Beautifying Data in the Real World: Beautiful Data and O’Reilly

I was recently privileged to co-author a book chapter entitled “Beautifying Data in the Real World” in a book called Beautiful Data, available shortly from O’Reilly. The list of authors is likely known to readers interested in Open Data and Open Notebook Science: Jean-Claude Bradley, Rajarshi Guha, Andrew Lang, Pierre Lindenbaum, Cameron Neylon, Egon Willighagen and myself.

This was a great example of “distant collaboration”. We didn’t get on the phone to talk about the manuscript. We didn’t connect via a conferencing system. Cameron brought us together as a group of interested individuals, interested in contributing to a chapter regarding the work we’d done together on crowdsourced solubility measurements and handling of the data. We collaborated via a wiki with a few emails here and there. I believe the result speaks for itself. It’s an excellent article regarding “Beautifying Data in the Real World”.

The book can be pre-ordered here. I’ve browsed through some of the articles already and I don’t think you’ll be disappointed by the contents of the book. The content is diverse “Join 39 contributors as they explain how they developed simple and elegant solutions on projects ranging from the Mars lander to a Radiohead video.”.

An Example of Creative Brilliance

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….

Three Articles Published Online in One Week

During my career I have had the opportunity to work with some of the best scientists. During my >10 year tenure at ACD/Labs I directly managed the NMR product line for a number of years and was involved with the development of both the NMR prediction and Computer Assisted Structure Elucidation software. Over the past couple of years since leaving ACD/Labs I have continued to co-author articles with two of my ex-colleagues, and still friends, Kirill Blinov and Mikhail Elyashberg. Three of these articles were released in one work. If you are interested in NMR prediction and CASE systems you might find these articles interesting.

The application of empirical methods of 13C NMR chemical shift prediction as a filter for determining possible relative stereochemistry

Mikhail E. Elyashberg, Kirill A. Blinov, Antony J. Williams
Published Online: Feb 10 2009 8:59AM

DOI: 10.1002/mrc.2396

The reliable determination of stereocenters contained within chemical structures usually requires utilization of NMR data, chemical derivatization, molecular modeling, quantum-mechanical calculations and, if available, X-ray analysis. In this article we show that the number of stereoisomers which need to be thoroughly verified can be significantly reduced using NMR chemical shift calculations for the full stereoisomer set of possibilities using a fragmental approach based on HOSE codes. The applicability of this suggested method is illustrated using a series of complex chemical structures.

A systematic approach for the generation and verification of structural hypotheses

Mikhail Elyashberg, Kirill Blinov, Antony Williams
Published Online: Feb 5 2009 4:33AM

DOI: 10.1002/mrc.2397

In this article we show that the most rational manner by which to create structural hypotheses is by the application of an expert system capable of deducing all potential structures consistent with the experimental spectral data. Empirical or quantum-mechanical (QM) NMR prediction methods are compared. It is shown that when an expert system is used the best structure(s) can be distinguished using either incremental or neural net (NN)-based NMR prediction algorithms.

Development of a fast and accurate method of 13C NMR chemical shift prediction

Available online 11 February 2009
Kirill A. Blinov, Yegor D. Smurnyy, Tatiana S. Churanova, Mikhail E. Elyashberg, Antony J. Williams

DOI:10.1016/j.chemolab.2009.01.010

In this article we describe a fast and accurate method of 13C NMR chemical shift prediction. The high speed of chemical shift calculation described is achieved using a simple structure description scheme based on individual atoms rather than functional groups. The systematic choice of an appropriate encoding scheme and the usage of partial least squares regression on a large training set has resulted in a robust and fast algorithm. The approach provides accuracy comparable with other well known approaches but demonstrates accelerated calculation speeds of up to a thousand times faster.

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A Request for Postcards from All US States

I am the proud father of twin 6 year old boys. They are in the middle of a project to get postcards from all US states around the country so I am making a request to those readers of this blog around the country. Would you be so kind as to send a state-specific postcard to our sons at the following addresses…it would be much appreciated! Thanks

 

Franklin Academy 1,

Mrs Rollin’s Kindergarten Class

Attention: Taylor Williams

604 Franklin Street

Wake Forest,

NC-27587

 

and 

 

Franklin Academy 1

Mrs London’s Kindergarten Class

Attention: Tyler Williams

604 Franklin Street

Wake Forest,

NC-27587

ACD/Labs and Pharma Algorithms Join Forces

An announcement today from the company where I spent 10 years of my career, the last few as their Chief Science Officer.

