Author Archives: pm286

Pubchem and Thomson – two cheers

Posted on November 8, 2006 by pm286

Noted in Peter Suber’s Blog: Additional 2.2 Million Structures Now Searchable in Freely Available Database Thomson Scientific, … provider of information solutions to the worldwide research and business communities, today announced the deposit of 2.2 million chemical structures from Thomson … Continue reading →

Posted in chemistry, open issues | 4 Comments

Mystery Molecule!

Posted on November 7, 2006 by pm286

This is a detective story. If you know the answer, please don’t reveal it (though I’d be pleased that you announce that you know it). (Anyone remember when Psycho came out? Hitchcock made the audience promise not to tell). Many … Continue reading →

Posted in chemistry | 8 Comments

"Open Data" on Wikipedia. Bloat and NOR?

Posted on November 7, 2006 by pm286

Latest report on the Open Data entry on Wikipedia – we are starting to get contributions. Remember always that WP is ours, not mine. And that it”s an encyclopedia, not a platform. This post is just to show how things … Continue reading →

Posted in "virtual communities", open issues | 1 Comment

Blogs as scholarly record? Should we reposit them?

Posted on November 6, 2006 by pm286

Blogs are increasingly becoming the grey literature of our time, and at least some may need preservation. I use this blog for many semi-reputable activities – an open notebook of thoughts – a means of presenting talks and snapshots of … Continue reading →

Posted in general | 3 Comments

Open Electronic Theses – should be simple…

Posted on November 4, 2006 by pm286

Theses are one of the most concentrated and valuable ways that science is published. Yet they could be so much more valuable. There a a few hurdles to overcome… From Peter Suber’s blog: Effective today, the University of Tasmania will … Continue reading →

Posted in open issues | 1 Comment

WordPress – help!

Posted on November 2, 2006 by pm286

This blog is now about 2 months old and I’ve made 70 posts. I have done all my editing with WordPress, the software that publishes this blog. Some things work well, others are driving me wild (and actually stopping me … Continue reading →

Posted in general | 4 Comments

"Open Data" Wikipedia NPOV, three revert, etc.

Posted on November 2, 2006 by pm286

The “Open Data” article on WP has already had useful attention from Wikipedians. Some minor typo corrections (and many WPians devote much energy to this, including developing bots). My reference numbering was a mess since I didn’t know WP had … Continue reading →

Posted in "virtual communities", open issues | 3 Comments

Creating "Open Data" on Wikipedia

Posted on October 30, 2006 by pm286

In an earlier post I mentioned that I was going to start an article on “Open Data” on Wikipedia. This is a blow-by-blow account (a few technical details are omitted). Do not be afraid. (I used to be afraid, but … Continue reading →

Posted in open issues | 1 Comment

Enjoyable version control with the Tortoise

Posted on October 30, 2006 by pm286

Update, merge, test, add, update, commit… that’s what I do when working in a communal software project. Update, merge, test, add, update, commit… So I’ve written some additional tests for JUMBO. Now I have to save them and share them … Continue reading →

Posted in programming for scientists | Leave a comment

Unit tests or get a life

Posted on October 29, 2006 by pm286

My unit tests have taken over my life this weekend. This post is a brief respite… Unit tests are one of the great successes of modern approaches to programming. If written briefly about them before and Egon has an introduction … Continue reading →

Posted in programming for scientists | 3 Comments