Sign in or Join FriendFeed
FriendFeed is the easiest way to share online. Learn more »

Egon Willighagen › Comments

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approaches to research and explicitly includes the making available of failed, less significant, and otherwise unpublished experiments; so called 'dark data'.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
Egon Willighagen
Over the past couple of years a number of articles have been posted claiming that we’re eating more food products containing nanoparticles than we know (remember this piece from a couple of weeks ago?).  One of the latest appeared on The Guardian website yesterday with the headline “Activists take aim at nanomaterials in Dunkin’ Donuts” (thanks to @HilarySutcliffe for the tip-off). - Egon Willighagen
Egon Willighagen
Extended-Connectivity Fingerprints - http://www.citeulike.org/user...
J. Chem. Inf. Model. In Journal of Chemical Information and Modeling, Vol. 50, No. 5. (28 April 2010), pp. 742-754, doi:10.1021/ci100050t Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure?activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their... - Egon Willighagen
Egon Willighagen
Egonw: {{Infobox scientist |name = Jean-Claude Bradley |image = Jean-Claude_Bradley.png |image_size = 182px |caption = Jean-Claude at The White House - June 2013 |birth_date = |birth_place = |residence = |nationality = |fields = {{Plainlist| * [[Chemistry]] }} |workplaces = {{Plainlist| * [[Drexel University]] * [[Duke University]]<ref name="DrexelMourning">Mourning Jean-Claude Bradley, PhD, Dept. of Chemistry, http://drexel.edu/chemist...</ref>}} |alma_mater = {{Plainlist| * [[Laurentian University]] * [[University of Ottawa]]<ref>http://chem241.wikispaces.com/extracr...</ref> }} |doctoral_advisor = Tony Durst |academic_advisors = |doctoral_students = {{Plainlist| * Patrick Ndungu * Khalid Mirza }} |notable_students = | thesis_title = The synthesis and reactivity of 2-benzylidenebenzocyclobutenones and derivatives | thesis_url = http://hdl.handle.net/10393... | thesis_year = 1993 |known_for = {{Plainlist| * [[Open... - Egon Willighagen
Egon Willighagen
Egonw: Added links to two books in which the data sets have been published. {{Infobox scientist |name = Jean-Claude Bradley |image = Jean-Claude_Bradley.png |image_size = 182px |caption = Jean-Claude at The White House - June 2013 |birth_date = |birth_place = |residence = |nationality = |fields = {{Plainlist| * [[Chemistry]] }} |workplaces = {{Plainlist| * [[Drexel University]] * [[Duke University]]<ref name="DrexelMourning">Mourning Jean-Claude Bradley, PhD, Dept. of Chemistry, http://drexel.edu/chemist...</ref>}} |alma_mater = {{Plainlist| * [[Laurentian University]] * [[University of Ottawa]]<ref>http://chem241.wikispaces.com/extracr...</ref> }} |doctoral_advisor = Tony Durst |academic_advisors = |doctoral_students = {{Plainlist| * Patrick Ndungu * Khalid Mirza }} |notable_students = | thesis_title = The synthesis and reactivity of 2-benzylidenebenzocyclobutenones and derivatives | thesis_url =... - Egon Willighagen
Egon Willighagen
Reshared post from NextMove Software: - https://plus.google.com/1041867...
