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Notes for Today: March 6, 2010

Back when I started my blog, I would have entries that were simply lists of links that I'd come across and thought worth sharing or brief events during the day.  Never mind "sharing with whom."  The impetus to share, presuming some sort of tenuous permanence seems like a decent rationale for blogging.

Today, one of the tabs open was a Wolfram|Alpha preview search for Academy Award nominations for the recent Star Trek movie (makeup, sound editing, sound mixing, and visual effects).  That lead me to the Star Trek wikipedia page where I read about some of the backstories on casting, etc.  I spent a few hours rewatching that awesome movie.

Saturday's my day to work myself into a little frenzy about savings etc, so I listened to Marketplace Money and called TiVo to follow up on cancelling my subscription from a long while back and that an acceptable refund was issued.  I still sort of want one of the new super cool HD TiVo Premiers because Comcast's DVR is just awful.

Later, I watch the latest episode of Caprica and lamented (privately) that the Facebook fan page for Caprica showed the closing climactic scene of Friday's episode as a preview last week, pretty much making episode 6 literally anticlimactic. I also looked up the word apotheosis that Sister Clarisse likes to say.

I read a recent first hand report of someone who attended Singularity U's executive conference and got to thinking about small-cap biotech ETFs as the next investment bubble.  A bit of Googling came to a decent seekingalpha article that mentioned XBI, BBH, and FBT.  Apparently, the Chinese government's bought $96m worth of Illumina genetic sequencing machines (@ $750k a pop) - the same machines used by personal genomics companies 23andme, decodeme, and counsyl. Will the new phrase be "cheap chinese genomes"?

Back to Singularity U, I watched Dr. Daniel Reda's talk on Biotechnology Fundamentals and wondered if I could memorize the RNA codes for all the amino acids. May be.  It's got to be like learning hex or anything else computational.

Optimization efficacy of evolutionary techniques

Natural selection
  • Slow!
  • Optimized for selecting the best replicators
  • Builds on previous adaptations (doesn't optimize best adaptations)
  • Optimization principle: Just good enough - ie selected for whatever's just good enough to pass on genes, not for any longer (healthy life, etc.)
Human Intelligence
  • Recombinant DNA technology - cut & paste via enzyme restriction endonuclease + ligase
  • DNA printer - writes DNA
  • http://www.bio-era.net/
Recursive AI


 If you haven't seen Harvard's BioVisions animation of the cell, you should.




Protein folding
    Game: http://fold.it/portal/

http://online.wsj.com/article/SB124207326903607931.html

"Killer Apps"
  • Drug metabolism
  • High-risk drugs

Edit, 04/25/2010 (DNA Day)

The new machine, the HiSeq2000, will begin shipping next month with a cost of $690,000 vs. $500,000 for Illumina's current model. It is being unveiled today at J.P. Morgan's investment conference in San Francisco. The Beijing Genomics Institute will be the first customer, purchasing 128 of the new machines.
Illumina's Cheap New Gene Machine Matthew Herper, 01.12.10, 03:00 PM EST
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Added lightbox2 (finally).  Since I'm still using a fairly old edition of CommunityServer, I keep forgetting where various settings are.  I had to add css and js's for lightbox as well as modify the LayoutTemplate.ascx (in the Themes dir) and the communityserver.config (in the web root) to accommodate for the "rel" attribute in the anchor tag.  Without the setting to allow "rel" attributes in "a" elements, CS was stripping the necessary annotations for lightbox to function.

Completely boring non informative post.
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Lots of network traffic lately and wireshark revealed that it's these guys Project Playlist, a "service" for myspace noobs and, what looks like, gang members, to stream mp3s. Well, our friend Cameron's blog playlist. somehow got on their site, causing my pipe to be filled. That's lame of them, but whatever. All fixed. Carry on.

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I just realized that blogs are stupid. The straw that broke the camel's back was a story related to me about the head technical guy of a company who goes home after work and listens to podcasts of other technical nobodies who've just discovered or put into use some technique instead of reading a book. It's like reading (or listening) to amazon comments about cars and expecting to understand how to drive a car.

