Category Archives: chemistry

Working with the NCI

I was intending to blog about our collaboration with Dan Zaharevitz and colleagues at the National Cancer Institute in the DTP (Developmental Therapeutics Program). Dan beat me to it: in a CMLBlog comment (February 4th, 2008 at 5:02 pm e) … Continue reading

Posted in chemistry, XML | Tagged , , , , | 2 Comments

Automatic assignment of charges by JUMBO

Egon has spotted a bug in our code for assignment of charges to atoms: Why chemistry-rich RSS feeds matter… data minging, The example shown by Peter was nicely chosen: something is wrong with that example. It uncovers a bug in … Continue reading

Posted in chemistry, crystaleye | 6 Comments

Semantic Chemical Computing

Several threads come together to confirm we are seeing a change in the external face of scientific computing. Not what goes on inside a program, but what can be seen from the outside. Within simple limits what goes on inside … Continue reading

Posted in chemistry, programming for scientists | Tagged , , , | 1 Comment

Does the semantic web work for chemical reactions

A very exciting post from Jean-Claude Bradley asking whether we can formalize the semantics of chemical reactions and synthetic procedures. Excerpts, and then comment… Modularizing Results and Analysis in Chemistry Chemical research has traditionally been organized in either experiment-centric or … Continue reading

Posted in chemistry, data, open notebook science | Tagged , , | 8 Comments

Is the scientific archive safe with publishers?

“In the pipeline” is an impressive and much-followed part of the chemical blogosphere. I’m a bit late on its post Kids These Days! which deals in depth with a case (Menger / Christl pyridinium incident) of published scientific error. The … Continue reading

Posted in chemistry | Tagged , | 3 Comments

Open Data: publishers are the problem

The Chemspider site and blog have been making rapid and valuable progress towards Open Data. This is particularly laudable for a commercial site where Openness in chemistry is a long way from being a proven business model and is actively … Continue reading

Posted in chemistry, open issues | 3 Comments

Open Access – Chemistry World reviews the dilemma

In this month’s Chemistry World (a magazine from the Royal Society of Chemistry) there is an important article by Rebecca Trager (US) reviewing the increasing fission within the chemistry publishing community: Chemistry’s open access dilemma   This was a commissioned … Continue reading

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Dog food is tasty!

I can’t escape… I have committed myself publicly. Here’s Peter Sefton:  Crossing curation mountain I’m looking forward to seeing Peter Murray Rust eat my dog food. He’s lucky cos at our place the hounds eat relatively benign dry food. […] … Continue reading

Posted in chemistry, open issues, XML | 1 Comment

CrystalEye: data loss and corruption through legacy files

Andrew Dalke raised the issue of data corruption: Andrew Dalke Says: November 4th, 2007 at 2:32 am e PMR: Moreover crystal structures contain problems such as disorder and partial occupancy which are impossible to hold in an SDFile as far … Continue reading

Posted in chemistry, crystaleye | 8 Comments

COST D37 Meeting in Rome

Tomorrow Andrew Walkingshaw and I will be off to Rome for the COST D37 Working Group. From the site: What is COST? COST is one of the longest-running instruments supporting co-operation among scientists and researchers across Europe. COST now has … Continue reading

Posted in chemistry, data, XML | 2 Comments