Monthly Archives: September 2006

OSCAR, the chemical data checker

Posted on September 17, 2006 by pm286

I spent yesterday reviewing the data in BJOC (the Beilstein Journal of Organic Chemistry) (articles). This is a new (ca. 1 year) and important journal as it is the first free-to-author and free-to-read journal in chemistry, supported by the Beilstein … Continue reading →

Posted in chemistry, open issues | 6 Comments

Linus' Law and community peer-review

Posted on September 17, 2006 by pm286

Linus Torvalds of Linux fame is creand dited with the law “given enough eyeballs, all bugs are shallow” In a communal Open Source project every developer and every tester (or user when the code is released) can contribute bugs to … Continue reading →

Posted in "virtual communities", open issues | Leave a comment

GIFs and other horrors

Posted on September 16, 2006 by pm286

The GIF (and its extended family of PNG, JPEG, TIFF, BMP, etc.) are major destroyers of scientific data. This post shows why they should be avoided for much scientific data. (The GIF has additional infamy through the patent fiasco). In … Continue reading →

Posted in chemistry, general | 5 Comments

Useful Chemistry: Publish and be…?

Posted on September 16, 2006 by pm286

It was great to meet Jean-Claude Bradley, the guru of the Useful Chemistry blog at the Am. Chem. Soc meeting. The Useful chemistry blog has a remarkable and valuale feature – J-C publishes chemistry as it is being done. To … Continue reading →

Posted in "virtual communities", chemistry, open issues | Leave a comment

The Blue Obelisk: A volunteer!

Posted on September 16, 2006 by pm286

I flew back from SF to Heathrow yesterday and, as usual, was hacking on the laptop (with difficulty as Virgin doesn’t seem to give enough space to open a laptop). After a while my neighbour (S) asked: S: “do you … Continue reading →

Posted in "virtual communities", programming for scientists | 2 Comments

Blue Obelisk Award – Geoff Hutchison of OpenBabel

Posted on September 14, 2006 by pm286

A major problem in chemistry is that there is a plethora of file formats and it continues to get worse. Each manufacturer thinks they are the centre of the world and everyone else will use their approach. So they make … Continue reading →

Posted in "virtual communities", chemistry | 2 Comments

Blue Obelisk Award – Christoph Steinbeck of CDK

Posted on September 14, 2006 by pm286

Last night we met at the Thirsty Bear pub in San Francisco. This was the second anniversary of the first BO meeting (in San Diego). There were nine of us, and the membership and programs are growing. People are taking … Continue reading →

Posted in "virtual communities", chemistry, open issues | Leave a comment

Blue Obelisk Award – Bob Hanson of Jmol

Posted on September 14, 2006 by ojd20

The Blue Obelisk Open Source group has now achieved a critical mass of high quality software, especially in chemoinformatics, chemical text analysis, editing and infrastructure such as markup languages (CML). We are begginning to be taken seriously and more collaborators … Continue reading →

Posted in chemistry, open issues | 2 Comments

Open Data – the time has come

Posted on September 12, 2006 by pm286

The term “Open Data” is now becoming commonly used and we (Blue Obelisk) are trying to define it (our mantra being ODOSOS. Open Data, Open Source, Open Standards). It was not commonly used two years ago although the concept is … Continue reading →

Posted in open issues | 8 Comments

Do you read journals, or "use a database"?

Posted on September 11, 2006 by pm286

We had a reception for the Chemical Information Division of the American Chemical Society last night and I spent a considerable time talking with several staff in the publications side of the Society. (I am not attributing personal views in … Continue reading →

Posted in open issues | 7 Comments