Turing in Life

Reading the Wikipedia entry on Conway's Game of Life answers the question of why it was developed "Conway was interested in a problem presented in the 1940s by renowned mathematician John von Neumann, who tried to find a hypothetical machine that could build copies of itself and succeeded when he found a mathematical model for such a machine with very complicated rules on a rectangular grid." It's interesting that von Neumann's idea of self replication actually predates the discovery of DNA by a few years.

So I asked Google the question and someone has implemented a Turing machine inside Coway's Game of Life; way back in 2000. A book called "Collision Based Computing" and a applet called LogiCell (which uses Conway's Game of Life to do simple calculations) is available here.

Indexing for Efficient SPARQL

Another interesting way of indexing triples: A role-free approach to indexing large RDF data dets in secondary memory for efficient SPARQL evaluation "We propose a simple Three-way Triple Tree (TripleT) secondary-memory indexing technique to facilitate efficient SPARQL query evaluation on such data sets. The novelty of TripleT is that (1) the index is built over the atoms occurring in the data set, rather than at a coarser granularity, such as whole triples occurring in the data set; and (2) the atoms are indexed regardless of the roles (i.e., subjects, predicates, or objects) they play in the triples of the data set. We show through extensive empirical evaluation that TripleT exhibits multiple orders of magnitude improvement over the state of the art on RDF indexing, in terms of both storage and query processing costs."

While looking around at arXiv I did a quick search and found two more interesting papers that seems related to a previous discussion on how the Semantic Web needs it's own programming language or I would say at least a way to process the web of data, both by Marko A. Rodriguez: "The RDF Virtual Machine" and "A Distributed Process Infrastructure for a Distributed Data Structure".

While you were away...

Now that I'm currently looking around for jobs, I came across a presentation on some of the work the the easyDoc project did at Suncorp, "Technical Lessons Learned Turning the Agile Dials to Eleven". It includes automating getter/setter testing, hibernate, and immutability. It's good to see the sophistication continued to increase after I left to reach quite a high level (like automatic triangulation and doing molecule level testing).

Cats Stealing Dogs' Jobs

Who knew that people from Japan read my blog. Tama the station master (actually in true Japanese style "super station master") is doing almost the exact thing I mentioned. Except they added merchandising - those damn cats.

A Billion Triples in your Pocket

At the Billion Triples Challenge this afternoon Cathrin Weiss showed off i-MoCo. It's a demonstration not only of a Semantic Web application with an iPhone using a stupid number of triples, but also of their indexing technique Hexastore which does all 6 indexes of RDF's subject, predicate and object in order to improve querying (they are ordered which allows you to do merge sorts). Actually, this made me think that the next steps in RDF triple stores will be indexes that are optimised for SPARQL operations and OWL inferences. Indexes for transitive closure perhaps? The data is regular and the storage is available to index triples that improve querying performance.

That wasn't the only impressive demo today. For me it's a toss up between another iPhone SemWeb demo, DBPedia mobile and SemaPlorer. DBPedia stood out because it was the only one that allowed you to write data to the Semantic Web rather than just read the carefully prepared triples. For a similar reason I thought SemaPlorer was good because they tried to do more by making it more generic like integrating flickr. But they were all excellent, all of them showing what you get with a billion or more triples and inferencing.

That combined with the guys at Freebase making all of their data available as RDF and it was a big day for the Semantic Web.

Update: I noticed that John Giannadrea's talk when he mentioned the three aspects to Freebase he went from the bottom up - probably reading too much into it.

Update: Also caught an interview with John Francis the guy who stopped talking, started walking, stopped taking mechanical transport and tried to change the world.

Update: ISWC 2008 awards have been published.

Time for REST

The best part of the latest release of JRDF is not code that we've written but Restlet. Restlet provided an excellent abstraction for providing RESTful web services and allows deployment without a container (the distributed and local server are both about ~6MB in size).

This has allowed us to quickly develop a web service that answers SPARQL queries that can be from one or many machines. We're using it to query the results from MapReduce tasks in our Hadoop cluster but it could probably be used as a general way to query other SPARQL services.

