Vote For MindTouch

November 21, 2008

MindTouch has been nominated for the wiki category by the Open Web Awards, an online voting competition that covers major innovations in web technology. This is quite an achievement since there were 43,000 verified nominations.

TOPSAN is built on MindTouch’s Deki platform and we are very impressed with it. TOPSAN requires performance, flexibility, nonrestrictive licensing, and customer support, all of which MindTouch does an excellent job of providing.

TOPSAN endorses MindTouch Deki and if you’d like to also, go to the voting widget on TOPSAN and cast a vote for them.

Collaborative Community Building For Video Annotation

November 19, 2008

TechCrunch has a nice article about video hosting site,, creating a “collaborative editing approach for video metadata” called WikiCafe. Apparently Metacafe believes that “…quality metadata is as important – if not more important – than the videos themselves.” And their strategy seems to be working out:

“So far WikiCafe is exceeding the company’s expectations. The system is currently logging 14,000 user Edit Actions per day, up from 4000 in September. In my book Metacafe deserves kudos in this respect as well because forming a collaborative community is in many respects far more difficult than delivering the collaborative technology.”

It’s nice that TechCrunch feels the same about this kind of venture as we do at TOPSAN:

“Time will tell whether Metacafe’s gamble on WikiCafe will pay off, but you have to admire the company’s vision and courage. Instead of sitting still it’s pushing the envelope in delivering its audience the most accurate video results.”


November 14, 2008

The Calit2’s StarCAVE is just undeniably cool and it recently got some more mainstream attention on G4TV, a television network that covers cool technology. At about 1:55 into the video StarCAVE is discussed with a simplified mention of the good work done by molecular biologists.

Vodpod videos no longer available.

more about “Calit2*Life: StarCave Mentioned on G4…“, posted with vodpod

More information about TOPSAN’s integration with the StarCAVE is provided in this interview with TOPSAN’s Krishna on the MindTouch blog.

“Obama” and “new media” found in Same SciAm Headline

November 12, 2008

Scientific American had a tiny posting that really doesn’t contain much interesting information. The headline, however, was something that might be interesting for TOPSAN users to consider:

Obama administration would create new “new media”

It hints that President Obama will be rather more sophisticated and progressive when it comes to exploiting new communication channels.

Obama’s website is more direct saying things like:

“We need to connect citizens with each other to engage them more fully and directly in solving the problems that face us. We must use all available technologies and methods to open up the federal government, creating a new level of transparency to change the way business is conducted in Washington and giving Americans the chance to participate in government deliberations and decision-making in ways that were not possible only a few years ago.”

This kind of thinking is also the foundation of the TOPSAN mission. Now let’s see how that works out in real life.

Eliminating Free Riding – Not Even A Coherent Objective

October 28, 2008

Some people have a difficult time understanding how a project that is generated purely by volunteer efforts can be successful and they’re especially puzzled when it’s normal for others to benefit from the project without making any contribution. I think it’s a pretty easy point to clarify and this article does a very good job of it.

One of the interesting points this article reminds us of is that “free-riders” actually are a motivational mechanism for the contributors and as such are actually, albeit in some very minor way, contributing. As this topic relates to TOPSAN, perhaps the most important idea from the article is:

“All that matters is whether the absolute number of contributors is adequate. And because some fraction of new users will always become contributors, an influx of additional “free riders” is almost always a good thing.”

Referring to one of his references (am I allowed to refer to such a thing?) the author quotes:

“…eliminating “free riding” is not only undesirable, but that it’s ultimately not even a coherent objective.”

I think these days everyone at least suspects that the old rules need not apply and what would be counter-intuitive five years ago is, today, proven with numerous examples.

Beating intruders at their own game

October 22, 2008

Bacteriophages (or phages for short) are bacteria-infecting viruses. Some phages can integrate into bacterial genomes where they lie dormant (in a prophage state) as long as host conditions remain stable. Upon detection of bacterial damage, prophages are released from the host genome and enter the lytic cycle, destroying the host cell.

Recently, bacterial proteins with substantial structural similarity to virus capsid proteins were shown to assemble into large polyhedral shells capable of sequestering enzymes involved in oxidative-stress response (Sutter 2008, News & Views in Heinhorst 2008). Many other virus-like bacterial proteins exist (see e.g. 3bjq, 3bqw) that could carry out similar functions.

Since the products of oxidative-stress, such as hydrogen peroxide, can induce DNA damage and the SOS response that triggers prophage release (Bol 1990), isolation of cytotoxic compounds by means of such bacterial nanocompartments, termed encapsulins, could provide a means for virus-infected bacteria to avoid lysis.

Subverting a viral intruder by means its own tools – an example of poetic justice?

The Deeper You Go, The More Convoluted

October 22, 2008

This is a very interesting article by Simpson Garfinkel, author of “Practical Unix and Internet Security” and “PGP: Pretty Good Privacy”, and probably some other excellent, well-written books that are not sitting on the shelf in front of me. In this article he draws attention to the fact that Wikipedia is successful, not fundamentally inerrant in its design.

He says something that we have known at TOPSAN for some time:
“An interesting thing happens when you try to understand Wikipedia: the deeper you go, the more convoluted it becomes.”

He specifically highlights some of the problems which have made the design of TOPSAN so much more complex than people initially assume such an undertaking would be. The exact issue he mentions concerning the unintended consequences of the original research restriction is a core issue of the TOPSAN philosophy.

This article was also referenced on Slashdot and I’m sure there are lots of comments there on the topic.