Archive for category Publications and Presentations
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.
Updated Presentation on Mobile Chemistry Apps and the SciMobileApps Wiki
Posted by tony in ChemConnector, Publications and Presentations, SciMobile Apps Wiki on October 23, 2011
I am presently in Barcelona at the ICIC meeting to give a presentation entitled “Mobile Chemistry and “Generation App”. I have been preparing by looking at what is new in the world of Chemistry Apps and in the process have updated my ongoing list of apps and updated it on SlideShare. I intend to keep updating it every couple of months to keep track of new apps as they become available. I have not had time to update the SciMobileApps wiki as yet.
Navigating an Internet of Chemistry via ChemSpider
Posted by tony in Publications and Presentations on October 19, 2011
The internet is a rich source of chemistry related data and, nowadays, if a chemist knows how to initiate a search, data can be sourced for millions of chemicals online. The nature of online data varies from simple molecule diagrams, to experimental and predicted properties, encyclopedic articles, synthetic routes, analytical data, patents and publications. The array of information now accessible is distributed across thousands of sites giving rise to the information overload commonly associated with the Google-type searches on the internet. In addition the purest language of chemistry, that of chemical structures, is not fully supported on the web as yet. This presentation will provide an overview of how the internet is being meshed together using data aggregation and standardization approaches to enable a structure-searchable internet for chemistry. The speaker will present an overview of the ChemSpider platform (http://www.chemspider.com), the challenges of linking together over 400 internet resources and 26 million unique chemicals, and discuss how members of the chemistry community can directly contribute to enhancing the availability of quality data online.
This is a movie of the talk I gave using the BigBlueButton platform to students and faculty at the University of Arkansas, Little Rock.
Open Drug Discovery Presentation Session with JC Bradley
Posted by tony in Open Science..all its forms, Publications and Presentations, RSC Publishing on October 17, 2011
I had the pleasure of co-presenting with my friend Jean-Claude Bradley today at the “3rd Annual Drug Discovery Partnership: Filling the Pipeline“. Jean-Claude gave a great talk, available on Slideshare here, and discussed the issue of data quality, how improve data gives improved models, the cross-validation of data and proliferation of errors. My talk is on Slideshare here and embedded below. In many ways I discussed similar issues, though not focused on melting point data but rather on structures, structure-identifier relationships, the cross-linking of multiple resources on the internet and how online resources can support Open Drug Discovery Systems. In this presentation I discussed some of the work we are doing on Open PHACTS.
Why I do not trust web statistics
Posted by tony in Data Quality, Publications and Presentations on October 15, 2011
Any of us that host websites like to use stats. We like to review our traffic, our hits, some of us follow our Alexa ranking or our Compete ranking. I have blogged previously about Alexa applied to ChemSpider and Compete applied to ChemSpider. The Alexa rankings and Compete rankings are available for the site online. These are PUBLIC rankings and the value of public rankings such as this is the relative ranking that you can observe…according to Compete ChemSpider unique users is about 1/2 that of PubChem and 9 times that of eMolecules.
Whether this is true or not is a whole different question. Why? Because I simply don’t believe most public stats on websites like this. For accurate measures of traffic I would choose internal Google Analytics code over any of the public website measures.
Here’s an example of how stats get distorted. I’d like to celebrate the result I am about to report but I DOUBT it’s true! Yesterday I gave a talk to a group of students and faculty at the University of Arkansas, Little Rock. The presentation is below.
Based on feedback from my host, Bob Belford, the presentation was well received. I enjoyed giving the presentation and used the BigBlueButton system to do it, using with skype for audio, and then sharing my desktop from Skype for a live demo of ChemSpider. However, I doubt it’s my best ever presentation! Within 5 hours I had received an email from Slideshare that it was being talked about on LinkedIn and was one of the top talked about presentations and they had put it on the home page of Slideshare! Overnight it had registered >10,000 views.
My Slideshare presentation on the Slideshare Home Page
Now, I wish that 10,000 people had looked at the presentation! That’s what it says now! But I believe the stats are likely biased and people have looked at the Slideshare home page 10,000 times while it was shown in the “Hot on LinkedIn” page. I may be wrong…maybe it is that popular! And if so thanks for reading.