Monthly Archives: November 2007

Talks on Open Notebook Science

Posted on November 5, 2007 by pm286

Two impressive blog posts from Cameron Neylon on Open Notebook Science: Talks on Open Notebook Science – some initial thoughts 13:44 05/11/2007, Cameron Neylon, cansas, open notebook science, us trip oct/nov 07, Science in the open So I have given … Continue reading →

Posted in open notebook science | Leave a comment

Open NMR: How good is the prediction?

Posted on November 5, 2007 by pm286

Egon asks about the quality of the prediction: Egon Willighagen Says: November 5th, 2007 at 5:58 pm e Peter/Henry, I was wondering about the carbon shifts for atoms in an aromatic ring? Can the QM method you are using work … Continue reading →

Posted in nmr | 3 Comments

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 →

Posted in crystaleye | Leave a comment

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

Is science copyrightable?

Posted on November 4, 2007 by pm286

I have been jolted into wondering whether scientific publications are actually protectable by copyright. I’m almost certainly wrong, but here’s my little journey. I found Tim O’Reilly (et al.): Publishing Digital Fair Use 23:26 03/11/2007, Peter Brantley, Planet SciFoo: Fair … Continue reading →

Posted in open issues | 5 Comments

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

CrystalEye and repositories: distribution and integrity

Posted on November 4, 2007 by pm286

Andrew Dalke has raised two useful issues and I will address them separately. The first is about integrity of a repository (I will start using that word rather than database). Andrew Dalke Says: November 4th, 2007 at 2:19 am eDuring … Continue reading →

Posted in crystaleye | 1 Comment

CrystalEye: data loss and corruption through legacy files

Posted on November 4, 2007 by pm286

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