Tranquil evening in the mesh sandbox

One of the other tools I've begun to appreciate more is Screenr. This short clip shows the structure of a pair of Escherichia coli ribosomes in one of their two native arrangements in polysomes (top-to-top in this case). It starts with the view in UCSF Chimera, then MeshLab and finally in SL. I am plainly not much good at machinima but that's not the point. It was easy and fun to make and stimulated me to investigate something I didn't know.

Things that go bump in the night

I just wanted to mark a few departures:

• Bloglines RSS reader: imminent closure, overtaken by the real-time web apparently
  
• The American Chemical Society and Centers for Disease Control, both leaving SL
  
• dabbleDb: on notice (and striking a happier note, the devs having been acquired by Twitter)

A lot of change in the system just now, one way or another.

Space, the final frontier...

... is a really terrible title for a blog post that features a single picture, albeit of three generations of SL mesh-type protein structure. Third in line on the left is Hiro Sheridan's sculpty version of human lysozyme, then the multi-sculpted version and, nearest to the camera, a "proper" space-filled mesh. Not perfect but it does at least give some feel for the kind of resolution that can be achieved.

My avatar is making the point that the PDB is not the only source of structures. He stands on EMDB Entry EMD-1644, the Borrelia flagellar motor (which does look a little like a spacecraft, no?)

All done with UCSF Chimera and MeshLab, the final frontier for me at the moment. The good news is that OpenSim does mesh too. Have mesh, will travel.

Fast, Easy, Fun (two out of three will do)

Well, my first semester SL sessions are already drawing to a close. They haven't exactly gone to plan and some of that was down to unexpected infrastructure issues when we moved to Windows 7. As you may have noticed, I also had to spend time devising mitigation strategies when Linden Lab decided on the price-hike/lockin for educators. As it happens, the students affected seem happy with the USB OpenSim solution, as am I, at least as an interim measure.

Looking on the brighter side, what has worked in the SL class (subtext: stuff I'd use again):

• TiddlySpace: we only scratched the surface but it was Fast and Easy.
• Pixlr.com: the best image editing/resizing site I've seen. Fast and Easy.
• Student base areas with scripted alignment prims so students can rez display boards that automatically position themselves over the pre-set marker prims. Fast, Easy and Fun.

OK, I'm biased but seeing prims self-locate (as per the video) made me smile. The students doubtless thought that this was just the norm and paid it scant attention. However trivial, Fast and Easy for them is still Fun for me.

[... and thanks to the Stilts Bitches at Burn2 for the excellent avatar freebies]

Putting my OAR in (well, almost)

It's Open Access Week. Last year Daniel Livingstone did a nice presentation on some of the OA issues for virtual worlds and mentioned the possible significance of OAR files. Pathfinder alluded to them in his blog on USB on OpenSim and they surfaced again at last week's VWER meeting (the transcript includes links to OAR repositories). Ener Hax among others has commented on both the importance and the sheer convenience of being able to archive a sim, a role that the OAR seems to serve well. However, their originator, Justin Clark-Casey, points out that the OAR format is potentially subject to change though he is personally committed to maintaining backwards compatibility (OAR-related posts on Justin's blog). The format also presently fails to preserve creator attribution.

I'd hoped to have an OAR to deposit in JorumOpen this week but have just been too busy. As the instructions below describe, however, it's possible to load and merge OAR files from the web and JorumOpen might be a useful repository for this though perhaps it's not best-suited to serving large OARs directly in this manner.

My contribution to OAW then are the brief instructions to getting started with OARs and USBs that follow hereunder. Please bear in mind that I am a complete beginner and am fully aware that some people have been using them for more than a year. You have been warned!

The instructions were tested on Windows XP and I've sadly yet to see anything analogous working on a Mac. Before we get started, I should also mention that the OpenSim wiki has the definitive guide to using OARs.

Getting started (if OpenSim not already installed)
1. Get a USB with 1-2 GB free space.
2. Download the zip file from http://dwellonit.taterunino.net/sim-on-a-stick/ and extract to the USB.
3. Download and install the Imprudence viewer from http://imprudenceviewer.org/wiki/Downloads
4. Copy the Imprudence folder over to the USB stick top level.
THANKS TO TATERU FOR HER PACKAGING OF THE USB OPENSIM

Starting and closing the sim
1. Swap to USB drive
2. Double-click usb-opensim folder
3. Double-click MOWSE icon and wait for application window to show Apache and MySQL are running.
4. Double-click Opensim.bat and press a key when prompted. Wait for the application to load (text stops scrolling for >20 seconds). Be patient!
5. Go to the Imprudence folder and double-click the Imprudence icon.
6. Login as Test User, password usbsim. The grid should be set to localhost in the dropdown. Ignore the error referring to Home as you login.
7. Note that you can set the daylight conditions via the World, Environment Settings menu. You can change the avatar appearance using the contents of the clothing folders in the OpenSim Library in the Inventory (button at bottom right). Just drag one of the folders in the Diva freebies, e.g. Ken or Paula, onto the avatar.

