One week left to submit - Symposium on Visual Analysis of Chemical Data (ACS Spring 2010)

Final Call for Papers:
Visual Analysis of Chemical Data
239th ACS National Meeting
San Francisco, March 21-25, 2010
CINF Division

Update(20/Oct): Closing date now 23rd Oct.

Dear Colleagues,

The submission deadline of 23rd Oct is approaching for an upcoming symposium focusing on innovative methods for visual representation and analysis of chemical data. Just as Edward Tufte has championed maximizing clarity and information content in statistical graphics, there is a need for methods to display chemical information that will maximize understanding, and allow rapid analysis and decision making.

We invite you to submit contributions that address various aspects of visualization of chemical data (such as structures, SAR data, literature, patents) including, but not limited to, the following topics:

• With an ever increasing pool of descriptors, along with new and more sophisticated machine learning methods, QSAR models are becoming more difficult to interpret. How can information on model reliability, the presence of activity cliffs, and the range of applicability of a model and other relevant model properties be easily depicted?
• Recently, virtual worlds 3D such as Second Life have presented new opportunities and challenges for the representation of chemical data. What is the potential of such a medium in education and communicating with the chemistry community?
• Social software allows for rapid and convenient sharing of chemical data. Examples include Google Spreadsheets, ManyEyes, DabbleDB, and wikis, including Wikipedia. What are the implications for chemical research and education?
• The visualization of the contents of large chemical datasets presents particular problems. How can an overview of the dataset be visualized so that it presents both the nature of the contents as well as the degree of diversity and similarity within the dataset? How can different datasets be visually compared?
• Depicting 3D chemical information in 2D involves a loss of information. However, innovative 2D visualization methods can restore the most relevant information.
• Chemical information comprises a diverse array of data types including chemical structures and diagrams (2D and 3D), associated assay results, conformations, QSAR models and their predictions. The visualization and integration of all these data into a single interface that aids interpretation and analysis is a continuing challenge.

We would also like to point out that sponsorship opportunities are available.

The on-line abstract submission system (PACS) will be open for submissions until 23rd October.

Please contact Andrew, Jean-Claude or myself if you have any questions.

Yours sincerely,
Noel O'Boyle

On behalf of the symposium organizers:

Dr. Jean-Claude Bradley,
Drexel University, PA
bradlejc@drexel.edu

Dr. Andrew Lang,
Oral Roberts University, OK
alang@oru.edu

Dr. Noel O’Boyle,
University College Cork, Ireland
n.oboyle@ucc.ie

Image credit: process/rum do/radial by Henry Cooke (CC BY-SA-NC 2.0)

Browser-based chemistry is here - its name is ChemDoodle Web Components

So...what's to say? Just check out ChemDoodle Web Components. It's Javascript. It's Open Source. It's running in your browser. It's doing funky chemistry.

Don't think it's going to affect you? Hear that noise? That's a paradigm shift.

Let's chart a brief timeline of what has led up to this:

• 1995 Nov - JavaScript (then LiveScript) first released
• 2008 Jul - Rich surveys all prior work at the intersection of Javascript and Chemistry, and identifies where Javascript can make the most impact on the web
• 2008 Oct - blahbleh implements a Javascript 3D molecular editor and viewer, molecools
• 2008 Dec - Duan Lian uses GWT to translate Rich Apodaca's lightweight Java cheminformatics toolkit, MX, into Javascript (website, demo)
• 2009 Jan - I develop a Javascript 3D molecule viewer, TwirlyMol
• 2009 Jan-Feb - Duan Lian releases a preview of the world's first Javascript molecular editor, jsMolEditor
• 2009 Aug - Kevin Theisen releases ChemDoodle Web Components

Keep your publication list up to date with Javascript and Google Spreadsheet

Adding a new publication to a HTML page is a fiddly business, especially if you want to add some markup or links. This might explain why there are so many websites of scientists whose last publication appears to be four years ago. If only adding a new publication were as easy as, oh, let's say...as easy as adding a row to a spreadsheet.

Well, you're in luck. The following procedure makes it as easy as just that. You can maintain the same list of publications on several web sites all of which will automatically be kept up-to-date. If you're familiar with Javascript and CSS, you can also easily change the markup used and its appearance. The result should look something like the following image:

Here's how it's done:
(1) Create a google spreadsheet, and use the same column names as shown in this spreadsheet.
(2) Add some information on your papers. Again, see the example spreadsheet for the format (note especially the author list format).
(3) Click on Share/Publish as Web Page, and make note of the key (i.e. the text between "key=" and "&single").
(4) Download addpapers.js, edit the line 'me = "N. M. O'Boyle";', and the line with the email address baoilleach@gmail.com, and put it in the same directory as a HTML page, papers.html (for example).
(5) Edit papers.html to load addpapers.js in its HEAD ("<script type='text/javascript' src='addpapers.js'></script>")
(6) Download publishious.css, and put it in the same directory as papers.html.
(7) Edit papers.html to apply publishious.css in its HEAD ("<link rel='stylesheet' media='all' type='text/css' href='publishious.css' />").
(8) Add the following to papers.html after replacing MYKEY by the value of the key for your spreadsheet:

<div id="paperentries"></div>
<script src="http://spreadsheets.google.com/feeds/list/MYKEY/od6/public/values?alt=json-in-script&callback=handlejson" 
type="text/javascript"></script>

Hopefully that works. If it doesn't, check your browser's error console (in Firefox Tools/Error console) for some idea of the problem.

