The Computational Infrastructure for Geodynamics

While reading a recent issue of Eos, I came across The Computational Infrastructure for Geodynamics (CIG)

… a membership-governed organization that supports and promotes Earth science by developing and maintaining software for computational geophysics and related fields.

According to their Web page, CIG consists of:

• a coordinated effort to develop reusable, well-documented and open-source geodynamics software
• the basic building blocks — an infrastructure layer — of software by which state-of-the-art modeling codes can be quickly assembled
• extension of existing software frameworks to interlink multiple codes and data through a superstructure layer
• strategic partnerships with the larger world of computational science and geoinformatics
• specialized training and workshops for both the geodynamics and larger Earth science communities

As of this writing, CIG has seven working groups:

• Mantle convection
• Long-term crustal dynamics
• Computational science
• Short-term crustal dynamics
• Geodynamo
• Computational seismology
• Magma migration

With these working groups providing the focal point, CIG facilitates events (such as workshps) and software coordination. There is already an impressive software repository (with additions to the geodynamo area imminent). In addition to the Web site, there are a number of mailing lists available.

Based on my cursory look, I have a few comments to share:

• Although frameworks such as ESMF are mentioned on a links page, it doesn’t appear that there is any related CIG-ESMF engagement. Further investigation is likely required.
• I’m keen to understand how the term geoinformatics is defined by CIG. I expect it relates more to GIS and related disciplines in surveying and space-science engineering. It’s for reasons like this, I referred to the new geoinformatics in a recent paper. Again, further research is required.

Google Notebook: A Tool for Annotation

According to one source, “… annotation means adding information (such as notes, commentary, links to source material, and so on) to existing web-accessible documents without changing the originals.”

Wikipedia defines it this way: “Annotation is extra information associated with a particular point in a document or other piece of information.”

My introduction to the term occurred when I worked for Platform Computing. While I was there, we worked on several projects whose aim was to annotate genomes.

Later on, working with Keith Aldridge of York University, I became interested in annotating data from The Global Geodynamics Project (GGP). Briefly, GGP data is collected by instruments called Superconducting Gravimeters (SGs). These instruments are incredibly sensitive to relative changes in Earth’s acceleration due to gravity. GGP is in fact a network of SGs that are distributed across the planet. Each instrument, each month provides three data files:

• Gravity and pressure data – The primary observables sampled regularly in time
• Auxilliary data – Complimentary observables (like groundwater levels) sampled regularly in time
• Log data – Other observables (like service events) that occur at irregular intervals

When Keith and I first started work on introducing an XML-based data model for the GGP, we thought it made sense to automatically represent each of these files separately, and then combine them using XIncude or XSLT. (This XML-based data model is described in detail elsewhere.) After additional exposure to the XML spectrum, XPointer emerged as another option. (I alluded to this in a follow-up paper with Keith.) XML Pointer Language (XPointer) is “… the language to be used as the basis for a fragment identifier for any URI reference that locates a resource …” It’s not by coincidence that the Wikipedia definition for annotation reads similarly to this definition of XPointer from the W3C. XPointer is the W3C’s vehicle for annotation.

It’s still my take that adoption of XPointer is rather slow. For example, the only Web browser that I know of that supports annotation is the W3C’s Amaya. When browsing annotated Web pages with Amaya, clickable icons of pencils provide a link to the annotations.

The utility of annotations, taken together with the poor adoption of XPointer in mass-market Web browsers, makes for exciting possibilities for Google Notebook. What follows are a few data points on Google Notebook:

• “Google Notebook makes web research of all kinds – from planning a vacation to researching a school paper to buying a car – easier and more efficient by enabling you to clip and gather information even while you’re browsing the web.”
• Google Notebook lives in your Web browser
• Google Notebook organizes, in an easily accessible way, your Web findings
• Google Notebook is accessible from any Internetworked computer
• Google Notebook is another prototype emerging from the Google Labs
• Google Notebook is searchable (of course, doh!)
• Google Notebook is publishable – click here for an example

In other words, Google Notebook is a tool for annotation!

Enthusiasm aside, I must note that:

• Google Notebook is not standards based – I assume it’s based on proprietary Googleisms, but this requires further research (Please see the comments on this post for additional dialog on this point.)
• Google Notebook is not a fragment identifier – The degree of granularity is the Web page itself, not a fragment on a Web page
  (Please see the comments on this post for additional dialog on this point.)
• Google Notebook is targeted at Mozilla Firefox only – It’s enabled as a plugin (Please see the comments on this post for additional dialog on this point.)
• Google Notebook makes use of a simple model of authentication – Username and password form the basis
• Google Notebook doesn’t allow for Access Control Levels (ACLs) – Published notebooks are accessible by anyone who picks up on the lengthy, randomly generated URL

On balance, Google Notebook is useful, and allows for an excellent introduction to annotation. I highly recommend investigating Google Notebook, and providing your feedback to Google on it.