Getting a molecule
1. Go to http://jorum.ac.uk/ and search on "OpenSim". Only one record exists at present.
2. Download the XML file for the caffeine molecule and copy it to the top level of the USB.
3. With OpenSim running, swap to Imprudence, select File, Import + Upload and choose the XML file. A ball-and-stick caffeine structure should appear.

Saving an OAR file
I SUGGEST DOING THIS ONLY WITH A SIM THAT IS EMPTY APART FROM THE CAFFEINE MOLECULE
1. Go to the OpenSim console window and type "save oar e:\caffeine.oar" (assumes your usb is drive E:). This saves everything in the sim (in this case the four regions comprising the Portable1 sim, i.e. all you can see). Delete the caffeine molecule (rightclick the object, More, Delete).
YOU CAN USE THIS PROCEDURE TO CREATE BACKUP FILES FOR SECURE STORAGE, I.E. *NOT* ON THE USB DRIVE
NOTE THAT REGION-LEVEL ACTIONS BY DEFAULT APPLY TO THE REGION CALLED PORTABLE1 WHICH IS 4x THE SIZE OF A SL SIM. YOU CAN USE THE OAR FILE CREATED HERE TO RESTORE THE STARTING CONDITION OF THE SIM.

Loading a local OAR file
I SUGGEST DOING THIS ONLY WITH A SIM THAT IS OTHERWISE EMPTY
1. Go to the OpenSim console and type either "load oar e:\caffeine.oar" or "load oar --merge e:\caffeine.oar" (the latter should in principle load the molecule and NOT replace/delete whatever is already there, unlike the first variant).
2. Delete the caffeine molecule.

Loading a remote OAR file
I SUGGEST DOING THIS ONLY WITH A SIM THAT IS OTHERWISE EMPTY
1. Go to the OpenSim console and type "load oar http://pcwww.liv.ac.uk/~pmiller/oars/caffeinex4.oar". This should load four caffeine molecules from file at the URL indicated. The merge option also works with remote OARs.

There are additional OAR files here:
http://www.opensimworlds.com/index.php?part=worlds

I haven't tested them all but the CSI one didn't work for me. In some cases it may be better to logout while the OAR loads. Note that the console window does accept pasted text, e.g. for URLs. Just rightclick and Paste.

Closing the sim
WAIT FOR EACH OF THESE STEPS TO COMPLETE
1. Close Imprudence.
2. Swap to the console and type "q", press Enter and wait for the prompt, then press a key.
3. Swap to the MOWES window, click "Stop server" and, when the servers show as stopped, click "End".

[edited to fix the link to dwellonit]

Meshes arrive

I eventually figured out that you had to go to a specific mesh sandbox on the Beta grid. Once there the rest was simple. I rezzed a couple of meshes I'd made earlier, neither at what you would call high resolution. Still the process was straightforward enough: load Model into inventory, press the Generate LOD button in the Model dialog and then Upload. The meshes seemed to rez at an enormous size and one was two big to do much with except delete. The mesh above is a resized version of my old friend 1rex, human lysozyme. The UV map needs some thought but generally, as I said previously, "well within the compass of students". The duck, by the way, was a test mesh provided by the Lindens.

The edu-revolution will not be streamed (well, not mine)

Dusan Writer would like to see the Lab stream Second Life. Doubtless many who base their online experience around the tablet form-factor are wishing for much the same. The desire to monetize that experience and the willingness to pay for apps seem natural bed-fellows. However, a harsh wind of economic reality is about to strike higher education in the UK and I only see streaming working if it reduces the cost to play and I don't see that happening.

Indeed, the Lab's continuing coercive behaviour towards educators and non-profits (as lock-ins must be viewed) increasingly leads me to seek a future primarily outside SL, not least as my renewal date hoves into view and my funding evaporates. That said, I acknowledge that for better resourced projects, SL remains the premier game in town. For the moment it is in most people's interest that SL flourish and that largesse in terms of viewer development continues to trickle down to third-party viewers.

What happens next, however, represents a fork in the road again, much like the one that led me to SL in the first place.

There are choices, most starkly in whether to join a public grid or not. In practice I do most of my own development and don't use other sims except as source of inspiration (one good reason to stay in SL in some reduced fashion). The SLED list saw evidence of coercive behaviour from an alternative edu-grid over the Summer and, suffice it to say, I won't be going there. Likewise, I'm not interested in manning any anti-Linden barricades. At best this is a distraction for me, at worst a catalyst for counter-productive grid wars.