It's still early days and there's a lot that still needs to be added (and re-added) such as limiting result sizes, being able to choose which format to return and better JSON support. A lot of it has been pushed out in time to show a front-end at SSWS.

It would be good to have a Javascript client that submits the SPARQL queries and handles the ordering and such rather than having the distributed query server hang onto all results until returning.

Download it here.

President of Real America

Yes, Virginians you may not be in the real part, "Jon Stewart Clarifies Palin Remarks, Expands To 'F%ck All Y'All'". America seems to have gone completely mental. The second video covers the current lunacy including the pro and anti American members of congress and the endorsement of Colin Powell, a black militant backing Obama, what a surprise.

Case Classes

Reading "Is Scala Not “Functional Enough”? linked to a post I've read before "Are Scala's case classes a failed experiment?" but hadn't blogged about it. In Java I simply avoid using switching based on type (for example, if foo.getClass() else if bar.getClass()) I really like case classes in Scala especially for language processing.

5TB Processing

Scaling Hadoop to 4000 nodes at Yahoo! "The 4000-node cluster throughput was 7 times better than 500’s for writes and 3.6 times better for reads even though the bigger cluster carried more (4 v/s 2 tasks) per node load than the smaller one." They did some performance monitoring of the cluster and achieved sorting 6TB of data in 37 minutes.

Update: Ex-Google and Yahoo employees create start-up (called Cloudera) and Hadoop Primer by Sun (PDF).

Update: Hadoop users group meeting with IBM talking about different join techniques and Cloudbase project which is an SQL abstraction over log files (tutorial PDF).

Update: Microsoft's first project is Hadoop.

Monks Practicing Evolution

Before the printing press allowed exact copies of texts, such as Bibles and other works, scribes would copy manuscripts by hand. These copies were imperfect and these mistakes would then be replicated as other scribes made further copies. The implication is that the church was practicing evolution before science had even discovered it. Darwin could've just popped down to his local monastery or church instead of cruising around the world.

Scientists have used phylogentic software to look at these texts in order to discovery the original document sources (creating a book of life if you will). Like evolution in the natural world, the mutations aren't random and you get errors such as recombination, lateral transfer, deletions, and even convergent evolution. There are some interesting relationships that can be determined, such as certain areas of text are more likely to have mistakes in them than others.

What's cool about a theory, such as evolution, is that it can be applied to many different areas such as natural languages, behavioural patterns, archaeological artifacts, and written works such as chain letters and medieval manuscripts.

More information, Manuscript evolution and Phylogenetics of artificial manuscripts.

Coffee Inspired

• The Global graphs in JRDF was inspired by the work done in MSG (minimum self-contained graphs, published in the RDFSync paper) and RDF Molecules. The former links to an implementation of DBin (P2P Semantic Web client) and there's also GVS (Graph Versioning System).
  
• It's a trap (cloud computing) It's a fairly typical Stallman statement - not wrong but not aware of the compromises people make. It is obvious that one of the reasons vendors are excited about cloud computing is because it is a chance for them to try and own your data (or at least make switching too hard). But you do have to do more than put data in the cloud - you do have to have executable services there. There are open source cloud computing infrastructure that you can run-up on your own servers like Hadoop or CouchDB. And it's not just back to mainframes and renting CPU time out by the hour it really is different to what has gone before.


• Live the Cloud Life lists the cloud computing applications in categories such as email, documents, data, music, photo editing and storing and browser synchronisation. Some categories are missing like RSS reading and calendaring.


• Apple drops NDA - the outrage worked.


• The main eResearch 2008 conference is over and some of the papers are available.


• Speaking of which, all development, and that definitely includes software, in whatever organisation (universities, governments, banks, etc) should have failure as an option. One sign of a truly stuffed culture is to never have a project fail.


• Muradora a refactoring of Fedora to allow pluggable authentication and enable metadata editing.


• Acer Aspire One links: Dual Monitor Support,
  Installing Firefox 3 on Acer Aspire One Linux and
  Updated repositories. It's a shame that OpenOffice doesn't support presenters view yet.

