Archive for category Publications and Presentations
Improving Online Chemistry One Structure at a Time
Posted by tony in ChemSpider Chemistry, Publications and Presentations, Quality and Content on February 13, 2012
Last week I was in the United Kingdom for numerous meetings and at the end of the week struggled to drive north to Macclesfield to the AstraZeneca site there to give a presentation on ChemSpider for an old colleague of mine from the Eastman Kodak company. I had not seen Tony Bristow in well over a decade but we reminisced about the good old days at Kodak (Tony worked in Harrow, UK and I worked in Rochester, NY. Tony is a Mass Spectrometrist and I am an NMR Spectroscopist by training). We also discussed how scientists are increasingly tapping into the ChemSpider resource to aid in the identification of chemical compounds using, especially, Mass Spectrometry. We have numerous examples now of when people are solving their structure ID issues directly by searching ChemSpider and are building up a portfolio of success stories.
The presentation I gave is below and loaded on SlideShare in case you want to download it.
Presentation Times and Titles at the Spring ACS Meeting in San Diego
Posted by tony in Community Building, Publications and Presentations on January 18, 2012
It’s going to be a busy meeting at the ACS Spring Meeting in San Diego. I am presenting five of my own talks and am co-author on 5 more. It’s going to be fun to get them all done! Read that as a challenge…and unfortunately despite my best intentions I NEVER get them written before I leave and am writing/tweaking them the night before. Such it is….
If you happen to be coming to the ACS and are interested in ChemSpider and how RSC informatics contributes to the world of chemistry please do find time to come and visit the RSC booth and, if you have time, let’s sit over a computer and a coffee and chat!
PAPER ID: 15442 PAPER TITLE: “ChemSpider as a chemical term resolver” (final paper number: 131) DAY & TIME OF PRESENTATION: March 29, 2012 from 10:00 am to 10:20 am LOCATION: San Diego Convention Center , Room: Room 27A
PAPER ID: 10915 PAPER TITLE: “Great promise of navigating the internet using InChIs” (final paper number: 101) DAY & TIME OF PRESENTATION: March 28, 2012 from 9:05 am to 9:35 am LOCATION: San Diego Convention Center , Room: Room 27A
PAPER ID: 10902 PAPER TITLE: “Chemistry made mobile – the expanding world of chemistry in the hand” (final paper number: 68) DAY & TIME OF PRESENTATION: March 26, 2012 from 2:45 pm to 3:20 pm LOCATION: San Diego Convention Center , Room: Room 25C
PAPER ID: 11299 PAPER TITLE: “Social networking tools as public representations of a scientist” (final paper number: 123) DAY & TIME OF PRESENTATION: March 28, 2012 from 2:25 pm to 2:50 pm LOCATION: San Diego Convention Center , Room: Room 25C
PAPER ID: 10893 PAPER TITLE: “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry” (final paper number: 61) DAY & TIME OF PRESENTATION: March 25, 2012 from 2:50 pm to 3:10 pm LOCATION: Westin San Diego , Room: Diamond II
A YouTube Cartoon Movie for ScienceOnline2012
Posted by tony in Presentations, Publications and Presentations, ScientistsDB, Wikipedia Chemistry on January 5, 2012
I have previousloy blogged on “Why are pornstars more notable than scientists on Wikipedia?”. It created a wave of comments and feedback, some on blog, a lot more off-blog. One of the results was a Xmas project that resulted in ScientistsDB that I discussed here.
I’ve been watching a number of amusing videos that have been showing up on YouTube of late and, as a bit of an exercise nut, I have posted a couple of funny ones to my Exercise blog [1,2]. Last night, while helping my friend Mark Jensen do some stopped-motion photography while he was painting a sign, I happened upon the process by which these types of movies are made. It’s possible to make them using XtraNormal. Since it is possible to make the first one for free…I had enough credits at least to do what I wanted to do…
So, I made an XtraNormal movie about the situation about “Adult Film Stars and Scientists on Wikipedia”and the development of ScientistsDB. I kind of dedicated the movie to ScienceOnline 2012 as that is where I suggested the fictional discussion between “Sean and Tony” would take place.
I’m sure there are going to be a lot of interesting discussions at ScienceOnline2012 and look forward to seeing everyone there. By the way, if you have been involved with any semantic web projects or projects using Linked Open Data please connect with myself @chemconnector or @kristiholmes on Twitter as we’d like to invite you to give a short (3-4 min) talk at ScienceOnline2012.
