This coming week I will be ScienceOnline 2012 representing my employer the Royal Society of Chemistry and our ChemSpider database. I will also have a book at the book table about Computer-Assisted Structure Elucidation , not exactly mainstream science but still something I am very proud of. I will be co-hosting two sessions…one on the semantic web with Kristi Holmes and one called Dealing with Data with Kaitlin Thaney. Both of these topics are part of my everyday role in my job, or part of personal projects I am involved with.

If any of you are attending ScienceOnline2012 or watching it via Twitter (for example), then you will likely see popping up as @ChemConnector.

If you want to know more about me I am on many of the Social Networks as listed below and actually am very passionate about teaching people about how to get into the Social Network as a scientist. My recent presentation on this is on Slideshare here.

If you are interested in hearing more about the ChemSpider database, a database of >26 million unique chemicals, sourced from over 400 data sources and linking many of these together on the web, then please comment on this post or email me directly at tony27587ATgmailDOTcom and if there is enough interest I will set aside some time to give a couple of demos in one of the rooms at the conference.

This weekend I have spent sometime helping to get some of the ScienceOnline attendees onto the ScientistsDB and they are presently adding/finishing their ScientistsDB pages:

Walter Jessen

Kristi Holmes

Bora Zivkovic

Sarah Chow

Sean Ekins

Myself

If you would like a page on ScientistsDB simply register here and then use this page to learn how to create an article. Ask me for help if you need it.

See you at ScienceOnline2012

My friend Mark Jensen is a very skilled man…gardener, painter, welder, carpenter. Last night I offered to try out a new experiment with him…capturing him in action using stopped motion photography using shots every few minutes as he spent four hours painting a sign. I assembled two versions of the video. I think you’ll agree they are fun to watch and Mark is a skilled painter!

The first video is the 60 seconds of stopped motion action ONLY

The second video includes the introduction and conclusion video shots by Mark.

I am a chemist.  I’ve been one since I had my first chemistry kit and mixed acids and salts and watched the results. Cool!

I didn’t know what science was until I was introduced to it in primary school by a visiting student teacher who took it upon himself to do science with us. He taught us the physics of lenses, the basis of photosynthesis, about the density of materials and the beauty resulting from performing paper chromatography with inks. The spark of interest was lit within me by that young man over 40 years ago. His passion was contagious…for me.

My mother used to provide bed and breakfast and once upon a time, for whatever reason, we had a metallurgist staying with us. I used to quiz him with questions and bugged him enough about what he did that one day he asked me whether I would like to visit his lab. At that age (9 yrs old I think) I imagined a Frankenstein lab, Tesla coils, large flasks of colored solutions…ah the imagination of youth. With the permission of my mother, and I have to assume his employer, he took me to his lab one evening and walked me through testing for ductility, corrosiveness and deposition coatings. I got to push buttons, watch metal snap and dissolve metals in liquids. No Tesla coils, no monsters but pure joy in being at play with the mysteries of science…demonstrated to me through the hands of someone who deeply understood and made it fun.

I have, of course, had many teachers over the years and the ones I remember, the ones who remain dear to my heart, are those with a passion for what they taught. These are the teachers who are willing to work after school to teach you more than the syllabus demands, those that have lunchtime clubs for us “geeks”, those that organize trips that immerse you further in what interests them and those that use their own passion to affect a child, stimulate a pupil and hopefully pay it forward with their inherited passions. I am fortunate that I have had a number of teachers who were willing to help me geek out…I wish there were more!!!

What I personally lack in teaching skills I hope I make up for in passion, in drive and a real want to evoke an emotional response in those I talk with about chemistry. I was trained as an NMR spectroscopist, became a cheminformatician and then moved into hosting chemistry data for the masses through the ChemSpider database. But I am proud to call myself ChemConnector! Whether I’m doing exploding Coke demos at our twins school, playing with Neodymium magnets with anyone who cares to handle them, educating the community about “inappropriate movie stars” versus scientists, or pushing for changes in the quality of online chemistry data, I hope that my passion comes through and just once in a while I create a convert to get interested and get active in science. If YOU have passion..then spread the love.

This blog post is part of the Vittana “Make a Difference” blogger challenge.