If that guy ever gets over the rat-race hump of keeping up with Constant Epiphany Guy's Blog of .NET Tricks Borrowed from Other Existing OO Systems he, himself, might warble into a bad microphone and podcast himself learning new technical abilities like marms passing around their favorite fruit-nut cake recipe. It's sad. It's also a hold over of the Big Bust - self-taught technurds trying their hardest to pretend relevance.

And, with that, I realized that there's really just no point to learning from the randomness. I thought that maybe, just maybe, nuggets of intelligence are to be gathered by sifting through the detritus and effluvia, but no, it's not to be. I actually don't want to hear someone else's path to technical nirvana or that some kid thinks they have the three-word-chant solution to peace in the middle east. That's the stuffing 'tween Pooh Bear's ears. To learn something, anything, there're books to read, courses to take, and (I can't believe I'm at this point) certificates to sit.

Sure, it's fun to look at a friends photoalbum or hear what they have to say, but Random Guy isn't going to be instructive at all for me. I might have some thoughts about politics, religion, or whatever, but it's just me making thinky into words for myself, ultimately, not for anyone's edification. I'm not a professional essayist or opiner of experiences beyond the average ken. Ok, maybe I have been to places that are uncommon and I have an interesting situation. Whatever, I'm, like, not good with explaining that. And, further, I'm no expert.

So, blogs, you're past being "on notice" (that's what all these absent days have been) and are now, officially "dead to me" ...

At least for getting information from. Unless, of course, it's meta-information and mockery about blogs themselves. And, yes, that means you, .NET "Informed" Comment and all you bleeding heart war profiteers.

This space for rent rant.

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Here's the weekend story, with it's sad ending, too:

"How cool would it be if I could capture visitor IPs for a certain url and plot them on a map, like Google maps?," I thought to myself.  "Very cool," myself responded.  Grab the IP from, say, the IIS logs or whatever and do a lookup.  No problem, right?  Wrong.  Innumerable ips to look up, lots of DNS, stupid IIS permissions.  "How about a javascript that calls a simple page to record the host ip and the datetime?," I said to myself.  Slightly concerned that I was going crazy, I replied tentatively, "Sure, that sounds good."

I grabbed the raw delegation ranges text file that ARIN has mirrored for RIPE, LACNIC, and APNIC (RIPE has AFRINIC's mirrored) and stuck them in a db (there're only about 70,000, a lot less than the max amount of ipv4 ips), made an IP address to IP number conversion utility, a quick lookup utility to get the IP block of a particular IP number and, finally, a little whois'er that queries the block registries (not domain registrars) and grabbed city and country name.  The last little bit was manually adding geocoords (lat,lon) to each city in the city table, but that's easy.  (I'm thinking about how to automate that bit, too.)   Phew!  Technical mumbo-jumbo aside, I get the visitor's city and plot on map.


The final result looks sweet. (Petah Tiqwa, Israel?) For example, this blog's hits come from all over, see here.

This morning, as I'm perusing some news I see that Google's releasing their analytics product for free (Free Web site therapy, Reuters, 11/14/2005; Google Press Release).  Yay!  I like Google.  Then it hits me:  I've just been housed!  Granted, they've probably had the idea for a lot longer, more resources than just one guy and a weekend, and much, much more data, but check out the neat picture from their main page:

It's (of course) got a map to track visitors! (Their map is Flash, though.  Odd, I thought, when they have a map tool. Seems like this analytics suite was bought/enhanced from some company called 'Urchin5'?  May have to look into it, may not care so much, either).  It uses a simple little javascript to ping their servers. It has pie charts.  Everyone knows that pie charts are the end-all-be all of cool.  Google:1, Me: 0.

Of course, I'm not competing with their product or even into "analytics," I'm just experimenting.  I learned a whole bunch, too.  For instance, NET 1.1 (which I used instead of Java, for kicks, or 2.0, which looks pretty neat, too) is pretty straightforward, once you get used to its quirks.  I dislike how it reformats HTML and how it doesn't compile in the background like Eclipse.  Parsing registry data into a db's easy, lookup reconciliation's not too bad, and generating javascript for the Google maps is a snap.  I'll keep playing around with my app, trying to make it more efficient and automated, but I'm going to stick on the Google Analytics' javascript on a few urls.  Since they're (Google, collectively) smarter than I am (and have a patent on address geocoding), I'll be interested to see how well my data tracks.