Presentations at ACS Spring in San Diego
Posted by tony in Publications and Presentations on January 2, 2012
I have received formal acceptances for five presentations at the ACS Meeting in Sam Diego in Spring 2012
PAPER ID: 15442 PAPER TITLE: “ChemSpider as a chemical term resolver”
PAPER ID: 10915 PAPER TITLE: “Great promise of navigating the internet using InChIs”
PAPER ID: 10902 PAPER TITLE: “Chemistry made mobile – the expanding world of chemistry in the hand”
PAPER ID: 11299 PAPER TITLE: “Social networking tools as public representations of a scientist”
PAPER ID: 10893 PAPER TITLE: “Teaching NMR spectroscopy using online resources from the Royal Society of Chemistry”
I’m also listed as a co-author on a number of other presentations and a poster. I’m glad the vacation is over. Time to get back to work, focus the mind and start being productive again! I love the holidays…it’s really a great time to connect with family but just like cardiovascular exercise I lose the ability to think clearly and multitask very quickly. I formally start back to work tomorrow and am already getting the gears rolling again to get myself back up to speed. 2012..here we come.
ScientistsDB – A wiki for scientists, about scientists, by scientists
Posted by tony in Presentations, Publications and Presentations, ScientistsDB on January 1, 2012
Join ScientistsDB
Recently I wrote about the issues of notability for scientists versus porn stars. It seemed to kick off quite a discussion…40 comments, 100 Tweets, comments off my blog on other people’s sites. It got mentioned on Wikipedia Signpost..and I take that as a compliment! There are some comments made on various Wikipedia pages [for example, 1]. Not everyone agreed with what I had to say and I received some GOOD guidance and input about how to improve the articles on Wikipedia that I had been writing. There were some supporting comments about how it was appropriate for me to write about people I know (in regards to the Conflict of Interest on Wikipedia).
When I originally wrote the post I was in a particularly “ranting” type of mood based on a few other things going on in regards to other systems, especially in regards to who makes final decisions. In retrospect some of the issues I blogged about had been brought up in various forms by other people over the years and in some ways my comments were “nothing new”. However, it is clear that the exposure the post got did resonate with a number of people.
I have sat with a number of friends and chatted, over a “cool glass of water” (or more), and chatted about exposure for scientists in general. We chatted about Wikipedia articles, about LinkedIn as a networking site for professionals, about the new systems such as ProSkore, and whether Klout would persist as a system for measuring influence.
Sean Ekins and I have introduced two wikis to the community…one for Scientific Mobile Apps and one for Scientific Databases. One addition to the family of scientific wikis that makes sense, based on the recent experiences with Wikipedia and the discussions around notability guidelines for scientists, is the new wiki ScientistsDB.
This wiki is for ANY scientist to have a wiki page about them online. We have no notability guidelines in place, and hopefully will not need them. Time will tell. The hope is that scientists will contribute their own articles, that the community will also contribute/edit/expand and that ultimately, when the article is in good enough shape, it might be used as the source of an article on Wikipedia. There it can be challenged, discussed, edited and moved through all of the potential phases of a Wikipedia article before it is accepted. We believe that all scientists are entitled to a presence that ScientistsDB can enable. As the data are gathered then we have the possibility of starting to form network maps, relationships and connections that would have been unavailable before. We have a way to introduce scientists working in the same domain, connecting people working on the same classes of compounds, diseases, genes, etc. This is all part of a potential future…for now the Wikipedia articles for scientists (almost 50,000 of them) have been harvested and kept categorized according to Wikipedia categories and all scientists are welcomed to add their own articles. All content is licensed according to CC-BY-SA 3.0.
For now we are starting to get articles. A good model article is from Alex Clark.
We look forward to your thoughts and comments!
Social Networking Tools for Scientists or How to Brand Yourself Online as a Digital Citizen
Posted by tony in Community Building, Open Science..all its forms, Presentations, Publications and Presentations on December 31, 2011
There are many social networking tools for scientists that can be used to share information, engage the social network and move information about activities across the web. This presentation provides an overview of some of the tools available and how they can be used by scientists to expose their activities, manage their profile publicly and participate in the network.
Who sets the price for our book and why does it vary so much?
Posted by tony in Book Reviews, Publications and Presentations, RSC Publishing on November 27, 2011
I have written a lot of book chapters over the years, probably about 20, and have another 4 in press . I also have 3 more waiting on me to write by end of year (agh…). I have co-authored three books over the past few years (1,2,3) but other than the first book, self-published with ACD/Labs, I was not involved with setting the price. That’s probably good as it would likely be randomly changed, as would the list of authors and the number of pages!
There has been a question on this blog about whether I think the price for the most recent book is appropriate and I will discuss that when I have more time. I would say that based on the likely number of copies that will sell for this very specialized area, the size of the book and the amount of work it took us to put together (almost 2 years of work describing about 15 years of work), that this is probably a fair price…about $220 (but with price variation to be discussed below). If you consider that our single articles can be $30-35 for ONE PDF for 48 hours of access summarizing only one point in time in our research then I do think that the price is fine. Having previously “self-published” and seen how many books can be sold in that way I’d say that price is definitely appropriate considering the quality of support we have received from the publisher, RSC, and the associated costs of set-up for printing that must be taken on. Maybe self-publishing would be better nowadays in terms of increased volume of sales, as my last experience was 10 years ago, but based on comments from people using Lulu.com (for chemistry books), sales volume is very low and for worldwide marketing to libraries a professional publisher IS necessary.
