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Egon Willighagen › Comments

Egon Willighagen
Hypothesis: The proprietary RDF is valid and uses common ontologies. Start date: 2014-07-23 End date: 2014-07-23. Description: For obvious reasons, this experiment will not disclose all details. It will outline, however, the steps I undertook to do the validation and evaluation. Methods: ... - Egon Willighagen
Egon Willighagen
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y - https://plus.google.com/1041867...
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y When assessing the impact of a published research article, it might seem logical to look at the Impact Factor of the journal that you find it in. But as journals and scholars have moved online, and citation indexing has been automated, the wealth of information for citation discovery and analysis has vastly increased. Citation counts can tell a more accurate story about the scholarly impact that an individual article has made than the journal Imp... - Egon Willighagen
Egon Willighagen
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y - https://plus.google.com/1041867...
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y When assessing the impact of a published research article, it might seem logical to look at the Impact Factor of the journal that you find it in. But as journals and scholars have moved online, and citation indexing has been automated, the wealth of information for citation discovery and analysis has vastly increased. Citation counts can tell a more accurate story about the scholarly impact that an individual article has made than the journal Imp... - Egon Willighagen
Egon Willighagen
As introduced in previous posts, SMARTS is a concise notation for describing chemical substructure queries. There are several aspects to a SMARTS implementation: subgraph graph matching, parsing, generating, and even optimisa... - Egon Willighagen
Egon Willighagen
Drug Discovery Resources Updates. 16 July 2014- Filed In:CytochromeP450 | ADME. I've added two new pages to the ADME section, there are now separate pages for CYP2D6 inhibitors and CY3A4 inhibitors. 22 July 2014 Updated to include CYP2C9 and CYP2C19 inhibitors. Nheterocycles ... - Egon Willighagen
Egon Willighagen
A strategy for grouping of nanomaterials based on key physico-chemical descriptors as a basis for safer-by-design NMs - http://www.citeulike.org/user...
Nano Today (July 2014), doi:10.1016/j.nantod.2014.05.001 Iseult Lynch, Carsten Weiss, Eugenia Valsami-Jones - Egon Willighagen
Egon Willighagen
#jcbms   As promised, I slowly set out to explore ONSSPs (Open Notebook Science Service Providers). I do not have a full overview of solutions yet but found LabTrove and Open Notebook Science Network. The latter is a more clear ONSSP ... - Egon Willighagen
Egon Willighagen
Hypothesis: Bioclipse works just as well with OPSIN 1.6.0 as it does with 1.5.0. Start date: 2014-07-20 End data: 2014-07-21. Description: Bioclipse in the development branch has OPSIN 1.5.0 exposed with the opsin manager. The intention of this experiment is to update Bioclipse with OPSIN 1.6.0, ... - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Original Post from Jan Jensen: Nice use of molecular graphics Why Women Are Stripey - Egon Willighagen
Egon Willighagen
Where's my supercarbon?? Oh, silicon, there you are! - https://plus.google.com/1041867...
Where's my supercarbon?? Oh, silicon, there you are! Warning: this comic occasionally contains strong language (which may be unsuitable for children), unusual humor (which may be unsuitable for adults), and advanced mathematics (which may be unsuitable for liberal-arts majors). BTC 1FhCLQK2ZXtCUQDtG98p6fVH7S6mxAsEey ... - Egon Willighagen
Egon Willighagen
Whilst cluster of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B40 to be specific.[1] My interest was in how the σ and π-electrons were partitioned. In a C40, one can reliably predict that each carbon would contribute ... - Egon Willighagen
Egon Willighagen
Nice chemistry infographics as CC-BY-ND-NC. - https://plus.google.com/1041867...
Nice chemistry infographics as CC-BY-ND-NC. There are few things better than an ice cold beer on a hot day. Chances are, when you crack open a beer this summer, you probably won't be thinking much about chemistry - but it's the particular ch... - Egon Willighagen
Egon Willighagen
That's exactly what the +Chemistry Development Kit is about! So, dear +Neelie Kroes, please add H2020... - https://plus.google.com/1041867...
That's exactly what the +Chemistry Development Kit is about! So, dear +Neelie Kroes, please add H2020 funding programs for clear +Open Science projects! (Which you could have done before... or your political party in NL...) I attended the Open Knowledge Festival this week and I had a blast. For three days (I also attended the fringe event csv,conf on Tuesday) I listed to wonderful presentations and was involved in great discussions - both within sessions, but more importantly all the informal discussions between ... - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Original Post from John May: CDK Release 1.5.7 CDK 1.5.7 has been released and is available from sourceforge (download here) and the EBI maven repo (XML 1). The release notes (1.5.7-Release-Notes) summarise and detail the changes. Among the new bug fixes and features, sev... - Egon Willighagen
Egon Willighagen
Open Notebook Science: also for cheminformatics Last Monday the Jean-Claude Bradley Memorial Symposium... - https://plus.google.com/1041867...
