Apparently, having a journal entry counts as a /. "achievement". It's about the only reason I can conceive of for making this journal entry. It's a fairly weak reason, at that, since most /. "achievements" are by no means achievements.

New JonesBlog update. Bionic implants

The device seen in these images is called the Utah Electrode Array (WARNING: potentially graphic image after the jump of an implant in a human brain). The Utah Electrode Array is a brain implant technology developed here at the University of Utah by Richard Normann. The purpose of this device, built by currently built for us by Blackrock Microsystems is to transduce signals from external devices to deliver to the brain for interpretation. Alternatively, the device can record impulses generated in the brain for delivery of neural signals to external devices. Our potential interests in this approach are manifold, but real use and implementation of these devices is some years away still.

New JonesBlog update. Bonneville Speed Week 2009

New JonesBlog update. Its spelt F-L-Y

I recently blogged a couple brainstorms on potential tools in the field of phylogeny-

Long-term alternatives to our current common-descent model in contexts where horizontal gene transfer is significant;

Logarithmic Evolution Distance, an intuitive computational approach to comparing genomes.

They were a lot of fun to think about; perhaps they'd be fun to read if you like theoretical biology stuff.

New JonesBlog update. USS Toledo SSN-769

New JonesBlog update. A Computational Framework for Ultrastructural Mapping of Neural Circuitry

We have just published a manuscript in PLoS Biology where we describe how to build a complete and accurate neural network. This of course is one of the long standing holy grails in neuroscience. So, this effort meets two goals: 1) It meets the goals of building a complete neural connectome (we'll be finished collecting all of the data with cell identity, physiologic response and all synaptic connectivity in approximately six days) and 2) It defines a workflow whereby investigators from around the planet can download and use the tools we are providing to build their own connectome projects using existing infrastructure. We are making those tools available here to enable other groups to assemble, browse and annotate the terabyte sized datasets required of connectome level projects.

About two years ago I wrote a piece of software that sits squarely in between two open source products. Two years later I'm no further along in getting my company to agree to open source the software. What suggestions do Slashdot readers have to help me convince the powers that be that the software should be open sourced?

Well, Mr. 4-digit UID asshat: I now know who you are. Let's just say my spies are everywhere. Oh, no, I'm not going to call you out. I want you to sweat it: does he really know or not? Because you don't want a war. You really don't want to pick a fight with me. I've been on this system at least as long as you have. Think about what that means. Or are you too stupid? Better watch your back, pal.

This is another open letter to Brad Smith, Microsoft's general legal counsel, in regards to their thinly veiled Linux patent threats and related lawsuit against TomTom.

(Disclaimer: As I am a nobody as far as Microsoft is concerned, I don't honestly expect Brad Smith or anyone at Microsoft to read this, and I don't care. Mostly I'm just blowing off steam and getting my beefs out in the open).

So it's come to this, is it? Suing over an ancient filesystem developed from the the 1970s (FAT) and the assorted ugly hackish kluges that have been necessary to keep the decrepit pile of garbage on life support? The one that only became a defacto standard because at one time its use was all but mandated by some older versions of Microsoft Windows that didn't support anything else? You know, the one originally developed for floppy disks?

Why don't you just stop your lawsuit now before you get laughed out of the courtroom? Seriously, you guys are starting to look more and more like your old sock puppet, The SCO Group? Remember them? Yeah, they're basically on life support now thanks to IBM, Novell and Red Hat practically bankrupting them. Guess they chose the wrong opponents to pick a fight with, huh?

So you thought maybe TomTom would roll over and play dead, eh? I guess they didn't. Especially now that they're backed by the Open Invention Network.

So you have $20 billion in the bank? Wanna watch that money continue to slowly dwindle whilst you fight the Linux community? You don't get it do you? A lot of people with serious cash have a vested interest interest in watching Linux succeed in dwindling your market share. You think others in the industry aren't prepared to enter the melee between you and TomTom? Wrong.

Give it up before you embarrass yourself. Seriously.

New JonesBlog update. Desire...

