Glycolysis, now with added molecules

I blogged previously about using the Mycobacterium tuberculosis maps from Bernhard Palsson's group to make a small metabolic browser. Somewhat inevitably and only thanks to Hiro Sheridan's Orac rezzer and Troy McLuhan's holo-emitter, I have now added some molecules, namely for glycolysis. As per the green prims previously, they rez dynamically as you change "page" on the browser. I'm sure this can be done better (there may well be errors too) but it's a start.

Mycolic acid is our foe

This is the lipid that forms the waxy outer membrane of Mycobacterium tuberculosis and underpins its ability to resist the entry of many antibiotics. I was unable to find a structure that I could readily rez but Hiro Sheridan's Orac had no such difficulty with the following SMILES code (for alpha-semegma mycolic acid which I assume is from M. smegmatis and therefore possibly misnamed/renamed in the databases).

smi=CCCCCCCCCCCCCCCCCCCCCCC(C(CCCCCCCCCCCCCCCCCC=CCCCCCCCCCCCCCC=CCCCCCCCCCCCCCCCCCC)O)C(=O)O

It would, however, be nice to know where the structure came from!

VWBPE: ISTE-on-Sea

I contributed to a panel chaired by Sheila Yoshikawa on subject-specific aspects of teaching in SL as part of the Virtual Worlds Best Practice in Education conference. Unfortunately, Sunday nights are the worst for me in terms of bandwidth and, as the picture shows, a quarter of the sim vanished and voice started to die on me (as it all too often does). I tried to use voice but this died on me completely on testing so I had to relog. Rather than risk this happening again, I decided to go with text but it appears that there was no chat relay in the auditorium, something I should have checked in advance. I failed to spot the cue from the Sheila that things were amiss and that I needed to shout. As a consequence people at the back could not "hear". My apologies to them and for their benefit, this is the gist of what I said:

I'm Peter Miller, lecturer in Microbiology, University of Liverpool
I've only been teaching for less than a year so am still learning
There's some overlap with the other speakers
I'm pleased to acknowledge Desi as an influence
And I have an interest too in molecules, albeit big ones, proteins
So Horace and Hiro Sheridan have been v helpful
Finally Max Chatnoir in the audience should be up here - she has been an inspiration :)
If you want see what I've been doing most recently, see
http://tidalblog.blogspot.com/2009/03/tb-build-video-with-subtitles.html
That was a build I did recently to mark World TB Day
And I'm blogging about it with a large class of Year 1 students
One of the aspects of the build is its use of multiple levels
I'm a microbiologist and its a subject that cuts a lot of ways
If you look at the build, it starts with people at the top level
A chance to discuss diease -- the history of the subject, its transmission, its real importance
At the next level down, I've been looking at cells
Their growth and some of their components and their significance
The final level is mapping data
There is now a vast amount of sequence data and I'm looking at novel ways to represeent and investigate that in SL
I'm very keen on the shared presence aspect Horace mentioned and really want to see collaboration in use of the features
More generally, there has only been a limited use of existing content in SL
I've borrowed ideas from people and sometimes tools but the amount of microbiology out there was v limited
I wanted to develop some tools that were immediately accessible and that was the genesis of StoryMachine
That is an evolved form of Eloise Pasteur's spidergram that Milton mentioned
Except it reads from a notecard so there is no need to hack prims to generate a 3D display
of a spidergram
There are some places inworld I can recommend
The excellent Max Chatnoir has some resources at Genome that are tangentially pertinent but probably of greater relevance to colleagues teaching genetics
It is certainly worth looking at how she does things though because her stuff is tried-and-tested
Like Horace, I haven't been doing virtual labs but I wouildn't rule that out
There are some govt organisations too
Although the US Centers for Disease Control (CDC) sim has some microbiology labs, they aren't really suitable for teaching use
I think CDC and some of the commercial folk are maybe missing a trick in terms of engagement here
Some of the talks and meetings held on Second Nature and some of the resources on the American Chemical Society sim are potentially useful
I wish UK learned societies were a little more open-minded given the costs associated with remote meetings these days
If I'm missing anything obvious, hopefully folk in the audience will let me know :)
If I include myself as a learner, then I have to say that the biggest opportunity is in networking and collaboration but I haven't done a good job on exploiting that yet
As far as limitations are concerned
A lot of science content in SL is directed towards the public understanding of science so is at rather a basic level
It isn't clear that using content on other sims is a strategy that is robust and scalable in the long-term
There is perpetual change and flux in SL and that makes it hard to plan
I think I want to finsih there and take questions when the time comes
Apologies for using chat

