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Interesting. Our group at CSIRO is interested in combining different studies of all kinds (such as public microarray datasets), in ways which are (1) “valid” and (2) increase their statistical power. Haven’t made much progress yet, but will definitely bear this kind of analysis in mind. – Neil Saunders

Jean-Claude Bradley, Ruchira S. Datta, Pedro Beltrao, Andrew Lang and Peter Miller liked this.

cool :) – Pedro Beltrao

thanks – I’m also thinking about making something similar for protein interaction networks, but first I would need to find a good algorithm for doing network layout in 3D – Lars Juhl Jensen

A few thoughts: I have a *very* limited setup on the giant TB genome with just one level of interactors and then you tp across the genome if you want to delve further. If you want something largescale, you are presumably looking at particles (to save prims) which are unfortunately limited by the fact that a node can only act as the source of one stream (so you need to duplicate/overlap nodes). Once you get your algorithm sorted, it might be worth talking to Erich Bremer about strategies for rezzing large numbers of nodes so as to avoid the grey goo fence. – Peter Miller

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Thanks for the analysis Lars. I had a look at issue you pointed out in what it relates to our study http://pbeltrao.blogspot.com/2009/06/reply-on-evolution-of-protein-length.html – Pedro Beltrao

It would be cool to know how much of the correlation you mention might be due to MS bias. – Pedro Beltrao

Thanks Pedro – redoing the same plot based on average number of phosphorylation sites per residue instead of on the raw counts was exactly what I wanted to do. It would just have been too much work to redo it without asking you for access to all your files. So I hoped that you would do it :) The result is as I expected; when I looked at protein lengths it did not explain the full signal, so there should be a correlation left after the length correction. – Lars Juhl Jensen

This is great discussion. One day, online papers will be wiki documents and you’ll be able to edit one another’s figures :-) – Neil Saunders

Intuitively, I would expect that due to biology the number of phosphorylation sites is directly proportional to the length of the protein (i.e. that the average density of phosphorylation sites is independent of protein length). When it comes to MS biases then I think that protein expression level is a much more important factor to take into account; a phosphorylation site on an abundant protein is much more likely to be picked up than one on a protein present in only one copy per cell. – Lars Juhl Jensen

Come to think of it: if there is a group of fairly small, highly expressed proteins (ribosomal proteins?), then this would explain the negative intercept with the y-axis in my plots. (Edit: rethinking the argument, this would give a positive intercept, not a negative one.) – Lars Juhl Jensen

Right; you can have small proteins with zero sites, but you can’t have zero-length proteins. – Neil Saunders

Neil Saunders, Jason Tsai, Michael Kuhn, Bill Hooker, Jason Stajich, Duncan Hull, Thomas Lemberger, Pawel Szczesny and Deepak Singh liked this.

I knew that there were limits to the coverage but didn’t know things were this disparate. Thanks :) – Deepak Singh

All the figures were already done, but ended up being leftovers; I might as well make them available by writing a blog post around them :) – Lars Juhl Jensen

Never a bad idea :) … now should be fun if someone actually ends up referring to that post in a more formal publication – Deepak Singh

It sure would be nice if someone would cite this (or another) blog post in a paper (not that it is my reason for blogging). In this respect, does anyone know a way to get DOIs assigned to blog posts? – Lars Juhl Jensen

Lars: http://www.doi.org/faq.html. Far as I can tell, DOIs involve paying a registration agency, somewhat analogous to DNS domain names. Just another internet scam, in other words :) – Neil Saunders

I just checked the prices and it almost looks like a scam: with the number of DOIs you or I would need, you are looking at 4-5 EUR per DOI plus sales tax! (Unclear if this is a one-time or an annual fee). – Lars Juhl Jensen

@Lars: webcite is another option: http://www.webcitation.org/#How_Cited – Bill Hooker

Thanks Bill :) – Lars Juhl Jensen

I have now added WebCite links for all my blog posts that I consider to be “citable material”. Hoping that some day someone will make use of it ;) – Lars Juhl Jensen

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The coverage they got is impressive. I would be more interested in post-translational modifications at this points :) – Pedro Beltrao

I agree, the coverage is excellent but it would have been even more interesting if one could compare PTMs between the conditions. Also, I would have liked to see microarray data for the exact same samples; I wonder how much that would improve the agreement between mRNA and protein levels. – Lars Juhl Jensen