The contest invites bloggers from around the world to discuss various ways to make a difference in the world, as well as share stories on who or what has made a difference in their lives.

The winning blog post will be the post that drives the most loans to students in need. Please support this cause (and this blog!) by making a loan in my name: “Antony Williams.” Be sure to type that in when you reach the checkout page (example screenshot) The more loans you make the more educations get funded and the more recognition and traffic my site gets!

Please support this blog and contest by using this special link to tweet about it (You can edit the tweet before it’s posted, but make sure this link ( http://bitly.com/w50Lsd ) and the hashtag #vittanachallenge is part of the tweet or Vittana won’t know you tweeted about me!)

Peter Murray-Rust and Henry Rzepa are the winners of the 2012 Herman Skolnik award. Details are below. Their impact on internet-based chemistry is obvious to those who work in our domain and this award is well deserved indeed! Congratulations to both and I look forward to their award symposium.

2012 Herman Skolnik Award Winners Announced

Drs. Peter Murray-Rust and Henry Rzepa are the joint recipients of the 2012 Herman Skolnik Award presented by the ACS Division of Chemical Information (CINF). The award recognizes outstanding contributions to and achievements in the theory and practice of chemical information science and related disciplines. The prize consists of a $3,000 honorarium and a plaque. The winners will also be invited to present an award symposium at the Fall 2012 ACS National Meeting to be held in Philadelphia.

Peter Murray-Rust and Henry Rzepa are recognized for their continued efforts to advance the field of chemical informatics, particularly in electronic and online forms, for opening standards to facilitate first-class science, and promoting new ways to collaborate and exchange chemical data. Through their efforts they have dramatically improved the ways in which molecular data are embedded in published scientific articles, preserving chemical identifiers and facilitating indexing and searching online. Their work has had a huge impact in the fields of chemical document analysis, chemistry on the Internet and in the orchestration of a viable strategy for making electronic chemistry information as widely accessible and usable as possible in our information age.

Henry Rzepa and Peter Murray-Rust have been closely associated with chemistry on the Internet, and were the only two chemists at an early WWW conference held in CERN in 1994. From this they were involved in the use of XML and development of the Chemical Markup Language (CML). Other Internet-related projects lead by Henry include how a chemical journal might evolve to benefit from the Internet (the CLIC project, jointly with Cambridge, Leeds University and the RSC), an exploration of online chemical conferencing (the ECTOC series), the ChemWeb discussion forum, the Molecule-of-the-month columns, and co-organizing the first ever Internet-focused session at an ACS national meeting (in 1995) dedicated to the Internet and the Web, along with dedicated workshops in Washington DC, the UK and at Imperial College. In addition to his Internet-related activities, Peter has also overseen development of software including OSCAR1 for experimental data checking and its extension to OSCAR4 for chemical tagging and other chemical natural-language processing; OPSIN name to structure conversion (delivered as Open Source to the community); Chem4Word add-in; and CrystalEye online resource of crystal structure data from the Internet. Peter has also been very active in the principles and practice of Open Data, in chemistry and elsewhere, and he was one of the team that defined the Panton Principles (honored by the SPARC Innovator, 2010).

Peter has B.A. and D.Phil. degrees in chemistry from the University of Oxford, and was a lecturer at the Universities of Ghana and Stirling. After a period in industry as Head of Molecular Graphics at Glaxo Group Research, he turned to academia as Professor of Pharmacy at the University of Nottingham, and is currently Reader in Molecular Informatics and Senior Research Fellow, Churchill College, University of Cambridge.

Henry has a B.Sc. in chemistry from Imperial College, London, and Ph.D. and D.Sc. (London). After a period as a SERC Postdoctoral Fellow at University of Texas, he returned to Imperial College, London, where he has held the Chair in Computational Chemistry since 2004.

Henry and Peter’s pioneering and continued efforts have changed the ways in which chemistry is handled, shared, stored and communicated on the Internet for the better of all, and they are worthy recipients of the 2012 Herman Skolnik Award.