And, after a few minor contributions, I ended with thoughts on research:

Modelling bacterial cells is a topic that has some currency: the most recent Annual Reviews of Biochemistry has a review paper on it
One small example is a class where I got students to rez components of the bacterial cell wall and then mount them in a (very basic) model cell
It illustrated quite nicely that one component was so large, it could only fit in one plane
That is an observation that is to the best of my knowledge original and might have consequences for that protein's role
You could reach the same conclusion on paper, of course, but model building in SL should hopefully stimulate a more questioning attitude
That's all :)

I thought the contributions from the other speakers were very interesting and certainly gave me food for thought.

StoryMachine: now you can have it both ways

The static image above belies a modestly significant enhancement to StoryMachine, viz that you can now appear to have multiple particle streams emanate from the same prim. This makes it much easier to convey a sequence of events wherein an interim node is linked to multiple outgoing nodes. Previously the streams would have had to link back to the common interim node as each can be the source of only one stream though the recipient of many. The result was not visually intuitive.

The limitation is inherent in SL and the work-round dodges it by permitting the creation of transparent prims. By convention the names of the trans-prims start with an underscore and end in a digit to distinguish them from the visible prim in the same location, e.g. myNode (visible), _myNode1 (trans), _myNode2 (trans) et seq.

The color command is therefore changed so it will recognise "trans" as a colour, e.g.

"color","_myNode1","trans"

The downside is that the map is now slower to rez and the trans effect is only applied after a normal node has rezzed and thus you do see the two prims briefly. I guess I should fix that...

TB build video annotated

Trivial really but you can obviously use more than one overstream with any video. The one above replaces some of the explanation with reflection on what needs fixing. And, of course, the students could do their own. Or you could provide feedback this way on their builds. Or you could pose questions about a scene. Or...

Of course, Overstream isn't the only company offering this service. Subyo does it for YouTube and Tony Hirst shows how tweets can be mashed to the same source.

On a related theme, Melanie Macbride extols the virtues of Kaltura which offers Wordpress bloggers the opportunity to let their readers remix video content on their pages. She plans to offer her Creative Commons session in this format.

TB build video with subtitles

In the end I used Overstream to add subtitles to the video record of the World TB Day 2009 build. This is web-based so adds a bit of lag at the start.

I had an improbable number of issues trying to audio dub locally in Movie Maker etc, mainly down to obscure file incompatibilities, so have gone with subtitling for the moment. I guess I could have used Splashcast but my login there seems to be borked.

Tour of the TB build

Click to Play

This was put togther for World TB Day on 24th March. There's no soundtrack and it isn't the finished deal visually either but it does give a feel for what was available. I'll do a better, more complete version at some stage in the future (maybe).

The background is provided by a blog post.

Edited to add tag (cross-posted originally without tag from blip.tv)

Evernote and text in SL, not to mention Ada

I was playing with the SL-based Medline bibliographic search tool I blogged many moons ago and somewhat pleasantly surprised to find it worked as well as ever (which is ~70%). The (rather poor) image above is part of a screenshot of a web page with a search result as displayed inworld using Daden Navigator.

One of the limitations of this approach is the disconnect between the visual environment and the need to record and search text. It isn't anywhere near a water-tight roundtrip solution (sounds like a cruiseship) but you can use the Evernote client to save a screenshot, synch with their server and after about 10 min or so the server will have indexed the image text so that the image is now searchable as text. As shown in the image, search terms are highlighted. I think that's neat!

I'll leave you, gentle reader, to ponder uses. For those of a techie (as opposed to trampolining) disposition, it may be worth bearing in mind that Evernote has an API so you can actually retrieve the text from images as well and, heck, feed it back inworld if you feel so inclined.

I believe today is Ada Lovelace Day so well-deserved plaudits to Eloise Pasteur for her ace SL building/scripting skills and general all-round pithy IT wisdom. Lots of other names I could mention who generally do a tremendous job of keeping the edutech social network wheels turning but I run the risk of leaving someone out so I'll stop there.

Marking World TB Day 2009

World TB Day is today, 24th March. I have put together a small collection of exhibits, mostly "works in progress", that I hope illustrate various facets of TB. The build is divided into 3 levels, the image showing Cellscape. You start at the top and then navigate via the orange arrows, clicking on the yellow info signs for explanatory text. You move between levels by means of the teleporter (TP) discs with concentric red circles. Barriers indicate that there is no further content in that direction. If you want some background, there is always Wikipedia!