My funding and infrastructure mean that I can only afford to join a commercial grid for part of the year; I prefer the idea of a high concurrency service when required rather than an affordable, low concurrency one simply for the purpose of maintaining a presence. The notion of being able to swap between the two is very attractive, however, and something that a few grids such as SpotOn3D are beginning to offer.

That said, the future for me (and I am likely atypical) lies primarily in OpenSim-on-a-stick -- and yes, I need a better name for it.

Put quite simply, it scales. It allows me to develop scenarios for different classes without buying/hiring extra islands. Assuming that students can download and run them satisfactorily, it means that I am not limited to small classes (and/or complex scheduling) and students cannot get lost on the way to or from class. Students can build or modify scenarios without interfering with one another and archiving for external examiner perusal is straightforward. As my classes are primarily face-to-face, collaboration could come at that level rather than inworld. That said, it is apparently possible to hypergrid-enable such sims. Outreach to schools and places with low internet connectivity can be achieved by physical exchange of USB sticks or, where practicable, downloads.

If there is one thing missing at present, it is the web but that is imminent and, of course, conditional on an internet connection. What would be ideal would be to be able to use TiddlyWiki while offline and TiddlySpace while online.

While some may see this approach as a marginal activity in the development of virtual worlds, I believe it could be important in taking such environments to a wider audience. There is plenty of scope for collaboration and sharing, carrying on the the ethos that attracted educators to SL in the first place. Ultimately it also gives students the keys to the walled garden and in due course develop a transcendant personal learning environment from which to explore the metaverse.

Check back later; this one may take a while

I'm slowly moving the giant TB genome onto the USB key OpenSim. The original was built using Cadroe Murphy's ShapeGen and I didn't change the rezzed prim so it bears his name as creator. Accordingly, I'm having to rebuild it. I do miss some of the neat tools in SL, most notably Puppeteer (which has a new edition out) and, indeed, this is one of the reasons for keeping a toe dipped in SL. And then there's the community, of course.

Pathfinder has a great blog on Roger Stack's USB-based OpenSim implementation -- his reaction pretty much mirrored my own first impressions. I'm really glad to see that he's as enthused as I am -- I think it has great potential and not just as a halfway house.

Look for me on a USB stick next year

The Rockcliffe meeting to discuss the ending of the SL edu discount was interesting but suffered from the same concern that I voiced in my previous blog, namely that we cannot assess the import of the Lab's actions without knowing their intent. Tateru Nino seems convinced that an attempted sell-off is imminent and debates the possible outcomes. Presumably if she were right, the Lab would be keeping it pretty quiet-- as it is. Equally, others see the discount announcement as a negotiating position.

Meanwhile I've ported StoryMachine across to OpenSim-on-a-stick. The nodes clearly haven't recoloured properly but the general effect is not dissimilar to SL and the interactive mode works as well. If only the code wasn't so utterly rubbish, it would still make a nice signature piece.

I also ported across the protein rezzer. This was fairly straightforward except that llLookAt isn't implemented in OpenSim. A quick Google showed a workround and that someone else had been porting Troy's scripts into OpenSim. Hiro Sheridan tells me that he is staying in SL for the moment but is happy for his molecule rezzers to go into OpenSim, as, indeed, they already have elsewhere.

I should emphasise that I'm not leaving SL entirely even though it seems 90% certain that the sim will disappear in November or shortly thereafter. I still think the outreach potential of SL is significant and I may even go back to Daxos as originally planned. That said, life on a USB is currently looking remarkably stress-free by comparison with SL.

Plan B?

I have neither the time nor the inclination for this really but I find myself driven into a corner by Linden Lab's decision to remove the discount for educational sims. It isn't so much the cost (though I could only afford a further six months) as the uncertainty implicit in this apparently arbitrary move. Is Linden Lab sending negative messages to its largest corporate sector, is it in desperate need of the money or is it trying to encourage educators to coalesce? Either way I find myself forced to act defensively and am actively investigating OpenSim alternatives.

Spurred on by Ener Hax's blog, I installed OpenSim and Imprudence on a USB stick and ported some objects over from the small Molecule Park display on our island in SL. As previously on ScienceSim, the ball-and-stick molecule generated by Hiro Sheridan's rezzer came across without problems. The multi-sculpted protein predictably came across without its sculpt maps so these had to be reapplied. The SlideBoard texture displayer required the script to be ported separately and the prim media commands to be removed but otherwise seemed to work fine.

I can't claim that the experience was entirely glitch-free. In particular, when attempting to export or save snapshots, the avatar was logged out though the save operation seemed to succeed. Also, while I am quite happy to have a ruthed avatar, not everyone will be. Nevertheless, I think this has significant potential for training purposes where I can give the student a USB stick and have them operational within seconds on a stock laptop. Prim limits are barely an issue on the four region island and the speed and zero cost of texture uploads is also a bonus.

Of course, OpenSim has limitations but it is looking very promising. The question of hosting can wait for another day.