Did a few tests for correlation of haploid/diploid ratio with other properties: CDK substrates, phosphoproteins, ubiquitinated proteins, D box motifs, KEN box motifs, PEST regions, and phenotype screens. Found weak correlations for ubiquitinated proteins and PEST containing proteins, but these correlations are not statistically significant after correction for multiple testing. – Lars Juhl Jensen

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Thats an interesting distribution of impact factors… – Duncan Hull

No “outrage” there, just some interesting facts. Anyone from Nature care to respond? – Bill Hooker

Thanks! No response from Nature so far – I guess they have given up responding to the flood of blog posts by now and just wait for the storm to pass … – Lars Juhl Jensen

When using the Media channel for rendering images from a website, these images are as sharp as a rendered HTML page in-world, which is enough for all slides I’ve seen so far.
(N.B.: It’s also not nessecarily so, that the movies played over the Media channel have to have a small resolution (like the 320 by 240 px you mention): On ZKM we have played a 1024×240 MOV stream with 1fps as a slideshow (which allowed us to broadcast 4 smaller images at once).
The common practice to reduce the movies in their resolution are just to keep the bandwidth down to a level that every viewe’s DSL line can handle, and to keep the outgoing bandwidth low, of course.)

Here are 2 screenshots from within Second Life, one of your Website:
http://www.flickr.com/photos/torridluna/3209885568/sizes/l/
And one with a screenshot of my browser, showing your website:
http://www.flickr.com/photos/torridluna/3209887456/sizes/l/

Both load with a minimal delay, and without blurring, since they don’t use SL’s jpeg2k approximisation, or the asset server at all, but instead get rendered from the user’s own builtin mozilla engine, included in the Viewer.

So much about “SL isn’t fit for scientific presentations.”. ;-)

Cheers,
Torrid (http://primforge.com)

http://maps.google.com/maps/ms?ie=UTF8&hl=da&msa=0&msid=117687718575072973123.00045c8043ee904df8750&ll=50.307433,6.934571&spn=19.69467,37.353516&z=4&source=embed

Originally found here:
http://worlds.ruc.dk/?p=393

I think the whole issue of slide shows being too slow is that Second Life is just not designed to do what we want to do. Using a separate high-resolution texture for each slide is a hack that results in much more data being transferred than the size of the actual slide show that the presenter made. I have been thinking along the lines of not having the presentation displayed on an in-world projector, but instead show it using a Flash-based viewer similar to SlideShare that could within the built-in web browser. All that is needed is a mechanism for synchronizing the slide changes, which should not be difficult to make.

However, I am also questioning the advantage of using Second Life for this purpose. What is the advantage over having a slide show, live video streaming, and interactive chat within a browser window? To be a bit provocative, the latter solution has clear advantages, namely that people would not need to install any new software and that we would not have to make hacks to circumvent the limitations of said software ;-)

The slow rezzing of textures is a technical decision Linden Lab have made. You can’t throw Megabytes (sometimes hundreds) of textures to every client at the same sim. So textues are send in several passes, where each pass adds to clearity of the texture.
Same solution was used in the early days of internet, and is stil a part if GIF and JPG file specification.

As for streaming movies, a MOV file in 320×240 (mobile phone screen) is rather good, blown op on at 10 meter screen, but you have to have a server that can stream to the number of people attending.
I have seen solutions where you “offset” the movie stream on 4 sceens, like when you put 4 flatscreens next to each other in the real world, to get “one” big screen.

Depending on your material, there are several ways to speed things up.
I’m sure other people happily will share their experiences, if you ask around.

I’m well aware of how scientists view such things, having been a college prof, and being married to one for 37 years. :-) What I’ve observed is the magic that happens when profs like Curious George from Cal Tech come into SL as skeptics, engage with the environment and residents with an open mind, and become converts.

Changing “…the perspective of a participant who cares about the conference and not about Second Life, which would be the majority of scientists…” is exactly my goal. If all you do in SL is attend the odd seminar, you are missing the power and potential. It’s about collaboration and community, not about yet another presentation venue. Webinars can do that more efficiently. I’ve come to believe that it’s essential for we as scientists to engage more fully with the world and to help students to do the same.

I’ve been asked to give a short talk and participate in a discussion at Kira Cafe. Have you been there? There is a world-wide physics community that meets regularly in SL to discuss the broader context of science. I taught college chemistry for 35 years, but now I’m interested in helping faculty to enter and acclimate to the virtual world.