Back to the point of this blog post. Who really sets prices for a book, taking just the chemistry book I am involved with as an example? Amazon want about $220, at present, for a copy of our book. That includes a “random 7% discount” that comes from where? However, then things get interesting….
Note that the author listing order for our book is: Mikhail Elyashberg (Author), Antony Williams (Author), Kirill Blinov (Author). Now then….
Borders sell it for $424 here and change the author order to by Antony Williams, Mikhail Elyashberg and Kirill Blinov.
BetweenReads.com.au have the price listed in Australian dollars, add the book editor as an author, change the order of the authors and add another random discount.
PowellsBooks loses two of the authors and leaves only Mikhail Elyashberg as the sole author but keeps the price as the original Amazon price, no discount.
Barnes and Noble give a 19% discount before the book is even released, not an uncommon situation of course.
In most cases the number of pages is underestimated to be 368 pages but if you consult the RSC page you will see that it is almost 500 pages and the LIST price is 146.99 UK Pounds.
Who knows where these various online book sellers get their information and how their prices get set, but clearly there are discrepencies. While this book isn’t a mainstream novel moving the basic info out to the sites should be easy. One has to assume that the various discounts are based on either the scale of the sales operation or, it seems, more random factors. All very interesting…and no resolution from me!
Our book published Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation
Posted by tony in Nuclear magnetic resonance, Publications and Presentations on November 10, 2011
Almost two years of work, a collaboration and friendship developed over many years of my tenure at Advanced Chemistry Development (with Mikhail Elyashberg and Kirill Blinov), a story about a decade of work to develop what we believe is the world’s premier Computer Assisted Structure Elucidation software, and multiple iterations later, our book is now at the printers.
Our Book COver
Our book is “Contemporary Computer-Assisted Approaches to Molecular Structure Elucidation” and is already listed on Amazon here.
“Computer Assisted Structure Elucidation (CASE) systems are powerful software applications capable of outperforming human data interpretation in terms of both speed and reliability. They combine software algorithms with tools for molecular structure elucidation using spectroscopic data. This book describes the principles on which CASE systems are based and concisely explains the algorithmic concepts behind the programs. It puts the technique in the context of its origins and describes the challenges that have been overcome to produce modern CASE systems. It uses the authors’ software development experience to discuss the present state-of-the-art and explains how the synergistic marrying of man and machine can provide superior results. Readers will gain a firm grounding in the fundamentals of CASE, an understanding of the challenges associated with algorithms, and an appreciation of the technologies underlying NMR prediction and structure verification. Scientists who have never used CASE systems before will find all the information necessary to master this new and very effective approach. Those with some experience will benefit from details on the latest developments.”
I willingly admit I’m glad it’s over…it feels great to have it finished, great to know its at the printers and good to know that we have likely written the definitive volume in this area for the time being. Now time to let my eyes recover before getting back to writing two more volumes about NMR applied to Natural Products, to be released next year all being well!
Open Notebook Science and One Future for Scientific Research
Posted by tony in Open Access Publishing, Open Science..all its forms, Publications and Presentations, Purpose and People, Quality and Content on October 30, 2011
A few weeks ago I was invited to give a presentation to the Board of Directors at Burroughs Wellcome. I was very interested in taking this opportunity to discuss my views on Open Science, Open Notebook Science, Open Data etc with this group of very esteemed scientists. However, it turned out it clashed with a planned vacation. Since my friend and frequent co-author Sean Ekins is an evangelist for open science for drug discovery, improving data quality, and Mobile Apps, and since we think alike on so many levels, I asked Sean whether he’d want to give the presentation. And, always welcoming adventure Sean jumped at the chance to present.
As it turned out Hurricane Rina resulted in us cancelling our vacation so I ended up attending the presentation with Sean. While we had bounced the slides between each other prior to the presentation Sean did a terrific job as the presenter and we had some very interesting questions regarding what is standing in the way of open science, especially around chemistry databases (of compounds), what are good examples of bioinformatics projects that are successful, and whether there are “risks” inherent to Open Science, especially in regards to what is shared online in public compound databases. I thoroughly enjoyed the meeting, short as it was and am glad that we were given the opportunity.
Sean has eloquently outlined the nature of the presentation at his site (he is Collabchem) and the presentation is below for your comments and review. I recommend that you check out Sean’s other presentations too!
Mobile apps for chemistry in the world of drug discovery
Posted by tony in Mobile Chemistry, Publications and Presentations on October 27, 2011
Our article “Mobile apps for chemistry in the world of drug discovery” is online here (still in press). The article focuses on reviewing what is possible today with Apps and what influence it may have on drug discovery.