Open Notebook Science: also for cheminformatics Last Monday the Jean-Claude Bradley Memorial Symposium was held in Cambridge ( slide decks ). Jean-Claude was a remarkable man and I spoke at the meeting on several things and also how he made me jealous with his Open Notebook Science work. I had the pleasu... Last Monday the Jean-Claude Bradley Memorial Symposium was held in Cambridge (slide decks). Jean-Claude was a remarkable man and I spoke at the meeting on several things and also how he made me jealous with his Open Notebook ... - Egon Willighagen
Egon Willighagen
Sextuple bond. A sextuple bond is a type of covalent bond involving 12 bonding electrons and in which the bond order is 6. The only known molecules with true sextuple bonds are the diatomic dimolybdenum (Mo2) and ditungsten (W2), which exist in the gaseous phase. There is strong evidence to believe that no two ... - Egon Willighagen
Egon Willighagen
Quintuple bond. A quintuple bond in chemistry is an unusual type of chemical bond, first reported in 2005 for a dichromium compound. Single bonds, double bonds, and triple bonds are commonplace in chemistry. Quadruple bonds are rarer but occur currently among the transition metals, especially for Cr, Mo, W, ... - Egon Willighagen
Egon Willighagen
Egonw: /* Awards */ {{chemistry|class=start|importance=low}} {{WikiProject Open|class=start|importance=low}} ==Awards== I have just added some awards from various blogs while on a fruitless search for some decent references. The current reference 4, to sourceforge does not seem to link to anything now about the awards. I know some of the Blue Obelisk members are active on wikipedia. Could you point us to sources we can use? --[[User:Bduke|<span style="color:#002147;">'''Bduke'''</span>]] [[User_talk:Bduke|<span style="color:#002147;">'''(Discussion)'''</span>]] 00:31, 13 July 2014 (UTC) [[User:Bduke|Bduke]], you can ask on the mailing list. [[User:Egonw|Egonw]] ([[User talk:Egonw|talk]]) 07:26, 17 July 2014 (UTC) [[User:Bduke|Bduke]], I have confirmed both awards with Peter and updated the Blue Obelisk wiki page (of which the link is updated too). [[User:Egonw|Egonw]] ([[User talk:Egonw|talk]]) 07:01, 18 July 2014 (UTC) - Egon Willighagen
Egon Willighagen
Recent news from the world of chemistry: the result is really the experimental observation of a special new molecule. People call it a "Boron Buckyball", but this irritates me since we know that th... - Egon Willighagen
Egon Willighagen
Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand - http://www.citeulike.org/user...
Basic &#38; Clinical Pharmacology &#38; Toxicology, Vol. 115, No. 1. (July 2014), pp. 50-58, doi:10.1111/bcpt.12257 Pekka Kohonen, Rebecca Ceder, Ines Smit, Vesa Hongisto, Glenn Myatt, Barry Hardy, Ola Spjuth, Roland Grafström - Egon Willighagen
Egon Willighagen
Renormalization of myoglobin–ligand binding energetics by quantum many-body effects - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences, Vol. 111, No. 16. (22 April 2014), pp. 5790-5795, doi:10.1073/pnas.1322966111 We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory. This combination of methods explicitly accounts for dynamical and multireference quantum physics, such as valence and spin fluctuations, of the 3d electrons, while treating a significant proportion of the protein (more than 1,000 atoms) with DFT. The computed electronic structure of the myoglobin complexes and the nature of the Fe–O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long-standing... - Egon Willighagen
Egon Willighagen
Direct observation of intermolecular interactions mediated by hydrogen bonding - http://www.citeulike.org/user...
The Journal of Chemical Physics, Vol. 141, No. 3. (21 July 2014), 034502, doi:10.1063/1.4885145 Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N–H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to... - Egon Willighagen
Egon Willighagen
Chemistry Development Kit - http://en.wikipedia.org/w...