[Edit: here's a story about how Google's liberation of the Urchin product effects analytics firms: WebSideStory Stock Falls on Google Plans, AP, 11/14/2005.
Urchin, also a San Deigo company, was acquired by Google in March 2005 and was, apparently, big news in the SEO community.  Urchin's service was a $199/mo.]

[Edit: replaced the link to the Google patent on USPTO with a link to Google's patent search on the patent. Neat!]

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One of the most annoying things to do is upgradinging this blog.  .Text to CS1.1 using Kevin Harder's converter read like it was straighforward, but it turned out it wasn't.  It's possible I missed some option to create a single stand-alone blog, because Community Server is geared towards one site, many blogs (photo albums and forums, too).  I wanted to replicate my single blog on my main url, not under some depth.  Seems like there's a lot of good in CS, but last night all I could do was get frustrated with it.

My goal was to migrate my base-url blog from .Text to CS.  I eventually found Dan Bartel's article on how to do a single blog configuration for 1.1, but not after completely messing up my directory structure.  Yeah, I know, I can just back out (which I plan to do) and redo it, since all of the changes are config files and not code at this point, but what's a blog for if not for kvetch?  Oh, right, as you might be able to tell, my css's hosed.

The Ideal Goal would be to get the multiple installs of .Text blog sites that I have on the server under one CS installation, yet still retain the individual URLs of these sites.  With the cursory look into the CS structure, it looks like I'll still have to have multiple CS installations, but possibly a single CS database.  I've a bit of trepidation in losing the authors of the comments when converting some of the more heavily commented blogs, though.  C'est la .net blogs.

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sage is pretty neat. I've just installed it at work to cut down on the endless yet numbered tabs I have open with blogs in them. I'm hoping there's a way to populate it via some bloggregation so that the problem with distributed bookmarks doesn't rear it's head for blogs.

Edit: There is an import/export, using OPML (Outline Processing Markup Language).
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It appears that CommunityServer 1.0 is out, which is a very big upgrade to .Text. Here's a converter that I may use.
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I screwed up Jack's password while trying to reset Amanda's.  The .Text blog software stores passwords as hashes, which we all know is smart.  In order to fix it, I wrote a password hasher, which was silly and annoying.

In doing so, I ran across some urls which were fun to read:
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So, after me telling them on 11/16 that it (connection cycling, dropping at the DSLAM or somesuch) was their problem (after calling FRII, of course), they said they found something on their end and were going to fix it. This morning, I call because DSL's still not training up and, yep, that's right, a coil's unplugged at the CO or somesuch. Thanks guys. I'm lobbying for a credit.
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I currently use the LuxInterior Dark skin, which i've slightly modified.  I'm planning on doing some modification to this skin and .Text in general, so I'll be keeping a running set of info here.

DotText Skin Directory
How To Create Custom Skins For DotText
tdhLuxLight - a variant on LuxInterior

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simple dts scriptoid pushed all my shappy blog entries into the .text db schema.  operation successful.
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Where're the other entries you ask, dear reader?  Well, I'm working on a dts to move over my previous notes from my handcrafted and poorly maintained blog, .shappy, to .Text's database schema.  Shouldn't take more than a few days, so fear not!

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So, the directory issue that I couldn't figure out wrt Ian's blog was because I have trouble reading the .Text wiki details about the ConfigProvider.  All fixed (for me).  Will have to look into fixing for Ian, and maybe Jack.

Setting up .Text was rather easy, relatively, mostly because this is the 5th time I've done it.  Preloading screwing up fase and cocking nek does help.

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for your fase: rss feed
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changed this look to be more subtle/conformist than the original, pushing more display control into css, rethinking a query or two, rss, more and less modules (allowing for per-date grouping, generic text box for sidebar, rss reader)
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new view, in prep for using this more.
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test of entry form. Yep, worked. I decided to start this mental dribble by creating mgmt functions first. This is only a test.
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