Cyclone Peter Murray-Rust moves away from Toowoomba. Cleanup continues.

Last week we hosted Peter Murray-Rust in Toowoomba. The ICE team have been busy getting ready for some other visitors, so I have not had time to write about the visit. Peter has blogged about his stay a few times, describing it as intensive talk and hacking. Intensive indeed.

He talked about ICE emphasis is mine:

Ive had the chance to look closely at ICE: The Integrated Content Environment- an authoring environment for academic material. USQ eat their own dog-food and over 100 academic staff at USQ use it routinely for authoring their course material. USQ is very committed to high-quality distance education – they have an impressive enrollment from overseas and they put a lot of work into the material which supports it. So their material can be repurposed as notes, lecturers copies, slides, summaries, etc. All this is managed through stylesheets – which are the key to ICE. The content is written once but delivered in many ways. Because the material is in XML it is also possible to amend it with XML-aware tools or to generate new material programmatically. A key aspect is that the structure of the document(s) can be managed in XML. So I am now convinced that for academic work it is (a) fit-for-purpose (b) reconfigurable (c) powerful. Its still early-adopter for theses, but as it can do so many new things I cant see any real competition.

http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=982

Here’s a quick summary of what the ICE team did with Peter on his visi.

We introduced Peter to ICE, and showed him how to blog with it. We’ll be very interested in feedback on this, does it work? Is it better for some posts than the WordPress editor? If so, which types of post? We’ll also try some other collaboration with Peter & team.

Oliver Lucido extended our work on embedding Chemical Markup Language (CML) into publications. CML lets your describe molecules and reactions and the like. We’ve come a long way since my first post on CML last year. You can now put a CML file into your working directory, and ICE will turn it into a variety of formats for you automatically. See Daniel’s screencast. Now we start to think about similar services for other disciplines, drop me a line or comment here if you have any suggestions.

Also related to CML, PMR is interested in being able to create what he calls a data overlay journal, taking bits of data gathered from various publications and aggregating them by type. So Ron Ward worked on something that turns ATOM feeds with chemistry in them into OpenDocument Format documents. Peter seemed pleased with the results, which are really just a proof of concept for now. Using Ron’s new code we scraped some data from the Crystaleye service, turned into an ODF, then PMR sent it to his blog over the Atom Publishing Protocol. You can’t see the PDF version just yet, or interact with the molecules via JMOL but we’ll sort that out soon. (When I say ‘we’ obviously I mean Oliver.)

We’re wondering if this might be useful in other situations, like for celebrity bloggers who want to turn their blog into a book. Point it at a feed of the relevant content and it will put it into a word processing format you can edit and send off to a publisher. Might also be useful when quoting web material. Me, I’d like to be able to get hold of posts from sources that I quote often in ODF rather than having to copy and paste HTML and re-style it.

Peter supplied a chemistry thesis and with a bit of word processor magic, I broke it up into a number of chapters which we fed into ICE. Daniel de Byl did a bit more work to fix up some character encoding issues. Oliver worked with Peter to find the chemistry that’s embedded in the thesis, which is authored using an application called ChemDraw. Peter has some code that can break open the proprietary ChemDraw format and extract open standard CML, and Oliver was able to hook this in to ICE to automate the process: find the ChemDraw pictures, turn them into CML and then re-render molecules using non-proprietary open source software. Still a lot of rough edges, but when Daniel’s back from a break in a couple of weeks we will show how ICE can be used to create a thesis in both HTML and PDF with the data linked-in and machine accessible.

Peter gave a spirited and inspiring performance of his genre of talk, this time on semantic publishing. I see lots of potential for the semantic web in some domains, particularly where the data are very bounded and structured like chemistry. But rather than trying to deal with the huge mess of unstructured data out there, the ICE team try to find or create the right tools to help people create a huge mess of structured data, with some semantic information embedded. It’s slow work, but PMR thinks 2008 is the year some of this will start to break out of the labs.

Peter presents using his presentation toolkit, which contains lots of material on a range of topics which he jumps around during the talk.

I gave my talk in HTML as normal – a series of ca. 100 major topic with 2-20 slides under each. I select each slide as I go along and stop at the time limit. At least this means I never overrun. The system has evolved over the years and now has a vertical menu for each topic and a horizontal one within the topic.

http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=960

I have been looking at how we might be able to capture Peter’s slides in ICE, and provide an interface that can assemble them into presentation packages (not necessarily linear). One thing that would be nice is for the slides themselves to have some notes. I’m going to see if we can do something like the ICE brochure where there is a document you can read, with a slide presentation that is automagically derived from it.

I was feeling a bit weathered after all of that hence the title of this post.

I was curious about cyclone naming. Turns out that Pete is on the list for a cyclone in the Brisbane region. The way I read it, it’s about 40th on the list. Found this:

Requests by the public for tropical cyclone names

The Bureau of Meteorology receives many requests from the public to name Tropical Cyclones after themselves, friends, etc. The Bureau is unable to grant all these requests as they far out-number the number of Tropical Cyclones that occur in the Australian region.

The Bureau will only accept requests received in writing (not e-mail). The request cannot be immediately granted but the name will be added to a supplementary list. When a name is retired of similar gender and initial, a name can be included from this supplementary list (subject to checks to ensure it is not on the Southern Hemisphere retired name list or offensive in any of the languages of our intern ational neighbours.)
Note that it can take many decades for a suitable slot to become available, then a further 10-20 years for the names to cycle through, so it is likely to be well over 50 years before your requested name is allocated to a cyclone.

http://www.bom.gov.au/weather/cyclone/about/cyclone-names.shtml