Egonw: Use the DOI of the Cinfony paper. {{Infobox software | name = Chemistry Development Kit | logo = [[Image:Cdklogo.svg|200px]] | screenshot = | caption = | developer = The CDK Project | released = {{Start date and age|df=yes|2001|05|11}}<ref>https://sourceforge.net/project...</ref> | frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! --> | programming language = [[Java (programming language)]] | operating system = [[Cross-platform]] | platform = | language = | genre = [[Chemoinformatics]]/[[Molecular modelling]]/[[Bioinformatics]] | license = [[GNU Lesser General Public License]] | website = http://cdk.sourceforge.net/ }} The '''Chemistry Development Kit''' is an [[open-source]] Java library for [[Chemoinformatics]] and [[Bioinformatics]].<ref>{{cite journal |author=Steinbeck, C.; Han, Y.Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E.L. |title=The Chemistry Development Kit (CDK): An open-source... - Egon Willighagen
Egon Willighagen
Egonw: Jens Thomas got the award for this NWChem work in 2011. {{Infobox organization |name = Blue Obelisk |image = BOicon.png |image_border = |size = 50px |alt = |caption = |map = |msize = |malt = |mcaption = |abbreviation = |motto = |formation = 2005 |extinction = |type = |status = |purpose = |headquarters = |location = |region_served = |membership = 23+ |language = English |leader_title = |leader_name = |main_organ = |parent_organization = |affiliations = |num_staff = |num_volunteers = |budget = zero |website = http://www.blueobelisk.org/ |remarks = }} '''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.<ref>P. Murray-Rust, The Blue Obelisk, [[Chemistry Development Kit#CDK News|CDK News]], 2005, 2, 43&ndash;46</ref><ref>{{cite journal | last1 = Guha | first1 = R | last2 = Howard | first2 = MT | last3 = Hutchison | first3 = GR | last4 = Murray-Rust |... - Egon Willighagen
Egon Willighagen
Template:Latest preview software release/Chemistry Development Kit - http://en.wikipedia.org/w...
Egonw: https://github.com/cdk... {{LPR | article = Chemistry_Development_Kit | latest_release_version = 1.5.7 | latest_release_date = {{Start date and age|2014|07|17}} }}<noinclude> [[Category:Latest preview software release templates|Chemistry Development Kit]] ➔ Back to article "'''[[{{SUBPAGENAME}}]]'''" </noinclude> - Egon Willighagen
Egon Willighagen
Reshared post from Anwesha Bohler: - https://plus.google.com/1041867...
Original Post from Anwesha Bohler: Reactome Version 48 Human Pathways now available in WikiPathways - Egon Willighagen
Egon Willighagen
Egonw: /* Awards */ {{chemistry|class=start|importance=low}} {{WikiProject Open|class=start|importance=low}} ==Awards== I have just added some awards from various blogs while on a fruitless search for some decent references. The current reference 4, to sourceforge does not seem to link to anything now about the awards. I know some of the Blue Obelisk members are active on wikipedia. Could you point us to sources we can use? --[[User:Bduke|<span style="color:#002147;">'''Bduke'''</span>]] [[User_talk:Bduke|<span style="color:#002147;">'''(Discussion)'''</span>]] 00:31, 13 July 2014 (UTC) [[User:Bduke|Bduke]], you can ask on the mailing list. [[User:Egonw|Egonw]] ([[User talk:Egonw|talk]]) 07:26, 17 July 2014 (UTC) - Egon Willighagen
Egon Willighagen
Egonw: /* Experimental */ '''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, [[lab notebook|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 [[Transparency (behavior)|transparent]] approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'.<ref name="wired">[http://www.wired.com/science... Freeing the Dark Data of Failed Scientific Experiments], Goetz, T. , Wired Magazine, Sept.25, 2007</ref> The practice of open notebook science, although not the norm in the [[Academia|academic]] community, has gained significant recent... - Egon Willighagen
Egon Willighagen
Reshared post from Björn Brembs: - https://plus.google.com/1041867...
And once again publishers fail to understand the idea... Original Post from Björn Brembs: The International Association of Scientific, Technical & Medical Publishers (STM) has published a set of open access licences (thanks to David Prosser f - Egon Willighagen
Egon Willighagen
Egonw: Added two links. {{Infobox organization |name = Blue Obelisk |image = BOicon.png |image_border = |size = 50px |alt = |caption = |map = |msize = |malt = |mcaption = |abbreviation = |motto = |formation = 2005 |extinction = |type = |status = |purpose = |headquarters = |location = |region_served = |membership = 23+ |language = English |leader_title = |leader_name = |main_organ = |parent_organization = |affiliations = |num_staff = |num_volunteers = |budget = zero |website = http://www.blueobelisk.org/ |remarks = }} '''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.<ref>P. Murray-Rust, The Blue Obelisk, [[Chemistry Development Kit#CDK News|CDK News]], 2005, 2, 43&ndash;46</ref><ref>{{cite journal | last1 = Guha | first1 = R | last2 = Howard | first2 = MT | last3 = Hutchison | first3 = GR | last4 = Murray-Rust | first4 = P | last5 = Rzepa | first5 = H |... - Egon Willighagen
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