]10.1039/D1SC06074K[/cite] At the Beilstein conference, Ian Bruno mentioned another type; tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.
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Tags:Chemistry, chloroform solutions, Conformational isomerism, Crystal, crystallography, gas phase, Ian Bruno, Isomerism, Polymorphism, Ritonavir, S-centre, Tautomer
Posted in Chemical IT, crystal_structure_mining | No 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.[cite]10.1039/b810301a[/cite]
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Tags:Applet, 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 Chemical IT | 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 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 Chemical IT | No Comments »
Tuesday, May 23rd, 2017
This is taking place in the idyllic surroundings of the Niederwald forest, Rüdesheim, Germany. Here I highlight only aspects of the first three talks.
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Tags:article processing charges, Bad Kreuznach, chemical shift, chemical terms, City: Rüdesheim, Country: Germany, Hesse, Hesse-Nassau, Ian Bruno, Jeremy Frey, Klaus Tochtermann, Leah McEwen, Martin Hicks, metadata tools, Niederwald, Niederwalddenkmal, Quotation, Rüdesheim, Rüdesheim am Rhein, Rüdesheim an der Nahe, Rheingau-Taunus-Kreis, Rhine, Richard Kidd, spectroscopy, States of Germany, Stuart Chalk, Technology/Internet
Posted in Chemical IT | 1 Comment »
Friday, April 28th, 2017
Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices. An important aspect of ensuring that such data remains fit for purpose is identifying what curation activities need to be associated with it. Here I revisit one particular case study associated with the molecular structure of a product identified from a photolysis reaction[cite]10.1126/science.1188002[/cite] and the curation of the crystallographic data associated with this study.
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Tags:assigned chemical name, author, chemical name, chemical name synonym, chemical names, chemical structures, editor, indicated chemical name synonym, Knowledge, radiation, Research, Scientific method, Technology/Internet, X-ray
Posted in Chemical IT, crystal_structure_mining | 5 Comments »
Friday, March 31st, 2017
Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[cite]10.1021/jacs.6b13229[/cite] has an SI which is paginated at 907; almost a mini-database in its own right!† Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[cite]10.1038/sdata.2016.18[/cite]
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Tags:Carbon, chemical databases, chemical graveyard, chemical spectra, Chemistry, digital signature, Nature, Organic, Organic chemistry, Organic compound, Organic food, search engines, Technology/Internet
Posted in Chemical IT | 3 Comments »