The top level is about people (Cityscape; slurl)

• Visit the laboratory of Robert Koch who discovered the bacterium, Mycobacterium tuberculosis, that causes TB.
• "The Cure". Witness the role for alpine vistas and revolving huts in the pre-antibiotic era.
• See James Nachtwey's moving TED Prize speech and images of the suffering caused by XDR-TB.
• The Trendalyzer video demonstrates the rising tide of infection from TB against a background of HIV in southern Africa
  

The middle level is about cells (Cellscape; slurl)

• The unexpected: M. tuberculosis forms biofilms (a rudimentary simulation)
• The nub of the problem: the porin in the sea of wax that limits growth and excludes drugs and disinfectants (the drop-through demo, shown above, is of a porin from a fast-growing non-pathogen but M. tuberculosis has something similar).

The lower level is about charting the growing body of subcellular data (Bioscape; slurl)

• The giant genome: take a tandem bicycle ride around the touch-sensitive genome and see the frontline drug molecules used to treat the disease
• Browse the metabolic pathways comprising central metabolism modelled in silico
• See how molecular data reveal the likely evolutionary pathways taken by the various lineages of the disease

I am conscious that there is a heavy emphasis on science and that some of the exhibits are less than complete and/or may contain errors of fact, omission or misinterpretation. I'm not an expert on TB so this is more than likely and the whole thing has been rather rushed. Please let me (avatar: Graham Mills) know if you find anything. If you manage to make it, I hope you enjoy our visit.

TB: Out of Africa

More maps but this time showing the evolutionary migrations of Mycobacterium tuberculosis in concert, presumably, with its human host. I decided to stick with the same layout as the metabolic map though this time all the browser function does is show an enlarged version of the chosen region. I've attempted to animate the map to explain what's going on and show the pathogen moving as it takes the routes. Sadly, it's spectator-only, which is not best use of SL. As time is tight, I went for a simple solution based on Puppeteer.

Puppeteer allows you to step-animate linked prims in relation to the root prim. It records position, rotation and scale (which can be changed) but it doesn't allow you to rez or delete prims so I have mine appear from out of the ground and, when done, return the same way. At the moment the animations are triggered by touching the coloured cubes but I really should make a better control panel.

The map is taken from an Open Access paper by Wirth et al. (2009) who studied the evolution of repetitive DNA sequences. Given our propensity to acquire bugs from animals (zoonoses), it is perhaps surprising to see that M. tuberculosis didn't hop from domesticated animal to human when they collectively settled in the Fertile Crescent but rather the other way round. Moreover, most of the sequence variation seems to have taken place over the past 180 years, i.e. since 1829, presumably alongside the trend to urban dwelling.

Given that similar data exist for Helicobacter pylori and Mycobacterium leprae, it would be nice to see how they compare but that is for another day.

(First accidentally published minus map)

Reference

Wirth T, Hildebrand F, Allix-Béguec C, Wölbeling F, Kubica T, Kremer K, van Soolingen D, Rüsch-Gerdes S, Locht C, Brisse S, Meyer A, Supply P & Niemann S (2008). Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 4, e1000160.

The Cure (for TB)

Prior to the advent of antibiotics, the cure for TB was believed to be fresh air (especially pure mountain air), sunlight and rest. Towns like Davos in Switzerland built sanatoria where those suffering from consumption (as TB was then called) and sufficiently well-off could recuperate under the supervision of specialist doctors and nurses. Many, many hours were spent on couches on the terrace exposed to the cold, fresh air.

A typical day (from Switzerland Unwrapped):

06:45 Rise. Nurse takes temperature and pulse.
Breakfast, then recline on Davos chaise-longue (couch) in open air, until
10-11:00 Free time
Lunch followed by silent session on terrace
15-16:00 Further free time
Back on the terrace until
19:00 Dinner
Followed by further resting (now indoors) until 21:00

There is a picture in a Flickr collection of US military archival images showing men undergoing similar treatment in sub-zero temperatures.

For those who couldn't afford Switzerland, some UK sanatoria and hospitals installed revolving garden huts to isolate the actively ill and give them what was believed to be the all-important fresh air and maximum sun exposure. Apparently huts were also used at Davos so the build is not entirely fanciful.

As ever, it is self-evidently a rough build. The hospital beds are not period but come from the paramedic box used by St Georges in their PIVOTE-based training. The backdrop uses the HUD-controlled RealView2 system purchased inworld on Jorah (slurl). It is rather unlikely that the picture is of Davos and we seem to be rather high up for grass to flourish so well.