Toronto, Canada (February 9, 2009)—Advanced Chemistry Development, Inc., (ACD/Labs) and Pharma Algorithms, Inc., have joined software development and business resources to better serve the extensive Chemical, Environmental, and Pharmaceutical markets, creating a new leader in in silico physicochemical, ADME, Metabolism, and Toxicology screening and prediction.” More here…

I know the experts from both companies who have been developing the physicochemical property prediction software for many years and this combination of knowledge and expertise in this area is going to be hard to beat now. It will be very interesting to watch what the joint efforts will deliver now.

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A New Service Provided by Elsevier

This particular feature might have been around for a while for authors in Elsevier publications but it is the first time that I have received a CiteAlert. I know that many of my other Elsevier publications have been cited, some quite highly, so I assume it is a new service. It’s a great idea and is something I would encourage other publishers to consider.

American Healthcare “Works great as long as you are not sick”

I stole the title for this blog post from American Citizen. Next week I will be sitting at his bedside with his wife after he goes through surgery. What he is going through is life-threatening and could disable him for life if things go awry. His experiences of what he is going through with our Health care system in America are amusing. Because of his wit, intelligence and work experience in the health care industry, his story from this point, through surgery and to recovery will be a fun and enlightening read. In his own words…

“This year, I find myself disabled with degenerative spinal disease and am awaiting surgery on Tuesday February 3rd. Since I have little else to do, I thought I would archive my experiences on this blog and also post some videos of the adventure.

As I write this stuff, keep in mind that I have spent numerous years working for my cause: universal coverage for all Americans and the deployment of a universal personal health record to prevent errors in clinical judgment and facilitate a smooth transition for all patients between systems of care.” read the rest of the blog post here…

A Family Emergency, The UK National Health Service and a Call to President Obama

Those who frequent the ChemConnector or ChemSpider blogs, or have these plugged into your Readers will have noticed a sudden silence from me in the New year. It was one of those “phone calls you never want” calls. My mother was rushed into hospital with a subarachnoid hemorrhage. That is NOT a bleeding spider deep in her waters (get it? A sub arachnid hemorrhage…) but a bleed in the brain. It is a form of stroke and as Wikipedia so nicely states (scary)  “Up to half of all cases of SAH are fatal and 10–15% die before reaching a hospital”. My mother made it to hospital thanks to the valiant efforts of my sister who had experience of exactly this medical emergency since her friend had SAH just over a year ago. By the time I got home three days later my mother was safely at the Walton Center,supposedly one of the best neurology hospitals in the UK. When I walked onto the ward for the first time after a red eye flight from the US and no sleep for about 30 hours, my mother was awake, but tired. She was bruised from all the lines running into her and had a drain running from her head to a bag draining fluid from the brain to prevent hydrocephalus. they must have been collecting over a half litre of fluid every day or so. Whenever I was there the bag was full of bloody fluid and seemed to get drained regularly. It’s very concerning and emotional for any child to see their parent in such a state….

In the first couple of days she was talkative but sleepy. With SAH it’s the few days following the event that are particularly telling and dangerous. No different in this case. All hell broke loose as she headed down from the normal ward and down to the High Dependency Unit (one nurse, per two patients) one day. We received a call and when we arrived she wasn’t conscious and non-responsive. Within a few days she had declined and had moved to the critical care (1 nurse, 1 patient it seemed) ward as a result of the drain from her head blocking and a build up of fluid, heart arrythmia, low blood pressure and an infection. They made a 6 inch cut across the scalp, drilled a hole into the skull and ran a fresh drain into a ventricle of the brain. The next three days were emotionally and physically draining (3 hours a day of driving and not knowing whether she would be able to talk that day or not or even know who we were. By the time she got back to High Dependency (who would have thought that would seem like a happy day…but after critical care it is!) she was on seven drugs, had mainlines running into her femoral artery and later the carotid artery. She was bruised and bandaged, cabled, wired and clearly in distress. At one point her eyes communicated “Enough…I can’t do this anymore” and it was one of the hardest moments of my life…but a singly defining moment in the nature of my relationship with my sister and my mother…and how closely connected we are.

During that period the doctors performed endovascular surgery to insert a coil as described in detail here. My mother now has Platinum in her brain and without it would likely not survive. The stress on her system would not been conducive to her surviving a more invasive surgery. When I left the UK, after almost 3 weeks, multiple changes to my flights (and lots of charges from United airlines!) my mother was off of all drugs, sitting up, had just drank her first glass of water in 7 days (she was on a nose feed for food for a long time and was receiving intravenous fluids the entire time) . I’ve been home almost a week and she is now eating soups, drinking hot drinks, can get out of bed and is learning to walk again…after three ways in bed there is a lot of muscle atrophy.

