Archive for category Uncategorized
A Survey about The Accuracy of Data on Wikipedia
Posted by tony in Uncategorized on July 26, 2011
This one should be very self-explanatory. I would appreciate your answers though!
Create your free online surveys with SurveyMonkey, the world’s leading questionnaire tool.
My presentation at the ORCID Meeting
Posted by tony in Uncategorized on May 22, 2011
FeedBurner subscription added to ChemConnector Blog
Posted by tony in Uncategorized on May 12, 2011
If anything I am saying on the ChemConnector blog is of interest to you, and you are interested in getting the blog posts directly to your inbox please sign up on the blog using Feedburner to receive the blog posts directly. The registration box is on the right hand side and looks like this:
Chemistry in Your Pocket
Posted by tony in Uncategorized on April 22, 2011
I am presently in the process of co-authoring an article regarding “Mobile Chemistry” and in the past few months have put together a short online article “Mobile chemistry – chemistry in your hands and in your face” and last month published an article with Harry Pence regarding “Smart Phones in the Classroom“. I’m up to give a few talks in this area in the next few months….and it is a fast moving field. For example…see Alex Clark’s recent presentation at the ACS! Alex is going some great work with his Mobile Molecular DataSheet. I recommend following him on YouTube!
Hosting a Compound Centric Community Resource for Chemistry Data
Posted by tony in Uncategorized on April 13, 2011
This is talk 2 from the ACS Anaheim collection. Talk 1 is here.
Hosting a Compound Centric Community Resource for Chemistry Data
Laboratories around the world continue to generate immense amounts of data that are non-proprietary and of value to the community. If available these data could dramatically reduce costs by minimizing rework and ultimately facilitating faster research. High quality reference data collections of chemical compound dictionaries, properties and spectra have been generated over many decades. With the advent of social networking tools and platforms such as Wikipedia, the community has an opportunity to contribute. The ChemSpider platform hosted by the Royal Society of Chemistry is a compound centric database with associated data. Already populated with almost 25 million unique compounds the community can deposit and host their own data, and curate and annotate existing data including those generated in Open Notebook Science Efforts. This presentation will provide an overview of progress to date and outline the vision of this community platform for chemistry and ensuring the longevity of chemistry reference data.
Of Course Scientists Have Good Imaginations and Especially at Halloween
Posted by admin in Humor, Uncategorized on November 2, 2010
Once upon a time I was told by a young lady I was dating that because I was a scientist I was too objective and didn’t have an imagination. I happened to be writing a children’s book at the time and had a tendency to solve some of the big problems I had with analyzing data by “sleeping on it” and, occasionally, dreaming solutions to a problem. On one occasion when trying to understand the complex molecular motions of N-trioctylamine I actually had a very vivid dream and walked my way along the chains, woke up in the morning and wrote a computer program to model the overall and internal motions of the chain to model C13 NMR relaxation. The result…a new model for alkyl chain motions that has been published a number of times and remains a useful model today for everything from lubricant-related systems to lipid bilayers. So, yes scientists have imaginations…and we tap into them in different ways.
I am the father of two dynamo guys…eight year old twins. They love Halloween and it’s a great time to truly apply my imagination for fun times. Working with my friend and neighbor Tom Barbieri, fellow scientist (physicist) and fun-guy extraordinaire, we collaborated to set up a “Halloween Path” for the neighborhood. We got a group of guys involved and our wonderful neighbor Beth was the “witch-for-an-evening” . We scared the living daylights out of a group of kids that evening, had a good time in the process and established a new standard for Halloween fun for the neighborhood. To be repeated? Maybe.
The “by light of day video” shows first.
The “darkness of night video” follows….you don’t see much but it’s worth watching for what you DO see…and that scream….I moved out of the woods at speed!
Continuing Conflicts in the Messy World of Internet Chemistry
Posted by admin in Uncategorized on August 16, 2010
I have been looking at the state of curated data on the internet and blogged last night about the messy world of curated data. I should emphasize…none of these commentaries are meant to be harsh. Believe me, I’ve gone through the process of validating data and it’s difficult. There will be mistakes but what we need are processes and systems to clean these data up efficiently. If I see an error I want to annotate it and let people know there is an error. With todays’s technologies it is not difficult.
Let’s take another example from DrugBank
That listed chemical name above the structure doesn’t look very consistent…I don’t see any stereochemistry, certainly no “dihydroxy” and overall…yes, it’s definitely wrong. The actual structure for that name is shown below. Looks like an entire half of the molecule is missing. The InChI and InChIKey are for the molecule shown in DrugBank but the link to KEGG is to the molecule shown below…here.