Reference

Campbell, M. (2005). What Tuberculosis did for Modernism: The Influence of a Curative Environment on Modernist Design and Architecture. Med Hist. 49, 463–488.

Reconstruction: Robert Koch's lab

There is a meme that says we shouldn't seek to recreate First Life in Second Life if we want to make the most of the experience. The one exception I would personally advance is historical reconstructions (First Life redux, if you like) and there are a number of such builds worth visiting. Three that spring to mind are the Alamo on ISTE, the Kristallnacht sim and Raoul Wallenberg's office on Second Sweden (links are slurls). Of course, there are many other period sims, including those with either a shopping or role-play subtext.

The image above is of a work-in-progress in which I am reconstructing a single rather blurry view of Robert Koch's lab at the Institut für Infektionskrankheiten in Berlin, presumably taken sometime between 1891-1904. Although this is sometime after his discovery of the bacterium causing TB (reported in 1882), I think it perhaps gives a sense of working in what is sometimes called the Golden Age of Microbiology. Koch is, of course, famous as the originator of the eponymous postulates but also did the seminal work on anthrax and cholera as well as TB. Arguably, he and Pasteur, together with their respective "schools", invented infectious disease microbiology as we know it today.

The image comes from a book called the History of Bacteriology, written by William Bulloch and first published in 1938 with my edition from the Dover Press in 1979. While there are lots of photos of Koch peering down microscopes, there are fewer that I can find on the internet of his lab.

The reconstruction isn't faithful to the picture (the windows and stool are entirely wrong, etc, and the purple sphere is, of course, a poseball) and it hasn't really progressed as far as the adjacent office seen in the background of the photo. Beyond issues of the lack of definition, context, scale and texturing, I'm not sufficiently knowledgeable about the history of microbiology as to be able to furnish an authentic period lab and commentary. Finding half-decent labware was difficult and the microscope I kludged together is rather obviously inaccurate. Still, if you half-close your eyes, set your lighting to midnight and use your imagination... I think Prof Koch is working late.


I am rapidly coming to the conclusion that I will not make Tuesday's deadline in any coherent sense (World TB Day 2009). Just too much other stuff going on.

Browsing central metabolism in SL

Following-on from my earlier post, I have now imported the map of central metabolism from Palsson's recent Mycobacterium tuberculosis paper. This is quite a big image so I decided to break it into sections. After playing with the UCL CASA image cutter for Google Maps and the PIL image library for Python, I eventually found the easiest path was to save the SVG as a PNG from InkScape and then use ImageMagick to first resize it (shrink by half) and then to generate 1024 x 1024 tiles (still large, I know). Sixteen of these sufficed for the map which works in much the same way as before except that I have added a highlight so you can tell roughly where you are on the browser map.

Inevitably there are some glitches: some things aren't fully legible and some pathways break across displays. Perhaps I should have a full-scale version as well and a HUD to go with it. However, having the smaller version available has the advantage that different groups might work with different parts of the map at multiple locations. Having some way of bringing their efforts together in the form of a composite map would be nice though.

Where might this go next? At the moment, apart from the browse functionality, the display is very static and 2D. I could put some touchpos data into the map. Another possibility is to use Troy McLuhan's holo-emitter to store extra info on a per map segment basis as the video tentatively illustrates.

I should like to think ultimately that this is something that students might do.

How (not) to make a bot

I needed what passed for a cook in short-order that could answer a limited range of questions, preferably getting some of the answers wrong in pseudo-random fashion. This sounded like a job for a bot. Big problem: I have no idea how to make one.

There are a few bots you can buy and, at the upper end (and ignoring the bots that requires their own SL account) is the J&M Creations robotar as typified by Naomi (slurl). She doesn't look like a chef but can, in fact, be retextured. She can also be hooked up to the Pandorabots.com site though I have found this on occasion to be so slow as to make programming the bot impossible.

Naomi is very capable (she doesn't cook but will run a camping site) but quite expensive for SL (you need body, brain and textures for starters: L$7750 in total). Anyway, I thought this might be an opportunity to see what a rank amateur could achieve in a couple of hours. If you want to find out how to do it properly, stop reading now.

Firstly, you need three textures for an avatar: head, upper and lower. These map onto the male or female shape, more of which anon.

I got the head texture from a resource pack I picked up on Southampton Solent’s resource centre on their main island (slurl).

For the upper and lower body, I downloaded and unzipped the 1024 size avatar templates from Robin Wood’s site.