"along with all of the millions of Caffeine SMILES variants outlined above, has the exact same InChI" Original Post from NextMove Software: Roger writes a SMILES string for caffeine. And then some. A recent posting to the CHMINF-L mailing list at the University of Indiana reiterates a point made by Steve Heller in his recent keynote address to the 2014 ICCS/GCC meeting in Noordwijkerhout. In that presentation, Steve argues for the need for chemical structure canonicalization by showing 172 ... - Egon Willighagen
Egon Willighagen
Koop Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents (3RD) door Andrew Lang (Paperback) online via Lulu NL. Ga naar de Lulu Marktplaats voor productinformatie, beoordelingen en recensies. - Egon Willighagen
Egon Willighagen
Original Post from Fon: This is how The Netherlands looks after the roll out of our joint network started. Amazing huh? There are lots of Fon Spots to connect to wherever you go! http://bit.ly/FonMaps Screen Shot 2014-07-16 at 10.05.49.png - Egon Willighagen
Egon Willighagen
Egonw: Updated the link out to the Blue Obelisk wiki, as SourceForge changed their set up. {{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 |... - Egon Willighagen
Egon Willighagen
Egonw: {{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 | last6 = Steinbeck |... - Egon Willighagen
Egon Willighagen
Original Post from Toxtree: Toxtree protein binding alerts  http://toxtree.sourceforge.net/protein... used in  Van der, J. W., Soeteman-Hernández, L. G., Ezendam, J., Stierum, R., Kuper, F. C., & van Loveren, H. (2014). Anchoring molecular mechanisms to the adverse outcome pathway for skin sensitization: Analysis of existing data. Critical Reviews in Toxicology, 1–10. http://www.ncbi.nlm.nih.gov/pubmed... Home. Toxtree. Download. Toxtree 2.6.6 · Toxtree 2.6.0 · Toxtree 2.5.4 · Toxtree 2.5.1 · Toxtree 2.5.0 · Toxtree 2.2.0 · Toxtree 2.1.0 · Toxtree 1.60 · Toxtree 1.51 · Toxtree 1.20. Plugins. Cramer rules · Extended Cramer rules · Verhaar scheme · Modified Verhaar scheme · Skin irritation ... - Egon Willighagen
Egon Willighagen
Scary... "Timeghost" http://feedly.com/e/ipDfWJSF < Prev · Random; Next >; >|. Permanent link to this comic: http://xkcd.com/1393/ Image URL (for hotlinking/embedding): http://imgs.xkcd.com/comics.... Selected Comics. Search comic titles and transcripts: RSS Feed - Atom Feed. Comics I enjoy: Three Word Phrase, Oglaf (nsfw), SMBC, ... - Egon Willighagen
Egon Willighagen
Fingerprint Searching Using Various Indexing Methods - Egon Willighagen
Egon Willighagen
Reshared post from Truthloader: - https://plus.google.com/1041867...
Of course, what we want is an interactive version, not an animated GIF... in fact, we want this in Google Maps... Original Post from Truthloader: I know you've all been waiting for it... so here it is #GIFTUESDAY    (on Wednesday) Unbelievable bit of footage from the ISS of this volcano erupting, BUT WAIT THERE'S MORE... For more International Space Station shenanigans, if you haven't heard of astronaut Chris Hadfield, he's pretty cool. Here's what he has done: Why astronaut Chris Hadfield is a legend - Truthloader #iss   #space   #volcano   volcano.gif - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Interesting! I see no reason to still implement HF in Fortran...  Original Post from Jan Jensen: Overview¶. PyQuante (Sourceforge Project Page) is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many “rate-determining” modules also written in C for speed. The resulting code, though not as fast as ... - Egon Willighagen
Egon Willighagen
Chimpanzee Intelligence Is Heritable - http://www.citeulike.org/user...
Current Biology (July 2014), doi:10.1016/j.cub.2014.05.076 William Hopkins, Jamie Russell, Jennifer Schaeffer - Egon Willighagen
Egon Willighagen
Dutch civilian rights organization calls for massive adoption for Tor and encryption in general, as ... - https://plus.google.com/1041867...
Dutch civilian rights organization calls for massive adoption for Tor and encryption in general, as reaction to new leaks showing NSA thinks anyone who cares about civilian rights is a potential "extremist". Geef de NSA meer uien om te pellen - Egon Willighagen
Egon Willighagen
Electrical stimulation of a small brain area reversibly disrupts consciousness - http://www.citeulike.org/user...
Epilepsy &#38; Behavior, Vol. 37 (August 2014), pp. 32-35, doi:10.1016/j.yebeh.2014.05.027 Mohamad Koubeissi, Fabrice Bartolomei, Abdelrahman Beltagy, Fabienne Picard - Egon Willighagen
Egon Willighagen
Reshared post from Vedrin Jeliazkov: - https://plus.google.com/1041867...
