Genome: check

I decided I had better add something to the giant cell to represent the genome, even if only on a temporary basis while I delve further into the literature. The blue DNA loops are sculpted prims made in SL with Cord Maker though I suspect I could have done the lot on New World Grid with the Devi sculpted prim gadget.

If you play with the lighting, it starts to look quite steampunk-ish. Of course, what it doesn't show is the intensity of the motion, even in such a crowded space. I have yet to grapple with that.

Once more unto the mesh, dear friends...

The New World Grid is now running a small beta grid with the newly released OpenSim 0.7.1. This includes both shared media and the early version of mesh shortly to be updated by Linden Lab. The picture shows a mesh molecule I made previously in SL and behind it a mesh of the building I work in. The latter was downloaded from the Google 3D Warehouse whence I assume it derived from some Google Earth-related building initiative.

I'm using Kirsten's S21(r7) for this and the whole thing's a little hit-and-miss, not least at my end. It will be interesting to see what innovations emerge on the back of this (rather protracted) development.

Adding a few (thousand) proteins to the giant cell

This is a minor update to show what 4000-ish average sized proteins (red spheres) look like when added to the slice of the giant TB cell. There should, of course, be some in the area of the nucleoid but I haven't worked out how many, nor what to do with them. That sounds lame but is actually the process I am undertaking, a journey that will take wrong turns at times. The aim overall is to provide a context for asking interesting questions, not least how Mycobacterium tuberculosis and Escherichia coli are likely to differ.


The grey structure in the closeup is the viewing platform. The prims themselves are non-randomly distributed, being linksets of 250 prims shift-copied and rotated/moved slightly in situ. Having them linked should hopefully make them easier to rez on demand. Overall, this is a useful shortcut for what is basically a feasibility study. More anon.

First visit to the giant TB cell

There are lots of eukaryotic virtual cells in Second Life (Max Chatnoir has a nice one, formerly on Genome and now on an adjacent sim) and last week I found them on ReactionGrid as well (Anatomy World region). What I'm trying to do here, however, is to give some immersive feel for the actual composition of the cell rather than just do a straightforward show-and-tell (though there is some of that too). This sounds intrinsically more demanding and in some ways it is, especially for bacteria where the small size makes it harder to resolve the detail.

There are, in fact, plenty of relevant numbers available although not that many for Mycobacterium tuberculosis so I will be employing a degree of "poetic" licence. Futhermore, the numbers may vary not only between species but between physiological states as well, not to mention between sources. Two useful websites at least got me starting to think in this context: BioNumbers and CyberCell from which the former draws some of its bacterial data. CyberCell in particular provides a useful compendium of Escherichia coli statistics though it would be nice if they linked directly to the source. Finally, there is a French group constructing a non-immersive model of the same species which can be visualized using a custom viewer called LifeExplorer. They published an interesting paper last year (paywalled, I suspect).

In the first instance I am constructing a 50 nm slice of the rod-shaped cell based in part on a recent transmission electron microscopy paper (paywalled). In the picture above you can see ribosomes (cyan spheres) as well as an average size protein (red sphere) and a much larger proteasome (green cylinder), both randomly positioned. The orange region at the centre is the location of the nucleoid and the long magenta filament is mRNA. The number and location of the ribosomes is roughly consistent with the paper though I suspect there are a few too many.

There is clearly a long way to go and this is just a token start compared, say, to the wonderful work of David Goodsell. That said, the build provides an interesting context in which students visualize key processes at multiple scales and in both static and, ultimately, dynamic modes, as well as learn about microscopy. The advent of mesh should hopefully add further visual interest.

If you build it, will they find it?

Firstly, I should point out that I haven't finished building -- I've barely started. That said, the issue of discovery is not insignificant. The Hypergrid is making inter-grid travel somewhat easier and that raises the issue of knowing where to go. The Welcome region on New World Grid showcases some of the best sims, several of which are intended, like mine, for educational use. Likewise I am sure there are regions on jokaydiaGRID and ReactionGrid that are of interest to educators and their students, if only to illustrate the range of pedagogic approaches that are being used. In all likelihood there are many more grids and sims of which I know little or nothing at all (I have not been to the regions owned by the universities and colleges hosted on the New Zealand Virtual World Grid, for example).

Putting together a search engine to help find content was very simple as it used only web sites, not inworld content. By comparison, finding educational grids and regions addressing particular subjects is much harder. Maria Korolov at Hypergrid Business has compiled the invaluable Hyperica directory and there is a list of grids at opensimulator.org as well. The inevitable lack of detail, however, is discouraging and my guess is that both represent a small fraction of educational use of OpenSim. Moreover, as many people build for their own use and interest, there is little incentive to rectify matters.

