Monday 30 April 2007

Adding trackback to a blogspot blog

Until I started blogging, I didn't realise that you could add lots of bells and whistles (aka 'widgets') to your blog that do everything from analyse hits from visitors to allow people to instant message the blogger.

I prefer to keep things simple. However, there is one feature I decided I needed to add to my Blogger blog: trackback. When I refer to someone else's blog post I'd like them to know about it, without me having to post a comment on their blog saying so. Similarly, if others are referencing my post, I'd like to know about it. Trackbacks are the glue that allow readers to follow a topic among multiple blogs. They typically appear as comments on a blog post containing a link to the referencing blog post, as well as an excerpt from the text.

Blogger blogs don't provide this feature, although they do have a related feature which in some ways is more powerful. Since Blogger is owned by Google, it is able to identify any websites that contain a link to a particular blog post and list them under "Links to this post". However, it's not clear whether the link is from a blog, nor is there any summary text included. Trackbacks are active acknowledgements by one blog of its link to another; the Google backlinks are passively harvested from the web.

Outgoing trackbacks can be enabled using the Greasemonkey script by Stephen Weber. When you are creating the blog post, there is a box for entering trackback URLs (typically found at the end of a blog post). To enable incoming trackbacks is slightly more difficult, as it requires the help of a third-party site HaloScan to manage the trackbacks. First you need to create an account. Then you need to manually edit your blog template as described on the HaloScan Forum (your mileage may vary). This adds trackback URLs to the end of your own blog posts allowing others to reference your posts.

Can anyone suggest any other 'essential' blog widgets?

Saturday 28 April 2007

Correction/Retraction Notice

"This article has been corrected, partially retracted or retracted in full. See below for the link to the original article and the correction or retraction notice."

Update: I am continuing to add retraction notices to this blog post

If you are browsing the Table of Contents (TOC) of an ACS journal online, and you come across an article which has subsequently been corrected or retracted, why doesn't the ACS provide a link to the retraction? And similarly, why doesn't the retraction carry a link to the original paper?

Thanks to Chemical Blogspace and my Greasemonkey script, the blogosphere can collectively do what the ACS fails to do. What do I mean? Well, both Peter Murray-Rust and ChemBark have recently blogged about corrections/retractions by Sames and Sezen, so I looked up some of the relevant papers and listed them at the end of this blog post. In a few days time once this post has been absorbed into Chemical Blogspace, if you go to the ACS website to download one of these papers, you should see a CB icon which contains a popup referencing this post. By clicking on the link, you will be directed here and you can search the list below to find the link to the correction/retraction.


Site-Specific Phenylation of Pyridine Catalyzed by Phosphido-Bridged Ruthenium Dimer Complexes: A Prototype for C-H Arylation of Electron-Deficient Heteroarenes
Godula, K.; Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2005; 127(11); 3648-3649.

Selective and Catalytic Arylation of N-Phenylpyrrolidine: sp3 C-H Bond Functionalization in the Absence of a Directing Group
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2005; 127(15); 5284-5285.

Oxidative C-Arylation of Free (NH)-Heterocycles via Direct (sp3) C-H Bond Functionalization
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2004; 126(41); 13244-13246.

Cobalt-Catalyzed Arylation of Azole Heteroarenes via Direct C-H Bond Functionalization
Sezen, B.; Sames, D.
Org. Lett.; (Letter); 2003; 5(20); 3607-3610.

Diversity Synthesis via C-H Bond Functionalization: Concept-Guided Development of New C-Arylation Methods for Imidazoles
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Article); 2003; 125(35); 10580-10585.

Selective C-Arylation of Free (NH)-Heteroarenes via Catalytic C-H Bond Functionalization
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2003; 125(18); 5274-5275.

C-C Bond Formation via C-H Bond Activation: Synthesis of the Core of Teleocidin B4
Dangel, B. D.; Godula, K.; Youn, S. W.; Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2002; 124(40); 11856-11857.

C-C Bond Formation via C-H Bond Activation: Catalytic Arylation and Alkenylation of Alkane Segments
Sezen, B.; Franz, R.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2002; 124(45); 13372-13373.

Added 01/06/07A Protein Folding Degree Measure and Its Dependence on Crystal Packing, Protein Size, Secondary Structure, and Domain Structural Class
Estrada, E.
J. Chem. Inf. Comput. Sci.; (Article); 2004; 44(4); 1238-1250.

Wednesday 25 April 2007

CIA on the move

If, like me, you like to keep up to date with CVS or SVN commits from SourceForge via RSS (rather than emails), you are probably tracking commits using CIA. This is a amazing light-weight website created by Micah Dowty.

This post is just to let you know that you should update your bookmarks; CIA has moved from to (where 'vc' stands for version control). Over the last few months, the ability to add metadata has been made easier, so that you can jazz up your personal and project websites on CIA with a nice photo or logo too.

Tuesday 24 April 2007

Chemical textbook blogging

By way of Peter Murray-Rust's blog (whom it's great to see back blogging), I came across a link to a Reactive Reports interview with Steve Bachrach who is the process of publishing a textbook entitled "Computational Organic Chemistry". One of the most interesting aspects of the discussion is that in order to keep readers of the book up to date, he has started a blog. Presumably, this will also form the basis of a subsequent edition of the textbook.

Blog entries on particular topics include full literature references with DOIs, as well as molecular citations using InChIs. If Egon adds this blog to Chemical Blogspace, it will be a valuable source of information for annotating molecules (via the InChI) and papers (via the DOI, and the Chemical Blogspace Greasemonkey script).

I wonder if the text of Open Access journal articles can be mined in the same way by Chemical Blogspace? This would allow users, while browsing the table of contents pages of any journal, to see whether any Open Access articles cite it, and to see the relevant quotes from that article.

Wednesday 4 April 2007

And so it begins...

I've decided to join the ranks of blue obelisk bloggers (bloblogs?) after realising that it gives me an excuse not to update my webage. I'll be talking about open chemistry software, and various random codings I'm involved in. Over at my sister publication, Paper Cuts, you can read some reviews of cheminformatics papers in the literature.