And so to the National Health Service of the UK. I have heard MANY nightmare stories and experienced some myself when I lived in the UK. However, I’ve lived in Canada and now live in the US. I have nightmare stories and experiences in both countries. Those stories are for another time… What I can say is that the treatment my mother received was outstanding. Her nurses and doctors were phenomenal. There were not only skilled at their jobs but sympathetic to us at a human level, listened to us when we were concerned and educated us when we asked. The coiling procedure is not available in every hospital and is state of the art surgery. Bottom line is my mother nearly died the moment the hemorrhage happened (50% of people do!) and, in my opinion, she went to the edge and back a number of times in 3 weeks. The medical staff clearly saved her life and I and my family are indebted to them for the treatment and the experience. one concern we didn’t have to deal with is “cost”. Even for the most mundane procedures in the US there is a cost concern. Having visited friends and hospital members in hospital I am conscious of the “how much per pill” mentality that persists here. Based on what I saw happen to my mother, and the 4 weeks of hospital stay to come and months of rehabilitation to follow my mothers treatment and recovery in this country would cost well over a hundred thousand dollars..probably more (maybe some one can give me an inform guess?). In the UK the National Health Service assumes those costs. There is no bill to come that we need to worry about. The focus can be on the patient, their rehabilitation and care. In this country I have sensed and discussed with some close friends the mentality of “what is a life worth?”. What child wants to be put in that situation?!

And so my plea to President Obama. “Please stay on task with your intentions to provide affordable health care for all families. Rich or poor none of us want to be faced with the challenging questions associated with the mentality of “What is a life worth” that will prevail unless health care costs are brought under control in this country. We have research investments in this country which have delivered incredible technologies to preserve life as we are threatened. We have drugs to support and enhance life when burdened by sickness and slowed by age. Yet, for many, basic healthcare remains out of reach. It is past the time for change. The majority of the populace, whether they voted for you or not, will lend their support to you to make the necessary changes. The world is watching and you can lead the change in healthcare. You have my support.”

My best friend is right in the middle of the challenges of “commercialized health care” in the United States. Jeff is a wonderful man and one of my life mentors. He is at once incredibly intelligent, thoughtful, caring, challenging and motivating. He is presently struggling with a health issue of his own and is about to enter into the challenges of dealing with the costs of excellent care, some of the (in)adequacies of the system, and going under the knife for a very scary yet incredible surgery. He has the blog American Citizen and is about to start posting videos about the challenges he is going through. Knowing Jeff they will be witty, amusing and straight to the point. Check out his blog and watch out for the movies.

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Chemical Information Mining Book - A Moment of Pride

As I recall last Christmas I was finishing up a chapter in a book that is now on the market and called Chemical Information Mining. What’s amazing is that I just found that the first 21 pages are ALREADY on Google Books. I could’ve seen the cover there before waiting to receive a copy…hell I could’ve read UP to my Chapter…that’s where it stops.

The product description on Amazon is: “This book focuses on information extraction issues, highlights available solutions, and underscores the value of these solutions to academic and commercial scientists. After introducing the drivers behind chemical text mining, it discusses chemical semantics. The contributors describe the tools that identify and convert chemical names and images to structure-searchable information. They also explain natural language processing, name entity recognition concepts, and semantic web technologies. Following a section on current trends in the field, the book looks at where information mining approaches fit into the research needs within the life sciences.”

I’m rather proud of the contribution Andrey Yerin and I made to the book. I worked with Andrey while I was at ACD/Labs and learned all about nomenclature from him. He’s one of the nicest, most competent and focused specialists in the domain of systematic nomenclature in the world. The book chapter contents are listed below. Makes for good Xmas reading if you care about that type of thing…

An Invitation to Bio-IT in Boston in 2009

I’m on the agenda to speak at the Bio-IT meeting in Boston next year (April 27-29 2009) to present on “Crowdsourcing, Collaborations and Text-Mining in a World of Open Chemistry.” In case you are assembling your calendar for next year here’s the announcement…

“Join the life sciences community in Boston, MA next April 27-29, 2009 for the 7th Annual Bio-IT World Conference & Expo (www.bio-itworldexpo.com).  Since its debut in 2002, Bio-IT has established itself as a premier event showcasing the myriad applications of IT and informatics to biomedical research and the drug discovery enterprise.  The 2009 program will feature best practice case studies and joint partner presentations relevant to the technologies, research, and regulatory issues of life science, pharmaceutical, clinical, health, and IT professionals. “