With a view to kindling a degree of enlightened self-interest, I have put together a region map gadget as shown in the image. If you put landmarks for the featured areas in your region into the map inventory and reset scripts, it will display the region map tile and generate pins with hovertext and sit teleports. If you add brief descriptions, these will be chatted to the user on touch. However, if the owner touches the pin, it also creates a notecard with appropriate wiki-formatted text for TiddlySpace. At the moment there is no connection between the inworld gadget and the web but I expect this to change in the future. Incorporation of http-in functionality going in the other direction is also a possibility.

Will this idea catch on or will we see the incorporation of hooks for more conventional search engines? Are the HyperGate networks and hgurl indicator boards all that are required? For that matter, would TiddlySpace scale? Finally, if our future experiences are to be increasingly based on HTML5, then maybe it will be the associated web-based text that makes sims discoverable. Time will tell.

(Thanks to Miley for her cam skills in generating the region map which I used in place of the default map tile)

Playing with OpenSim search and trails

Firstly the good news. I put together a Google Custom Search Engine (CSE) so people can find free content more easily on five of the web-based stores that have come online recently. Yes, it was very simple to do but that's how it should be.

In the "watch-this-space" department, I have also been playing with the super-amazing TiddlySpace again. The aim originally was to generate search results that another Google CSE could index but that seems to be problematic (and, given the dynamic nature of TiddlySpace and its increasing focus on the social, I'm not surprised). Nevertheless, I've made a start at generating records for OpenSim grids, regions, builds and trails that might be of use to educators. The seriously smart aspect of TiddlySpace is that it lets you "include" spaces (sites comprising multiple knowledge chunks known as tiddlers, if you prefer). Each of the spaces above (grids, et seq) inherits from the preceding one and, more to the point, can be "included" in other people's spaces too. Moreover, when I update mine, their space changes too. Of course, you do have to trust me...

The trails are slightly awkward to code (not to mention that I'm severely out of practice) but basically comprise a series of locations together with "secondlife://" style Hypergrid links. You copy and chat these links in your browser (Imprudence, for example) , then click the link generated in chat history and, whoosh, you are teleported to your destination. There is slightly more to it that that, needless to say, but I am using the "broad brush" here!

The links themselves are picked out from the (included) region record by a process known as tiddler transclusion -- hence the slight awkwardness (you can see the code simply by double-clicking the tiddler). The big benefit over conventional wikis, of course, is that a change in one place is automatically propagated through all the tiddlers. Doubtless a skilled TiddlyPerson could also work out ways to simplify matters further. If you want to edit a tiddler you own, just double-click it, make the changes and then Ctrl-Enter to save. There are icons to help you too but the actual editing involves wiki-style text formatting so it's not necessarily for those who depend entirely on WIMPs.

Of course, it's very early days but I'm fairly encouraged, even in the absence of a CSE. It's great to have a couple of open source projects play nicely together. You can see the OpenSim-trails space here. It's very crude but nevertheless, I think, an intriguing approach.

In which I am unwisely invited to pontificate

OpenSim: an Educator's Perspe...

More PowerPoint presentations from Peter Miller

There have been some great OpenSim presentations recently, including a couple from Diva Canto and Fleep Tuque. I gave my first ever RL pitch on the topic today at a JISC West Midlands RSC meeting in Coventry. I don't think I got the tone quite right and, as predicted, I ran short on time (I inserted a simonastick demo at the start which didn't exactly help). Nevertheless, it was great fun for me and many thanks to Jane for the invite and marvellous to see other folks from my SL friends list, including Annabeth (a tough act to follow!), Dave, Mark, Rob and "Tim", inter al. Annabeth also covered Unity3D and, for completeness (!), there was a nice blog on this recently by ArianeB.

Anyone who gets as far as the final slide of my presentation will see my concluding that OpenSim is "just about" ready for the big-time (I will, of course, be using it but I am small-time). I should qualify that by saying that I'm still using 0.6.9 at present for most things (NWG is about to move to 0.7.0.2) and that just this week 0.7.1 emerged (along with a new Diva Distro) so YMMV. That said, I still think that getting the hardware matched to the class size is a critical step. I also want to thank Pathfinder for his many great Hypergrid "finds" via the HGAC.

The slides have got multiple links that are unpacked via multiurl. Just bear in mind that the /l/ is a letter L (for list) and the O, as you might imagine, is the capital letter.

The (Not So) Faraway

AM Radio recently announced that his sojourn in Second Life (and virtual worlds in general) is drawing to its natural close. His builds are tremendously atmospheric and I was delighted to discover that OpenSim Creations has a CC licensed version that you can download and install on a USB stick. Much kudos to V at OSC for providing this.

Another landmark of note: OpenSim 0.7.1 was released today. Many thanks to all the hard-working developers for their sustained efforts in bringing this to fruition. Much to admire about this release and an important milestone for educators with shared media on a prim a notable addition.