Jean-Claude Bradley

Polymers are where the problem with assuming that chemistry is structure centric come home to roost of course. Nico Adams has been looking at developing ways of describing polymers effectively and it really isn't straightforward. The whole notion of substance, chemical, and structure get very very messy. - Cameron Neylon

Michael...drop me an email at antonyDOTwilliamsATchemspiderDOTcom and let's discuss how you want to use information and what you need to get at and it might be an issue of simply pointing you to the right web services. Lots of people are using ChemSPider through web services at present. We'd love to help you - Antony Williams

Article on Chemistry in Second Life by Lang and Bradley published in Chemistry Central Journal automatically republished in PubMed. Gotta love Open Access. - Jean-Claude Bradley

The did a good job of porting it over too. - Andrew Lang

One of my students used AcaWiki to summarize her chosen paper on ultra performance liquid chromatography and did a great job summarizing each paragraph. - Jean-Claude Bradley

When is it? - Egon Willighagen

Anna - good it would be nice for those videos to get some use outside my class - Jean-Claude Bradley

The fifth Chemical Information Retrieval class at Drexel University on October 22, 2009 started out with covering the new 3D structure viewer introduced recently at PLoS ONE to provide ideas for students doing a multimedia project this term. The current student answers to the chemistry publishing FAQ are then discussed. The reason for removing glatiramer acetate from ChemSpider is explained and a few databases (Wikipedia, PubChem, DrugBank) are visited that still contain the incorrect SMILES, 3D structure and related properties. An overview of an Open Access site (OAD) suggested by Bill Hooker is provided to suggest additional questions for the FAQ. Examples of questions discussed include primary and secondary sources, peer review, article level metrics (a PLoS ONE article on malaria is used as an example), citation searching, Impact Factors and whether one should use one's real name in the blogosphere. Databases Scirus, Web of Science and PubMed are also reviewed. - Jean-Claude Bradley

Pascal Lapointe - Ce texte est paru initialement dans l'édition de novembre 2008 de la revue Découvrir - Jean-Claude Bradley

a 30 year time frame is unpredictable IMO - Jean-Claude Bradley

This is the lecture from the sixth Chemical Information Retrieval class at Drexel University on October 29, 2009. It starts with a review of some of the new questions answered by students from the chemistry publishing FAQ, which covers patent information and accessing electronic journals at Drexel. Tony Williams submitted a puzzle to resolve conflicting structures in ChemSpider, which is too difficult to be a regular assignment. It requires re-analyzing spectroscopic data in papers where stereochemical assignements are determined. An example is paromomycin which has three entries. The regular assignment for the week is then introduced and it involves obtaining 5 different sources each for 5 different properties for a molecule of the student's choosing. To demonstrate how to do the assignment strychnine is chosen as an example. Melting point information is obtained from ChemSpider (ultimately MSDS sheets), Wikipedia, Wolfram Alpha and in a JACS article via SciFinder. By investigating... - Jean-Claude Bradley

Now that's good to know! - Cameron Neylon

Mummi - I had experimented with it a long time ago and there were some issues that led me to drop it. There are still issues - for example when they alert you to the fact that your submission is archived they don't give you all the citation information - have to remember to copy and paste all that info given on the website itself right after submission. I also don't know what happens to... more... - Jean-Claude Bradley

My Xstreet account has seen a very sharp uptake on the number of people getting our stuff. I have had to log in to SL just to make sure my messages are not capped. I'm sure it will die down soon but pretty cool to see. - Andrew Lang

The final format just got published http://journal.chemistrycentral.com/content... which is nice because you don't have to download the pdf for the full text version - Jean-Claude Bradley

It's great Anthony! I put it up on the ONSclaims page as the first animated gif http://onsclaims.wikispaces.com/ (for some reason I image Andy's orac (or a Dalek) speaking the words as they pop up) - Jean-Claude Bradley

I think it should be autotuned, where is T-Pain or an iPhone when you need one? - Anthony Salvagno

some 'open data' on ChemSpider. - Andrew Lang

I think you can download the whole lot from sf.net/projects/nmrshiftdb, but never installed the full thing myself... - Egon Willighagen

what a crazy notion :D - Mike Chelen

Rufus does interesting work on (inter alia) the size and value of the Public Domain. - Bill Hooker

Egon Willighagen's thesis is a must-read for chemists who seek to understand the emerging role of cheminformatics. The topics covered include molecular chemometrics, molecular descriptors - with an emphasis on those derived from NMR spectra, and crystal packing modeling. There is a strong emphasis on the sharing of Open Data and Open Standards, detailed in the description of the Blue Obelisk Repository. Novel methods of disseminating chemical metadata - such as CMLRSS - are highlighted. Most of the chapters have been published as separate articles and are available from links provided on the chem-bla-ics blog: http://chem-bla-ics.blogspot.com/2008... - Jean-Claude Bradley

Email me your address if you like a copy. I still have a few around :) - Egon Willighagen

looking for speakers for Visualization of Chemistry at ACS - Jean-Claude Bradley

Mike - you might find a few more SL in Chemistry slides and discussion at a recent ACS talk Andy and I gave: http://drexel-coas-elearning.b... - Jean-Claude Bradley

hmm Preso-Matic Game kit - Jean-Claude Bradley

Thanks Allen - looks very straightforward - which educational groups are mainly using the Preso-Matic? - Jean-Claude Bradley

Downloaded from Oxford and installed OK for me under Vista. Data download for the paper was (unsurprisingly) slow on home wifi and browser (Ff) failed to close on first attempt but eventually up and running without problems. Slightly sad that we are back to ugly frames but otherwise nice (this from someone who is not a structural biologist). - Peter Miller

It worked ok for me but crashed on exit. - Andrew Lang

Yup, want that for SL (or whatever). - Peter Miller

chickens and career changes - Jean-Claude Bradley

As a youth I worked at a battery chicken farm collecting eggs - I only lasted a month. Put me off both eggs and chicken for years. - Andrew Lang

Working on a dairy farm put me off milk for a long time too. - Jean-Claude Bradley

Of course the next step is to put a cat on another controller and set up a virtual deathmatch. I wonder if they can learn to use the Quake weapons? - Jean-Claude Bradley

I'm sure they could be trained to use weapons, maybe other stuff too - maybe we could use mice for crowdsourcing - mousesourcing? - Andrew Lang

All kidding aside it would be cool to play Quake against mice. They don't seem to be harmed by running in the maze. Of course I'll be playing the side of the cats :) - Jean-Claude Bradley

Lisa Balbes has a great list of resources for those looking for chemistry careers today. She also provides a link to her own book: Nontraditional Careers for Chemists: New Formulas in Chemistry. - Jean-Claude Bradley

This is a recording of the fourth class on Chemical Information Retrieval on Oct 15, 2009 at Drexel University. It starts with some tips on removing formatting from Wikispaces pages, the Drexel Cisco VPN client for accessing paid subscriptions off campus and how to link to a DOI. The first two assignments for the class are then described. The first involves summarizing each paragraph of an article and an option to use AcaWiki is demonstrated. The second involves filling in an FAQ for publishing in chemistry. FriendFeed is then presented as a resource to help answer questions followed by an extensive overview of available information on ChemSpider, covering SMILES, InChIs, InChIKeys, experimental and predicted properties, linked databases and contributed spectra. Finally a demonstration of Beilstein Crossfire is presented with an emphasis on doing substructure searching. - Jean-Claude Bradley