More Data

Neurocommons have released their integrated RDF datasets. It is composed of different modules or bundles including MeSH, Medline, OBO and others.

Who Holds the Power?

On Monday I went and saw John Wilbanks talk on "Publishing in Today`s Environment" (I can't seem to find a decent URL but a good overview of some of the topics discussed is "The Open Access Interviews: John Wilbanks"). I didn't take many notes but a few things have stuck with me:

• Libraries providing a role as repositories of data (both public and private).


• The idea of "free as in puppy" in relation to digital curation - a great metaphor. When someone gives you a puppy it is initially free but the upkeep of it is anything but.


• The Queensland Government has its own Creative Commons initiative and the Australian Government is following suite.


• There's a power struggle occurring between researchers and publishers to make data, papers and the like freely available. The power used to be on the side of publishers but as the producers band together (by country, university, faculty and so on) the power is going back to them.


• Creative Commons are continuing to fight, in cunning ways, to get back to decent copyright law.

The kind of behavior that publishers have exhibited appears to be on the way out and seems to be going the other way. This is where databases interoperate with each other, papers can link to the original data, and tools, data and papers are all part of an integrated experience. The linking and integration of papers and other artifacts seems to be a one way process, it's hard to imagine a developer, scientist, arts graduate or anyone else spending huge amounts of money and time finally wresting control from one bunch of people only to tie it to another.

This leads to the T-Mobile G1 announcement. The announcement was very underwhelming - guys speaking for the first 10-15 minutes saying what a wonderful job they had done and the guy talking about how good an experience the phone was at playing Pacman. The more intersting part is the open platform. Much like the publishing area the ability to have open access will be a massive differentiator. It reminded me a bit about the discussion on how AOL, Prodigy and the other closed networks quickly died when faced with the open web:

By contrast, the proprietary networks of CompuServe, AOL, Prodigy, and Minitel were out beating the bushes for content, arranging to provide it through the straightforward economic model of being paid by people who would spend connect time browsing it. If anything, we would expect the proprietary networks to offer more, and for a while they did. But they also had a natural desire to act as gatekeepers—to validate anything appearing on their network, to cut individual deals for revenue sharing with their content providers, and to keep their customers from affecting the network’s technology. These tendencies meant that their rates of growth and differentiation were slow.

The closed versus open network is not quite the whole picture with respect to the iPhone versus Android. While there is competition between iTunes versus Amazon, Streetview versus normal Google Maps and there will be other content battles, I don't think that's the source of the real innovation. I think it's probably the technical innovation that the online providers couldn't match that was decisive and will be for phones:

The software driving these communities was stagnant: subscribers who were both interested in the communities’ content and technically minded had few outlets through which to contribute technical improvements to the way the communities were built. Instead, any improvements were orchestrated centrally. As the initial offerings of the proprietary networks plateaued, the Internet saw developments in technology that in turn led to developments in content and ultimately in social and economic interaction: the Web and Web sites, online shopping, peer-to-peer networking, wikis, and blogs.

Is developing on an iPhone going to lead to more technical innovation over Android? Does the ability to have open source code on Android beat the Apple NDAs?

Apple will probably recognize that it's the developers that will ultimately have the power but like publishing it depends on the actions of both parties. At the moment both of these new phone platforms are a little limited - the ability for people to innovate on iPhones using iTunes, Mail is out but it doesn't seem terribly better for Android (being DRM free is a good start though). If history is any guide, it would seem to favor open development over closed.

Update: Similar more succinct explanation.

Update: No Pragamatic book due to NDA - the outrage!

For Silver

So now I can finally run Silverlight on Chrome on Windows, all the ducks are aligned.

Make Every Web Site a Semantic Web Site

Back in March this was news but I completely missed it. Dapper has a rather nice way of turning web sites into data - XML, JSON, etc but it also includes a semanify service. It includes using existing namespaces (FOAF, GSS, Creative Commons, Media RSS and Dublin Core) supported by Yahoo's search engine.

