Archive for January, 2010

Over the past three years I’ve carried a double-edged sword on the ChemSpider Blog: the honor and the burden.

As anyone who runs a blog would likely tell you hosting a blog can take a lot of time and effort, especially if you are passionate about communicating. Fortunately, since ChemSpider was acquired by the Royal Society of Chemistry we now have a lot more people involved with the platform including support staff and our colleagues in the Cambridge, UK-based Informatics team. Since we are working hard to further integrate various processes, systems and projects it makes sense that more of the team discussing our activities around ChemSpider can post here. In particular there are a number of activities going on regarding the technical aspects of ChemSpider development that will start to show up on this blog and we encourage your participation, comments and feedback. ChemSpider is, after all, about community participation so do engage us!

Over the next few days a number of my colleagues will introduce themselves to the readers of this blog. I welcome them all to the “honor and the burden”…it’s a pleasure to share this space with them.

In the first of many integration projects presently underway inside the RSC to bring together the benefits of ChemSpider with existing systems we’re happy to announce that the Prospected compound pages are now using structure images from ChemSpider as shown below. We spent a lot of time creating aesthetically pleasing structure images for ChemSpider and especially for display on webpages and blogs so we’re happy to see them show up in other venues too.

We unveiled the ability to embed chemical structure images as well as embedding spectra last year. Now there are multiple blogs using the embed functionality, structures are starting to show up on Wikipedia and our web services are being used for structure image retrieval. We encourage you to make use of the resources we are delivering and any feedback.

prospect

I will be speaking in a Science Commons symposium on the Microsoft Campus in Redmond in February. If you are interested in hearing John Wilbanks, Cameron Neylon, Heather Joseph, Jean-Claude Bradley, Stephen Friend and myself talking about accelerating scientific discoveries come and join us.

sciencecommons

A couple of days ago I came across a video on YouTube about “Water Marbles”. I’ve inserted it below…I recommend watching it…it’s excellent!

It’s excellent because by time I had finished watching this I was both excited and confused. Confused because how could I not of heard of this experiment. Even if it was to work why were those spheres so big and uniform? Excited because I’d been looking for some good kitchen chemistry to do with my kids and this would be a great example. I couldn’t really get my head around how the observations were working but on a rushed grocery expedition prior to going into ScienceOnline2010 #scio10 this part weekend I threw everything necessary into the grocery basket to repeat the experiment.

At ScienceOnline2010 I was involved in a number of discussions, as usual, regarding data quality, curation and assertions….this being based on my experience with curating the ChemSpider database. Today I sat in on a discussion entitled “Getting the Science Right: The importance of fact checking mainstream science publications — an underappreciated and essential art — and the role scientists can and should (but often don’t) play in it – Rebecca Skloot, Sheril Kirshenbaum, and David Dobbs.” it was an interesting exchange with comments such as “newspapers and magazines don’t check facts” and the urban myth that a one minute kiss burns 26 calories while the fact is that a Hershey’s Kiss contains 26 calories.

Post ScienceOnline2010 I got home this afternoon to find my kids desperately wanting to do kitchen chemistry so, with pessimism I started to work through the experiment with them. They mixed and stirred and cooled and heated. They got to see a lot fizzing and to see crystals grow which they thought was great. It of course failed dismally as it has for many other people, including this guy, but they had a great time. In parallel I was doing some fact-checking to see whether or not to prepare them for disappointment.

There have been a lot of exchanges online about this topic of water marbles with chemists exchanging concepts about the science behind it if it did work. See here for example. The video has gone viral across many sites. Very impressive for a hoax really…and it did get me interested in doing kitchen chemistry. The truth is a lot easier though…and still good chemistry! Watch Steve Spangler in action below…

The polymer beads can be bought here.

There’s more Kitchen Chemistry to come but I think I’ll stick to some of Theodore Gray’s guidance …maybe time for some Mad Science at home

I’m off to ScienceOnline2010 in a few minutes. It’s the last day of the conference and the experience has been a highly positive one. I’ve finally met people face to face that I have been connected with for over 2 years….and congruency is always good…they are as interesting, passionate and generally nice people face to face as they are online. I also managed to catch up with a number of old friends. I got to meet some new people focused on changing the flow of communication for ScienceOnline and working hard to do so. #scio10 is different….there’s an energy in the air that I haven’t experienced at any other scientific gathering other than SciFoo. This is an audience that is introducing me to social networking tools that I’ve never heard of…that doesn’t happen often. It has to be that over half the attendees are twittering. iPhones are everywhere. Flips are out capturing video in the sessions and are uploaded online shortly thereafter. The conversations are open, opinionated, full of energy and motivating. This is MY type of conference and I’m fortunate to live less than half an hour away.

The dinner event was fun, giggly, five minute “Ignite” talks were given (I gave two …one on Curating Chemistry online and one with JC Bradley regarding the spectral game). The first of those is linked here and shown below.

Today I will be giving a live demo of ChemSpider to anyone interested and around at the end of the conference. It’s nasty weather so people might be leaving early.

I found myself a virtual running partner for my 1000 miles in a year challenge assuming my calf muscle tear heals. We’re going to try and figure out how to raise money for asthma. Anyone want to join us as to form a virtual team let me know…

Bora and Anton have done a tremendous job organizing the conference. Clearly there is a great team supporting them and the Sigma Xi facility is excellent. Terrific conference all around….glad I spent the weekend this way…

scienceonline2010It’s one week to ScienceOnline 2010. Last year I missed it because of the threat of weather and this year I’ll likely be hobbling in on crutches. I’m listed to give a few presentations/demos and a joint session regarding Citizen Science and Students with Sandra Porter and Tara Richerson. I’m going to have the chance to catch up with people I know such as Cameron Neylon and JC Bradley who’ll be covering Open Notebook Science. I notice that Bill Hooker is in town and look forward to connecting with him too. I’ll get to meet Hope Leman who runs the blog “Significant Science” and released a blog this weekend regarding an interview with me. It was a real pleasure to work on that with Hope.