The links on DrugBank to PubCHem and ChEBI are to the molecule to the left. All of the data in the DrugBank record in terms of outlinks are for the structure on the left EXCEPT the actual structure on the record, and its associated SMILEs and InChIs are for the ”2-amino-3,5-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one” moiety. Oops.
Recently I pointed out to David Wishart, host of DrugBank, some of the issues I had been seeing and it appears there will be a major update to DrugBank in the next few weeks that, in theory, will address some, and hopefully all of these observations.
Participating in a Sprint Triathlon to Raise Money for Cleft Lip and Palate
Posted by admin in Uncategorized on June 18, 2010
Last week I ran a 5km race to raise money for the Susan G. Komen Race for the Cure. I managed to raise past my target. I knew a young woman who had a double mastectomy at quite a young age. My dad died of liver cancer. As far as I’m concerned if I can push some money towards the charities based on my participation in a sporting event then I will. If I can get my friends, family and network to encourage me to push harder and contribute to the cause I’m running for I’m not shy to ask for support!
This coming weekend, on June 27th, I will be doing a sprint triathlon to raise money for SMILE TRAIN, a charity founded with the intention of providing free cleft lip and palate surgeries to any family affected. Examples are shown below.
This cause is special to me. We are friends with a neighborhood couple who have a son who was born with cleft lip and palate. Liam is a funny, gentle, loving and hug-every-time kid. He hangs out with our kids and together the three of them are a force of nature…young boy attitudes with a laugh for every occasion. He knows he was born with cleft lip and palate and just gets on with it. Fortunately he had surgery when he was 10 weeks old and additional surgeries since. The photos below show him at 10 weeks old before surgery and his handsome face in a photo taken at 5 years old, about 2 weeks after a plastic “revision” surgery to give more symmetry to his lip and nose. He is now six years old. He will most likely require a bone graft for the missing bone in his jaw about age 8, and lots of orthodontics will follow to address crooked and missing teeth.You can see the impact of the surgery. Imagine the challenges that Liam would have in life without such a surgery. Imagine the lives of the 1 in 700 children in the world born with cleft lip and palate and how their lives can be changed forever by this surgery.
In the last week of June here in North Carolina it’s going to be hot, damned hot, unless we have a surprise weather system. I’m going to swim 250m, cycle 12 miles and run a 5km at the end. I swim like a brick, I cycle ok and I run pretty well despite tearing my calf muscle earlier this year. Either way…I will push like a madman and it’ll hurt 
. I’m going to do my part and I humbly ask you to sponsor my efforts and help raise money for the Smile Train and provide for children born with this condition.
Ways to Give
Mail: Checks made payable to Smile Train can be sent directly to Rebecca Warriner, Race Director, at the address below. Please put my name, Antony Williams, in the memo.
RebeccaWarriner, Race Director
The Smile Train Triathlon
908 Heritage Greens Drive
Wake Forest, North Carolina 27587
Online at www.smiletrain.org/goto/milesintosmiles: Use Smile Train’s secure giving Web site created especially for the Smile Train Triathlon. Please list me in the Recognition Name field.
Matching gifts: Many employers match charitable giftsmade by employees, spouses, and retirees, which could easily double or triple the value of your contribution! Check with your HR department or visit www.smiletrain.org/site/PageServer?pagename=donate_matching for details.
A Nice Review of Our Recent Book Chapter on Nomenclature
Posted by admin in Uncategorized on July 5, 2009
Last year I co-authored a book chapter in a book regarding Chemical Information Mining. A recent review for the book was recently written by Peter Willett and it was nice to get a good mention for our section:
“This book discusses the use of text-mining techniques that would enable such operations to be carried out by purely computational means. The techniques are clearly attractive in terms of cost-effectiveness but would appear, from this volume, to require considerably more research before they can provide a realistic alternative to human processing. Two chapters – Automated identification and conversion of chemical names to structure-searchable information and Identification of chemical images and conversion to structure-searchable information – stand out, providing critical, wide-ranging reviews of their respective topics that I am sure that I shall return to in the future. ”
It’s nice to be appreciated for “after-hours” work.
An Example of Creative Brilliance
Posted by admin in Uncategorized on March 14, 2009
A friend of mine passed this on to me. it is an example of creative brilliance…I hope my children are a part of this future….