Category Archives: programming for scientists

OPSIN/OSCAR: you + us = we; please help

Posted on October 14, 2007 by pm286

I’m exploring how you and we may be able to work to improve OSCAR and OPSIN. Even if you aren’t interested in chemical names, you may find the general principles useful. One of the drawbacks of full Open Source and … Continue reading →

Posted in chemistry, open issues, oscar, programming for scientists, XML | Leave a comment

Open NMR

Posted on October 13, 2007 by pm286

As I have already blogged (WWMM calculation of spectra) we are hoping to provide Jean-Claude Bradley and others an Open service to calculate NMR spectra from structure. This  needs a lot of software components and a lot of glueware. With … Continue reading →

Posted in blueobelisk, nmr, open issues, open notebook science, programming for scientists, theses | 6 Comments

Dave Martinsen reviews ACS and Greasemonkey

Posted on August 15, 2007 by pm286

Noel O’Boyle has highlighted a review by Dave Martinsen of the American Chemical Society. Dave has been very supportive of the new technologies and ideas that are emerging and has run sessions at the ACS meetings highlighting them. Here he … Continue reading →

Posted in data, open issues, programming for scientists | 1 Comment

scifoo: academic publishing and what can computer scientists do?

Posted on August 14, 2007 by pm286

Jim Hendler has summarised several scifoo sessions related to publishing and peer-review and added thoughts for the future (there’s mote to come).  It’s long, but I didn’t feel anything could be selectively deleted so I’ve left only the last para, … Continue reading →

Posted in cyberscience, programming for scientists, scifoo | Leave a comment

Chemistry in MathML and CML – comments?

Posted on July 3, 2007 by pm286

[warning – WordPress is not very math/chem friendly so forgive formatting] Michael Kohlhase and I are trying to come up with a synthesis of MathML and CML for representing the numerical aspects fo chemistry. By chance we have started with … Continue reading →

Posted in chemistry, mkm2007, programming for scientists, XML | 2 Comments

MathML and CML communities

Posted on July 2, 2007 by pm286

I was delighted to meet old friends from the MathML/OpenMath community last week at Mathematical Knowledge Management 2007 – Patrick Ion, Robert Miner, James Davenport and Michael Kohlhase (apologies to any I have omitted). OpenMath (1993) was one of the … Continue reading →

Posted in chemistry, mkm2007, programming for scientists, XML | Leave a comment

Synergy between "MKM"-math and "CML"

Posted on June 28, 2007 by pm286

In this post I am using the context of the Mathematical Knowledge Management 2007 conference to try to construct similarities in the MathML and CML communities and their thought processes. I’ll show this list in my presentation tomorrow – I … Continue reading →

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CML on ICE – towards Open chemical/scientific authoring

Posted on June 23, 2007 by pm286

Because WWMM had outages my blogging is behind and I’d written a post on Peter Sefton’s ICE. Peter and I met at ETD2007 and immediately clicked. But WWMM went to sleep and I haven’t reposted. Peter has beaten me to … Continue reading →

Posted in "virtual communities", blueobelisk, chemistry, data, etd2007, programming for scientists | 2 Comments

The soul of the Blue Obelisk

Posted on May 30, 2007 by pm286

There has been a discussion on the Blue Obelisk mailing list about whether we should move the mailing list to Google to attract the less geeky community. I drafted a contribution to this discussion and then felt it would be … Continue reading →

Posted in blueobelisk, programming for scientists | 1 Comment

Bioclipse – Rich Client

Posted on May 25, 2007 by pm286

I’m at the Bioclipse workshop in Uppsala – excellently run by Ola Spjuth and colleagues. Rich clients – where the client has significant functionality beyond the basic browser – are critical for the interchange of scientific information. A typical example … Continue reading →

Posted in blueobelisk, chemistry, data, programming for scientists | Leave a comment