I painted them mainly using the freebie version of ArtRage (you might get a better result with [i] talent, [ii] almost anything that can edit JPGs, but ArtRage was at least quick).

For the body I used the mod/trans/no-copy “Additional poses” mannequin from Chakra Nova (L$950; slurl). This appears to be the foundation for the mod/copy Naomi bot which can be retextured by changing texture ids on her notecard; texture ids are available by rightclicking the texture in Inventory.

If you click on the mannequin and choose “Textures”, you cycle through Head, Upper, Lower and at each stage you can Ctrl-Drag the textures onto the mannequin. If you press Reset, the mannequin reverts to what is called the UV map and you can retexture if you like from scratch (though you can use the normal texture cycle as well).

One benefit of choosing a male shape is not having to worry about hair though you could splash out on a hat from ::MIA:: chef on xstreetsl.com (L$200 for a full avatar).

Programming the bot was done using the freebie Eliza script from Dedric Mauriac (slurl) added to a transparent prim. This reads a notecard, attempts to match text chatted to it and chats back a response from a list of options.

Adequate for our purposes. Could we have done it cheaper? On reflection an image + the script might have sufficed but, hey, we learned something new!

Metabolic maps

The giant Mycobacterium tuberculosis genome has a large central area that is presently empty, save for a few molecular models. That is not for lack of potential content ideas and I'm presently pondering how best to represent metabolism in the M. tuberculosis bioscape (as I call it until I can think of a better name).

The pathways in the image above are from an Open Access paper from Palsson's lab and go with a metabolic model they published recently. The chequerboard in the background is a touchpos-based menu; the image next to it is a one-prim representation of the 4-prim map my avatar is standing on.

Many of the images in the Palsson paper are large and getting them into SL is going to take some work. I'd like to be able to hack the SVG they come in but suspect I may have to settle for raster image format. Using QuickTime or HTML would also be nice but there are limitations in terms of the number of media URLs.

The Palsson model presently contains 661 genes catalysing 939 reactions and is presumably a subset of what the real bug can do with its 3800-odd genes, though admittedly not all encoding enzymes. From an educational perspective, completeness at a fine-grained level is not a major issue though making connections between genome and metabolome.

At a basic level, the exercise of mapping the gene id onto the unrelated enzyme abbreviation on the metabolic map makes a useful point regarding naming and databases. The gene markers on the genome can rez physics-based prims representing proteins. These can be taken into inventory and used to decorate the metabolic map.

So far as the TB build is concerned, I think we are looking at a proof-of-concept within a proof-of-concept so I shall start with just a few pathways in the first instance.

Technology that isn't Second Life... yet

I (and almost everyone else) blogged the World Builder video. Now Patti Maes in her TED talk shows how hand-based virtual menus already exist. But why stop at 2D when you can generate a 3D augmented reality display?

Some of this stuff needs to come inworld and vice versa.

Pot-pourri of PIVOTE, pfText and pStoryMachine

The JISC-funded PIVOTE simulation authoring system was released today and I went to St Georges sim to check it out. Two very patient avatars guided me through the use of a simulation (paramedic attendance at a road traffic accident as per the image). You move through the simulation by a mix of selecting options and media from the noticeboard (on wall to left in image but also available as HUD) and interacting with objects rezzed automagically or from inventory, some of which in this case function in different ways depending on context.

There was the odd glitch but overall I thought it worked rather well. I've no idea how the authoring is done but my guess is that it is fairly straightforward and that the system will find wide application. The developers, Daden, are probably going to offer a hosting service for those, like me, who don't have immediate access to the necessary Perl-based server. You do still need customised inworld objects so it hasn't solved all our problems just yet!

Torrid Luna released a simplified xyText system called pfText. I'd always been put off by the apparent complexity of xyText but this works very nicely for me and I quickly made a simple label maker that takes text from the description field. I think this will be useful for the students.

One of the students is thinking of using StoryMachine so I have improved the documentation slightly (in case anyone else is using it and interested). And despite this post's title, I haven't changed it's name.

I may, however, have to change the title of one of the layers in my TB sim, viz Cellscape, as it transpires there is a Canadian commercial developer producing an immersive sim of the same name. Ah, well...

Not like that, like this

World Builder from Bruce Branit on Vimeo.

I gave an impromptu talk about SL to some Masters students today as a follow-up to a less-than-stellar inworld session. I explained that the current SL was just one step on a journey. This video by Bruce Branit (via the npirl blog) says it so much better.