There are multiple structure drawing editors on ChemSpider. And we could add more! For example, one we don’t have is JSDraw and we also don’t have the ChemDoodle components in place, yet, though I am VERY impressed with the spectral display components that are integrated into the SpectralGame that ChemSpider supports. Compared to just a few years ago there is now an abundance of structure drawing editors in the form of Applets and JavaScript Editors. So many in fact that it can be confusing to the user. The user in reality should not worry about the technology behind the editor. It should be quite simple, especially when it comes to something as simple as the editor being the interface to querying ChemSpider. It should display perfectly on the browser(s) and platform(s) used by the user, it should be intuitive and easy to use (preferably without having to resort to reading help files), and essentially, it should “do what I want it to do”. Not at all an unreasonable list of demands right? Not so easy to deliver on mind you!

On ChemSpider we have multiple structure drawing editors. If you visit this page and open up the selection window by using “Click to Edit” you will see the editor below and, underneath the editor shown, a series of editors that you can choose from.

There has to be an order of listing the editors…the listed order is NOT a preferred order from our point of view. Just a list. We have heard feedback from numerous people about their preferred editor. Some live and breath the Java Molecular Editor (JME). Some prefer Accelrys JDraw because they already use Accelrys Draw. Many think that Elemental is a great Javascript Editor.

We are left with a choice….leave all editors (which has a cost in time to support them, keep them updated, tested etc) or reduce the number of editors to just a couple (or three). So, we welcome your input, on this blog post as a comment, or via the survey on SurveyMonkey here. We’d like your input to help steer our decision. Thanks

The ACS meeting in Denver is next week and we hope that the ChemSpider mobile app developed in collaboration with Alex Clark will be available via the iTunes store in time! The full details of the app, and some associated screenshots, are outlined on the SciMobileApps wiki here. A brief overview is given below…

“ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page.

Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the Royal Society of Chemistry.”

Unless you have no interest in sports, or have your head under a stone, you will be aware of the fact that the next Olympics will be held in London in 2012. Peter Scott (one of the editors of ChemSpider SyntheticPages) and I were recently discussing how much of a role chemistry plays now in modern sports. I’m a runner, cyclist, swimmer and overall sporting type of guy and depend on wicking materials to keep me cool, nutritional support to get me through my 100-150 mile bike rides in a day, glide stick to “stop me chafing” (ow!) and graphite grease to silence the rattling chain on my bike. In fact it doesn’t matter what sport I am doing it is easy to notice the influence that chemistry has on my improved performance at my tender age of, ahem, just over 40 (and holding, for a while now).

I was reminiscing with Peter that Sir Graham Richards and I were chatting about pyrenes about a year ago and we lamented on how Benzo[CD]pyrene, shown here, looks just like the Olympic rings. There is another rather well known “Olympic molecule” of course, already captured on Wikipedia and named Olympiadane. It looks rather complex to synthesize and personally I think the benzopyrene looks a lot more like the Olympic rings so I attached the synonym Olympicene to it! In fact, if you search ChemSpider using the name Olympicene you will find it.

In a recent discussion about our online crowdsourced database of syntheses, ChemSpider SyntheticPages,(and not distracted at all by the conversation about the Olympics going to the UK next year!!!)  I mentioned again to Peter the molecule Olympicene and he searched ChemSpider to find it. We agreed that it would be fun to know how easy it would be too synthesize it and if it was done it would be a good synthesis to add to ChemSpider SyntheticPages. That was enough to trigger Peter into action and chat with one of his colleagues to see if he can make it.

And so it starts…the trials and tribulations of how to synthesize the chemical Olympicene will be captured on ChemSpider SyntheticPages step by step. We’re not sure how complex a synthesis it will be..time will tell. It will be great to add the analytical data to ChemSpider too as it gets generated..including all the intermediate reaction steps and associated data. ChemSpider and CSSP were designed to support projects like this so it will be a fun story to watch it work through.

If YOU have any thoughts about good synthetic approaches for what seems like a simple molecule post them on this blog. Actually, why not try synthesizing yourself and add your syntheses to SyntheticPages!? Every contribution is issued a DOI for your publication list!

It might be ideal to get a  number of synthetic approaches posted on ChemSpider SyntheticPages and see which one is the best! Watch this space. Also, I’ve set up a Twitter account to capture the progress at @Olympicene. Enjoy!

This one should be very self-explanatory. I would appreciate your answers though!