I don’t see a huge learning curve–I see an environment with powerful tools waiting to be used. It’s surely not that scientists are averse to learning difficult concepts. But what’s the point if not to go beyond making it easy to watch yet another talk? I spent my whole career interacting mainly with scientists. That was not such a great idea in retrospect. Look me up in-world sometime. Cheers!

I have already participated in Metanomics events, but I don’t think that these are a fair comparison with scientific conferences. From what I have seen, Metanomics is more a kind of interviews where you need the video to see the person speaking. At science meetings you need to be able to easily read text, even when it is written with a fairly small point size. Unless you can do streaming video in at least 640×480 resolution then this will simply not deliver. The preloading of textures on hidden faces of prims seems a good solution. It would be interesting to try to preload an entire 100 slide presentation in this fashion.

Concerning chat bridges, I agree that it is a very good idea. So far, however, my experience has been that most scientists at Second Life meetings have been very, very quiet on the chat. This is largely a cultural issue, but in at least one case I found myself unable to make any intelligent comments because technical issues hindered me in understanding the presentations.

Even then, what worries me most is the high barrier to entry and the steep learning curve of Second Life. You have to realize that most people in the scientific community do not read blogs or use of RSS readers yet. The most common reason is “I don’t have time”. If you want them to invest the time it takes to get a Second Life account, install the client, and figure out how to do the most basic things (like navigating and talking to people) then you really want to make sure that they have a good experience. Otherwise, I’m afraid they will turn their back on Second Life and not give it a Second Chance.

By now you are probably aware that the problems which prevented you from reading the slides at your first conference are a normal part of life on SecondLife. They are part of the overall problem known as “lag” and arise whenever a large group of avatars gather together in one place. LindenLabs feels lag is due to excessive drain on the computer server because of the many avatars.

In the excellent courses offered inworld by New Citizens Institute, the presenter often uses two slide displays, putting odd numbered slides on one and even numbered slides on the other. This allows time for each slide to rez before beginning that section of the course lecture.

But there are many, many organizations who are doing conferences and events in Second Life, with a large and creatively talented audience beyond (but also including) scientists. Much progress has been made with many of the problems you mention. For instance, presenters can rez their slides on a small scripted prim prior to speaking so that they load quickly during the talk, and Chatbridge technology allows simultaneous chat in SL and on a webpage with a video stream.

One of my goals is to bring science students and faculty into contact with the other vibrant cultures and communities in SL. Attending events like Metanomics (http://www.metanomics.net), Orange Island programs, and the business, NMC, or other Edu-sponsored events that occur several times a week is a good way to learn the latest on the tech front and to meet professionals from around the world.

I can only touch on the many possibilities in this comment. I frequently have conflicting events in SL, and more that interest me than I can possibly attend. Please contact Chimera Cosmos in Second Life, friend Liz Dorland on Facebook, or follow ldinstl_chimera on twitter for more information.

I have a Danish friend who is researching teaching and learning in SL, I collaborate in a space on the Australian Jokaydia sim (http://www.jokaydia.com), the NMC virtual conferences are fabulous, talks by famous authors…artists, social media experts, faculty, event planners, machinimatographers like Draxtor Depres who recently won an international award for the Virtual Gitmo video, international relations experts…limitless possibilities for students and the rest of us.

I very much hope that others don’t miss out because they are convinced by your initial impressions!

Regards, Chimera Cosmos (Liz Dorland in RL)

Evolvability and hieracrchy in rewired bacterial gene networks    
Isalan et al. Nature 452:840                                                    
PMID:18421347    

It was discussed at the Molecular Evolution club at your workplace last month. They seem to have a pretty cool platform for studying network topology.

I fully acknowledge your point, though, that it is obviously easier to interpret the word cloud for a paper when you have already read the paper – not to mention when you have written it.

We also fully agree that looking at a word cloud is no substitute for reading a paper. However, I think that with improvements in the visualization, it could be an alternative to rapidly looking through a pile of abstracts. My question is rather what can convey most of the content of a paper in 10 seconds: a word cloud or an abstract?

For example, reading the first tag cloud I thought STITCH could have been a novel protein, whose interactions with different chemicals were examined in the paper.

Just to put the general euphoria into relation.