Useful for all your research under EC-funded project NDAs.... Original Post from Vedrin Jeliazkov: This service could make big waves in the webmail swamp. Secure email with absolutely no compromises, brought to you by MIT and CERN scientists. Follow us for live updates. - Egon Willighagen
Egon Willighagen
#JChemInf Volume 5 as PDF on @FigShare One of the things I do to prepare for holiday, is get some reading... - https://plus.google.com/1041867...
#JChemInf Volume 5 as PDF on @FigShare One of the things I do to prepare for holiday, is get some reading stuff together. I haven't finished Gödel, Escher, Bach yet (a suggested from the blogosphere), with a bit of luck there are new chapters of HPMOR , and I normally try to catch up with litera... One of the things I do to prepare for holiday, is get some reading stuff together. I haven't finished Gödel, Escher, Bach yet (a suggested from the blogosphere), with a bit of luck there are new chapters of HPMOR, and I norma... - Egon Willighagen
Egon Willighagen
Reshared post from Joerg Fliege: - https://plus.google.com/1041867...
We must never forget that wars normally do not end because the opponent was convinced about your argument, but because the number of soldiers and civilians left ran out... Original Post from Joerg Fliege: The First World War, in new pictures Headline chosen with care, as some of the pictures displayed have only recently been digitized,  and the curator has trawled extensive collections of the war to find and display photographs that have not been shown on mass media before. So, 'new' in this sense. A poignant, well-chosen display, executed with great care. The full collection is available at http://www.theatlantic.com/static... and subdivided into 10 subsections. The picture here shows Royal Army Medical Corps men, searching the packs of the British dead for letters and effects to be sent to relatives after the Battle of Guillemont, Somme, France, September of 1916. w_32.jpg - Egon Willighagen
Egon Willighagen
Investigating the contribution of CYP2J2 to ritonavir metabolism in vitro and in vivo - http://www.citeulike.org/user...
Biochemical Pharmacology (June 2014), doi:10.1016/j.bcp.2014.06.020 Rüdiger Kaspera, Brian Kirby, Tariku Sahele, Ann Collier, Evan Kharasch, Jashvant Unadkat, Rheem Totah - Egon Willighagen
Egon Willighagen
The human circadian metabolome - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences, Vol. 109, No. 7. (14 February 2012), pp. 2625-2629, doi:10.1073/pnas.1114410109 The circadian clock orchestrates many aspects of human physiology, and disruption of this clock has been implicated in various pathologies, ranging from cancer to metabolic syndrome and diabetes. Although there is evidence that metabolism and the circadian clockwork are intimately linked on a transcriptional level, whether these effects are directly under clock control or are mediated by the rest–activity cycle and the timing of food intake is unclear. To answer this question, we conducted an unbiased screen in human subjects of the metabolome of blood plasma and saliva at different times of day. To minimize indirect effects, subjects were kept in a 40-h constant routine of enforced posture, constant dim light, hourly isocaloric meals, and sleep deprivation. Under these conditions, we found that ∼15% of all identified metabolites in plasma and saliva were... - Egon Willighagen
Egon Willighagen
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. - http://www.citeulike.org/user...
Journal of cheminformatics, Vol. 1, No. 1. (2009), 10, doi:10.1186/1758-2946-1-10 Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets. Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate standardised comparisons typically reduced source counts by between 5% and 30%. The pair-wise overlaps between 23 databases and subsets were determined, as well as changes between 2006 and 2008. While all... - Egon Willighagen
Egon Willighagen
Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database. - http://www.citeulike.org/user...
Molecular informatics, Vol. 32, No. 11-12. (December 2013), pp. 881-897 ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database are resources of curated chemistry-to-protein relationships widely used in the chemogenomic arena. In this work we have extended an earlier analysis (PMID 22821596) by comparing chemistry and protein target content between 2010 and 2013. For the former, details are presented for overlaps and differences, statistics of stereochemistry as well as stereo representation and MW profiles between the four databases. For 2013 our results indicate quality improvements, major expansion, increased achiral structures and changes in MW distributions. An orthogonal comparison of chemical content with different sources inside PubChem highlights further interpretable differences. Expansion of protein content by UniProt IDs is also recorded for 2013 and Gene Ontology comparisons for human-only sets indicate differences. These emphasise the expanding... - Egon Willighagen
Other ways to read this feed:Feed readerFacebook