This is covered in more depth in Semantify Hacks - Creating a your own RDF schema using Dapper:

So now, building a Dapp means you also built your own RDF compatible schema, that you can use wherever by just pointing to the webservice:

http://www.dapper.net/websiteServices/dapp-scheme.php?dappName=MYDAPP

The given example is MSN's search engine which you can see in all its RDF/XML glory.

ReadWriteWeb has step-by-step instructions.

Into Thick Air

Chrome, JavaScript, and Flash: Two (Mostly) Opposing Views the second comment closely follows a reason update on CounterNotions, Google Chrome: Bad news for Adobe.

But a full-fledged browser. One that behaves, however, as a platform to host applications best tied to cloud computing with built-in local persistence for offline computing. Sure, in its current form Chrome can’t compete with Silverlight or Flex/AIR for what Adobe calls “expressiveness,” meme-speak for rich graphics, animations, integrated video and other visual UI goodies.

Chrome may shut it off for good. It’s possible that various open source Chrome technologies could melt into Safari and Firefox. But –– whether as a stand-alone product or a progenitor of fast, powerful and expressive browsers –– Chrome signals to anybody but the diehard Microsoft constituents that the browser itself, not a proprietary plug-in or a separate runtime, is the future of RIAs. With its huge ecosystem, Microsoft can live with that. At least until its enterprise monopoly seriously erodes. But Adobe cannot.

In a world where the online pie is divided among the .NET army of Microsoft, the browser-gang of Apple+Mozilla+Google, and the lone Adobe, it’s not difficult to predict whose share will shrink into insignificance. If the exclusion of Flash from the iPhone wasn’t a wake-up call for Adobe, Chrome should certainly be one.

Most of the commentary is focused on the browser within an operating system angle. Although one of the easter eggs is a familiar screensaver. I think it's more helpful to concentrate on the fact that these browsers are getting rich enough to remove the applications embedded within browsers. There is already a lot of functionality developed or being developed such as SVG and storage (part of HTML 5). Chrome ships with Gears though and Webkit, to see how HTML5 and Gears relates see Aaron Boodman's talk on implementing HTML5 in Gears. They create two namespaces one for implementing the standard APIs and one for non-standard APIs - it seems like it has quite a solid development process behind it. Is there really a lot of reason left to support these proprietary applications within applications?

More MapReduce Groovy

A very good post on Cascading (covered previously), GOODBYE MAPREDUCE, HELLO CASCADING

Cascading’s logical model abstracts away MapReduce into a convenient tuples, pipes, and taps model. Data is represented as “Tuples”, a named list of objects. For example, I can have a tuple (”url”, “stats”), where “url” is a Hadoop “Text” object and “stats” is my own “UrlStats” complex object, containing methods for getting “numberOfHits” and “averageTimeSpent”. Tuples are kept together in “streams”, and all tuples in a stream have the exact same fields.

An operation on a stream of tuples is called a “Pipe”. There are a few kinds of pipes, each encompassing a category of transformations on a tuple stream. For instance, the “Each” pipe will apply a custom function to each individual tuple. The “GroupBy” pipe will group tuples together by a set of fields, and the “Every” pipe will apply an “aggregator function” to all tuples in a group at once.

One of the most powerful features of Cascading is the ability to fork and merge pipes together.

Once you have constructed your operations into a “pipe assembly”, you then tell Cascading how to retrieve and persist the data using an abstraction called “Tap”. “Taps” know how to convert stored data into Tuples and vice versa, and have complete control over how and where the data is stored. Cascading has a lot of built-in taps - using SequenceFiles and Text formats via HDFS are two examples. If you want to store data in your own format, you can define your own Tap. We have done this here at Rapleaf and it has worked seamlessly.

Senior Re-Searcher

Someone who continues to search (re-search) Google until he finds what is required. Senior in that he remembers a time before Google.

Stats for Nerds

I read "Is google chrome under / partially reporting RAM usage ?" which seems to be the typical problem with Microsoft's task manager. A better way to check out Chrome vs others is to hit Shift-Escape, click on "Stats for Nerds" and it has a comparison there.

Antimetabole

Bill Clinton had an interesting one recently in his Democratic convention speech: "People the world over have always been more impressed by the power of our example than by the example of our power."