Category Archives: crystaleye

Automatic assignment of charges by JUMBO

Posted on January 31, 2008 by pm286

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

Chemistry Repositories

Posted on January 30, 2008 by pm286

Richard Van Noorden – writing in the RSC’s Chemistry World – has described the eChemistry repository project, Microsoft ventures into open access chemistry. This is very topical as Jim Downing, Jeremy Frey, Simon Coles and me are off to join … Continue reading →

Posted in crystaleye, repositories | Tagged , | 1 Comment

Microsoft eChemistry Project and molecular repositories

Posted on December 13, 2007 by pm286

Some of you may have picked up from – e.g. the Open Grid Forum – that Microsoft (Tony Hey, Lee Dirks, Savas Parastatidis) have been collaborating with Carl Lagoze (Cornell) and Herbert van de Sompel (LANL) on bringing together Chemistry … Continue reading →

Posted in crystaleye, open issues | 5 Comments

SPECTRa tools released

Posted on November 30, 2007 by pm286

The SPECTRa tools allow chemists (perhaps group or departmental analytical spectroscopy groups) to submit their data (spectra, crystal structures, compchem) to a repository. From Jim Downing SPECTRa released Now that a number of niggling bugs have been ironed out, we’ve … Continue reading →

Posted in crystaleye, nmr, open issues | Leave a comment

CrystalEye: using the harvester

Posted on November 7, 2007 by pm286

Jim Downing has written a harvester for CrystalEye. I thought I would have a try and see if I could iterate through all the entries and extract the temperature of the experiment. This is where XML really starts to show … Continue reading →

Posted in crystaleye | 1 Comment

CrystalEye and repositories: Jim explains the why and how of Atom

Posted on November 5, 2007 by pm286

Since Atom may not be familiar to everyone Jim Downing has written two expositions on his blog. These explain his thinking of why a series of medium-sized chunks is a better way to support the download of CrystalEye than one … Continue reading →

Posted in crystaleye, open issues | 3 Comments

CrystalEye: request for subsets

Posted on November 5, 2007 by pm286

Egon Willighagen has made a clear and appropriate statement/request of what he would like from CrystalEye: Egon Willighagen Says: November 5th, 2007 at 11:09 am e Depending on the differences between the RAW and COMPLETE CMLs or maybe CIF files, … Continue reading →

Posted in crystaleye, open issues | 1 Comment

CrystalEye and Open Data and Open Notebook Science

Posted on November 5, 2007 by pm286

There has been more interesting discussion on the contents of CrystalEye, derived data, and the concept of OpenData . I shall address some of the issues and welcome more discussion. Since I have been critical of others I am quite … Continue reading →

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CrystalEye and repositories: distribution and integrity (cont)

Posted on November 5, 2007 by pm286

Continuing our discussions on how to disseminate CrystalEye without too much effort or breaking too much. In reading this please remember that CrystalEye – like many bioscience databases – was created as a research project. It had the following aims: … Continue reading →

Posted in crystaleye | 1 Comment

CrystalEye: what should InChIs reference?

Posted on November 4, 2007 by pm286

In response to my post on the technical issues of CrystalEye, Egon has asked about InChIs (see Unofficial InChI FAQ): Egon Willighagen Says: November 4th, 2007 at 1:43 pm eRegarding the InChIs: I would prefer one InChI for each moiety, … Continue reading →

Posted in crystaleye | 2 Comments