It's probably not a good idea to rely totally on Google spreadsheets, so what I do is view the generated HTML code using the Web Developer plugin and paste it into the HTML page as the content of the paperentries div. That way, even if Google spreadsheets goes down (or changes its API), a couple of papers will still appear.

Feel free to adapt this code for your own use, although I'd appreciate if you could add a comment below with a link to the resulting webpage.

ANN: Cinfony 0.9 released

The most anticipated software of the year, the one we've all been waiting for, has just been released. But enough about Google Wave - Cinfony 0.9 is now available.

Cinfony allows you to access RDKit, the CDK and OpenBabel from Python (and Jython) all with the same API.

What this all means is that you can quickly get up and running testing out any of these three toolkits. The Cinfony API makes it easy to read in a file and carry out some basic manipulations, and for anything more complicated you still have access to the underlying toolkit. For a complete description, see the docs.

This release supports OpenBabel 2.2.3, CDK 1.2.3 and RDKit Q2_2009.

Running the Windows OpenBabel GUI under Linux on the Windows desktop - Need some Wine?

A friend of mine (Ed Cannon) recently showed me the OpenBabel GUI running on Linux. The surprising thing about this is that OpenBabel currently does not have a Linux version of the GUI (Update 16/Sept/09: Now it does). He was running our Windows release on Linux using Wine, the Windows emulator ("sudo apt-get install wine"). Cool, I thought - I didn't realise that that would even work. Cue blog post.

To get a screenshot I needed Linux. As I described earlier, it's easy (and free) to run Linux on Windows using VMWare Player. This time I installed an Ubuntu 9.04 image. And then (after running "sudo vmware-config-tools.pl") I discovered a new feature called Unity mode. This allows you to use the virtual machine to start Linux applications that appear directly on your Windows desktop (rather than enclosed in a Linux desktop). So I decided to get a screenshot of the Windows OpenBabel GUI running under Wine/Linux together with it running natively on Windows.

The only catch is that I wasn't able to screen capture the Linux application in Windows so in the end, despite all my hard work, I had to Gimp two images together. The resulting image is accurate though, and you can click for a larger version.

Moving to pastures new, but still in the same field

Friday was my last day at the Cambridge Crystallographic Data Centre (CCDC). I've been a postdoc there for the last three years working on the GOLD protein-ligand docking software, specifically on scoring function improvements for virtual screening. It has been a great learning experience, and I've enjoyed working there a lot.

Recently I was awarded my first grant, a career development fellowship from an Irish funding agency, the Health Research Board. From today I will be an HRB Postdoctoral Fellow based in University College Cork (UCC) working on pharmacophore software based on OpenBabel.

I am very grateful to the HRB for giving me to chance to do this, and I'm really looking forward to getting started on this project. It's early days yet, but I am very much interested in collaborations with experimental drug design groups especially those working in the absence of protein structural data (for example, GPCRs). Feel free to drop me an email at baoilleach@gmail.com.

Image credit: Kman999

Now open for submissions - Symposium on Visual Analysis of Chemical Data (ACS Spring 2010)

Second Call for Papers:
Visual Analysis of Chemical Data
239th ACS National Meeting
San Francisco, March 21-25, 2010
CINF Division

Dear Colleagues,

We are now accepting papers for an upcoming symposium focusing on innovative methods for visual representation and analysis of chemical data. Just as Edward Tufte has championed maximizing clarity and information content in statistical graphics, there is a need for methods to display chemical information that will maximize understanding, and allow rapid analysis and decision making.

We invite you to submit contributions that address various aspects of visualization of chemical data (such as structures, SAR data, literature, patents) including, but not limited to, the following topics:

• With an ever increasing pool of descriptors, along with new and more sophisticated machine learning methods, QSAR models are becoming more difficult to interpret. How can information on model reliability, the presence of activity cliffs, and the range of applicability of a model and other relevant model properties be easily depicted?
• Recently, virtual worlds 3D such as Second Life have presented new opportunities and challenges for the representation of chemical data. What is the potential of such a medium in education and communicating with the chemistry community?
• Social software allows for rapid and convenient sharing of chemical data. Examples include Google Spreadsheets, ManyEyes, DabbleDB, and wikis, including Wikipedia. What are the implications for chemical research and education?
• The visualization of the contents of large chemical datasets presents particular problems. How can an overview of the dataset be visualized so that it presents both the nature of the contents as well as the degree of diversity and similarity within the dataset? How can different datasets be visually compared?
• Depicting 3D chemical information in 2D involves a loss of information. However, innovative 2D visualization methods can restore the most relevant information.
• Chemical information comprises a diverse array of data types including chemical structures and diagrams (2D and 3D), associated assay results, conformations, QSAR models and their predictions. The visualization and integration of all these data into a single interface that aids interpretation and analysis is a continuing challenge.

We would also like to point out that sponsorship opportunities are available.

The on-line abstract submission system (PACS) is now open for submissions until 19th October.

Please contact Andrew, Jean-Claude or myself if you have any questions.

Yours sincerely,
Noel O'Boyle

On behalf of the symposium organizers:

Dr. Jean-Claude Bradley,
Drexel University, PA
bradlejc@drexel.edu

Dr. Andrew Lang,
Oral Roberts University, OK
alang@oru.edu

Dr. Noel O’Boyle,
University College Cork, Ireland
n.oboyle@ucc.ie

Image credit: prehensile