ScienceOnline is THE place to be to discuss online science based on what I’ve heard from previous attendees. It always fills up early, is incredibly well organized in terms of workshops, guest attendees and social events based on what I’ve seen. I am looking forward to experiencing the event, sharing space with some of the leaders in the domain of online science and seeing some old friends. One week to go…lots of preparation work to do.

I’m presently building a list of examples of Citizen Science in Chemistry. If you have any examples you believe are worth highlighting please feel free to send them through. Thanks

Wired Magazine is my favorite monthly read. I get a lot of magazines delivered to the house for our family to browse through and these include Popular Mechanics, Popular Science, Science Illustrated and then additionally Chemistry World, C&E News, Drug Discovery News and a lot of the other trade magazines. Nevertheless, after the books I am reading (and I am presently reading Dr Mary’s Monkey as a follow on regarding the SV-40 cancer causing monkey virus in polio vaccines) Wired magazine is always the next thing I pick up.  It’s an easy read, some great short snippets for when I’m sitting on a stationary bike flipping pages or some long interesting articles, always well written. I recently read an old Wired magazine that had been on my stack for a few weeks and wish I’d read it earlier. We’ve been discussing the importance of user interface on ChemSpider and it’s impact and influence on the users of the website. This connected to the article on Craigslist that was covered in Wired Magazine.

Now, if you don’t know what Craigslist is then how about eBay? I’ll assume you know, and use, eBay. I use eBay…I like it. I’ve used Craigsist and like it, but for a different reason than I like eBay. Here is an interesting statement about Craigslist from the article: “With more than 47 million unique users every month in the US alone—nearly a fifth of the nation’s adult population—it is the most important community site going and yet the most underdeveloped.” The article goes on to tell the story about how confusing the site is, how poor the aesthetics are and how non-Web 2.0 it is in terms of integration access etc. I recommend it as a fun read, if nothing else to get a handle on Craig Newmark, the interesting (and VERY rich man) behind the initial concept. As a historical article regarding how early technology can morph over time into something more flashy but not necessarily more successful it’s a great read.Wired was convinced that people would want to give some input on how Craigslist should be improved and set up their Extreme MakeOver: Craigslist Edition for user comments. I doubt that Newmark and colleagues will pay much attention and, based on stats available to date, they don’t need to.

Another interesting read is a separate article regarding eBay vs Craigslist and the fact that Google and Microsoft actually tried to get into the same sector and both failed. What’s the magic, the secret sauce, the USP (unique selling points) for Craiglist? I’m read a number of suggestions but am not sure of the conclusions. I think its a combination of: 1) old and less complicated technology for novice users (searching means scrolling in a lot of cases) 2) traction …it’s been around a long time and 3) price for people to post ads. The bottom line though, of relevance to our discussions, is that “it ain’t the user interface!”.

Let’s be honest, technology is fun, especially when you work in our domain of building an internet for chemistry. Over the past few years I have upgraded from computer to computer, operating system to operating system (with Vista the worst transition but now loving Windows 7), from browser to browser (i have three installed: IE8, FireFox and Google Chrome with FF my preferred). I would say that while I am not at the bleeding edge of technologies I have access to more advanced systems than the majority of users in schools, homes and the rest of the world especially when taking into account that I have good, solid high speed access, both wireless-N and cabled in our house. If you truly want to see how a site works in the “hands of the masses” it is necessary to look at it on another computer where the latest and greatest browser isn’t installed and they are still running on 512Mb of RAM. In my new “personal adventure” of running 1000 miles in a year I am using the NikePlus website to track my performance but it uses so much Flash, so much animation and “looks” so modern and beautiful that I am struggling to use it even on my most recent laptop. It needs a “dumb down” button (maybe its there but I’m dumb enough to not see it).

We know we need to change some of the ChemSpider website for ease of navigation, for ease of use and to cater with all of the browser dependencies that we see with just things such as copy and paste of long strings, word wrapped strings etc. They can all be fixed. We know that there is an abundance of functionality on the site that only a fraction of the user base will care about. Our focus since starting the ChemSpider project was to establish a high-quality dataset (much progress but a long way to go), provide useful functionality to our diverse user base (lots in place, more to add, some to remove), provide a “successful” experience that meant that users could get answers to questions/queries they asked and that the experience wouldn’t so challenging or mundane as to provide no value. Feedback to date suggests we’re doing okay but we’d like your feedback. Ultimately I’ll likely assemble this into a SurveyMonkey questionnaire but for brevity and early feedback I am interested in your comments to some of the following questions

1) What is your favorite piece of functionality on ChemSpider?

2) What is your LEAST favorite piece of functionality on ChemSpider?

3) If there was one new function you would like to see added/improved what would it be?

4) Assuming a scoring system of 1 to 10, 10 being the best, how well does the ChemSpider interface support your usage of the system?

5) Which public dataset would you most like to see integrated to ChemSpider?

Any other comments are of course welcomed. We will be working on usability over the next few months and it’s hard to please everybody but we’ll do what we can with the resources we have. A Survey Monkey questionnaire will show up in the future with more questions. Watch this space and check out the Craigslist article…I think you’ll enjoy it.