Sys-Con.tv is reporting that The Pirate Bay is currently offline due to massive DDoS attack:

I just got word that "someone" is currently DDoS'ing the thepiratebay.org. Even more interesting it may be a hijacked botnet causing the problem. More details as they come in.

Interesting. Now we'll know if the theories about the BitTorrent network experiencing difficulties if/when The Pirate Bay gets taken down are true.

In related news Wired is reporting that the prosecutor and Hollywood are demanding prison sentences for the four defendants in The Pirate Bay case.

Think SSDs are so much wickedly faster than top of the line mechanical drives like the Western Digital Velociraptor? Maybe not. Bill O'Brien has an article on his site debunking three common myths about solid state drives (SSDs):

Myth 1: A Solid State Disk will boot faster than mechanical hard drive.
This is true but it's partially smoke and mirrors as well. When SSDs first appeared, they were rather pathetic 8GB and 16GB devices. Not much fits in that size. Even at 32GB you'll still be somewhat cramped if you have hardware drivers and applications. But when you get to 64GB or 80GB or 128GB -and you have some room to feel confident about carrying the additional software you need around with you--you start to add time to the boot process.

Some of you may remember Bill O'Brien from his stint at Computer Shopper, where he co-wrote The Hard Edge with Alice Hill.

I've seen a bunch of complaints lately about the new beta index. Now, I know that it's been in a state of rapid flux in the past few weeks as they try different things -- sometimes the thing doesn't even render right. Of course, this is 'beta', so you take your lumps as they work out the bugs.

Other than the occasional rendering problem and associated weirdness, though, I have to say that I rather like the new interface.

Wha? Why are you all looking at me like that?

Seriously. Listen. Okay, I don't like the green "idle" look very much, either. I personally think it's a bit difficult to read. But, other than that, I think the changes improve the usefulness of the site. Firehose has become more integrated with the main page, for instance. The whole thing is more dynamic, more AJAXy and overall the feel is much faster and much easier to sort through to find what you're looking for.

If you don't like it, you can always use the RSS feeds.

I welcome your opinions and comments, especially opposing viewpoints.

Okay, so I'm a little slow at jumping on bandwagons. Having written code to parse everything from XML configuration files to Windows-style .INI files, I've always thought that writing code to create and parse configuration files sucked. And that things like ConfigParser and xml.dom.minidom in Python made it suck a little less.

So, having worked with XML, I had heard of JSON as an alternative to XML and always thought "Wow. I'm going to have to write ANOTHER parser? Ugh." Obviously I just didn't get it.

So I wrote a little proggie the other day and needed an object-oriented-type configuration file for it and thought, for some strange reason, they I should do something a little lighter weight than XML. Flat .INIs weren't going to work because, well, they're flat. ;) So I decided to give this JSON thing a try.

I looked at the JSON documentation for Python 2.6 (and simplejson for Python 2.5, which the Python 2.6 json module is based on) and went huh? That's it? That can't be it. I'll need to write more methods than that surely.

As I looked more and more at it, I realized uhhhh...a JSON file looks rather like a Python dictionary (like a hash table in Perl or C) with str and numeric values. And lists! (Values can be lists!) Perfect. And when you parse it, you get exactly that -- a big Python dictionary. Wow! *slaps forehead* How much easier can you make it than that?

So you can have

{
        "window": {
                "width": 150,
                "height": 200
        },
        "bookmarks": [
              {
                  "name": "Slashdot - News for Nerds. Stuff that Matters",
                  "url": "http://slashdot.org" },
              { "name": "Google Docs",
                  "url": "http://docs.google.com" },
        ]
}

(forgive me if Slashdot mangles the indentation as it usually does)

and then you can access the whole shebang via

>>> import json
>>> configFile=open('foo.rc','r')
>>> config=json.load(f)
>>> config['window']['height']
200
>>> for bookmark in config['bookmars']: print bookmark['url'] ...
http://slashdot.org
http://docs.google.com

And the JSON file can be entirely self-documenting: You can put literally anything you want for each of the key:value pairs.

And since writing out the JSON file is just easy (just in reverse), you can easily write a configuration GUI, with the same brand of direct access to the JSON structure.

Now that's easy.