Dictionary Evangelist

2008-11-16: I just watched a TED presentation on the dictionary by Erin McKean — http://dictionaryevangelist.com/ — I love reading the dictionary.

I have the American Heritage Dictionary With Thesaurus, Fourth Edition, installed on my laptop, along with the New Oxford American Dictionary, which comes with Mac OS X. I spend a lot of time browing these dictionaries.

Resuscitating a PowerBook G4 (2)

2008-11-16: I removed Debian 4.0r5 from my PowerBook G4 and installed Mac OS X 10.5. I’m very pleased with how fast the computer still is.

Yesterday, I installed Debian 4.0r5 for PowerPC on my 1.5-GHz PowerBook G4. Unfortunately, it wouldn’t connect to my Airport Extreme base station, and I didn’t have the patience to twiddle with the configuration files. I read the documentation for Mac OS X 10.5 and discovered I could install it on the PowerBook, so that’s what I did, and it runs great.

Working on the Weekend

2008-11-17: @pyyhkala My observation is that working four hours on the weekend is equivalent to eight hours on a weekday. There’s a problem here.

I usually work several hours every weekend in order to keep up with the demands of my job. I often put off until the weekend those tasks where I need several hours to concentrate.

Pandemonium Bookstore

2008-11-17: I went to Pandemonium in Central Square (Cambridge) tonight to buy a book for vacation. I bought A Fire Upon the Deep, by Vernor Vinge.

Pandemonium is a book store in Cambridge that specializes in gaming, science fiction, and fantasy. Their selection of science fiction is very good because they have a lot of used books.

Not a Smartphone

2008-11-18: My new cell phone will be delivered today. It’s so not a smartphone that it doesn’t even have a camera. It’s just a phone, nothing more.

I thought about buying a smartphone, and I looked into it carefully. But I’m on the Internet all day long at work, and then I’m on the Internet when I’m at home, so I don’t really need a smartphone. So I ordered a Samsung Knack (see the CNET review), which is a no-frills cell phone and nothing more.

If Verizon had the iPhone, I would buy one. But after billing problems I had with AT&T several years ago, I vowed never to do business with them again.

Charles Stross and Vernor Vinge

2008-11-18: @agbiotec Stross is on my list of authors to read. Vinge’s A Deepness in the Sky is the best science fiction book I’ve read this year.

@agbiotec is the second person to recommend books by Charles Stross. I’ll get to Stross soon.

Testing PowerBook Batteries

2008-11-18: I’m testing three old batteries in my PowerBook G4 to see how long they last after charging. One battery has a cycle count of 753!

These batteries have seen hard use. None of the batteries lasts longer than one hour forty minutes. I need to buy a new battery.

Missouri No Longer a Bellwether State

2008-11-19: McCain is finally declared the winner in Missouri. We lived in Missouri for seven years; we’re much happier in Massachusetts.

Missouri is blue in St. Louis and Kansas City, red otherwise. My wife and I are very liberal, and we sometimes felt uncomfortable in the conservative Missouri culture. Obama did a great job challenging McCain in Missouri, and he almost pulled it off. This breaks Missouri’s string of casting its electoral votes for the winner of the presidential election.

Vacation Reading

2008-11-19: I’m on vacation, so I’ve been reading today: Hallelujah Junction, by John Adams; Mac OS X Leopard: The Missing Manual, by David Pogue.

I’m reading David Pogue’s book using my Safari Books subscription, which has saved me a lot of money so far. I bought John Adams’s autobiography at Porter Square Books, one of my favorite local bookstores.

Trading in an iPod mini for an iPod touch

2008-11-20: I erased my three-and-a-half year old iPod mini this morning. I’m going to trade it in today for the 10% discount on a new iPod nano.

2008-11-20: I went to the Apple store on Boylston today to buy an iPod nano, but I came home with an iPod touch. I got 10% off for my old iPod mini.

Oh, did I mention that you can trade in an old iPod at the Apple store and get 10% off on a new iPod? I wasn’t sure I believed it, but it’s true. I had to fill in a form with my name, address, email address, and the serial number of the old iPod.

My initial plan was to buy an iPod nano, but the 8-GB iPod touch is only $80 more, and I wanted the larger screen to watch TED videos on, so I splurged.

The Long Now and Anathem

2008-11-21: The Long Now, a project to build a clock that will last 10,000 years, provided inspiration for Stephenson’s Anathem.

I learned about the Long Now project from a TED presentation by Steward Brand. Neal Stephenson’s connection to the Long Now project is described in this post. Anathem is a book that has remained in my head after I finished it; I will probably reread it in December.

iPod Touch 2.2

2008-11-21: iPod touch 2.2 update is 277.7 MB in size. I updated iTunes to 8.0.2 first, but I don’t know if that is a requirement. Downloading now….

2008-11-21: iPod touch 2.2 update was problem-free. I’m still in novelty mode in the App Store. Complete works of Shakespeare for free is awesome.

The 2.2 update for the iPhone provided Street View for Google Maps, but not on the iPod touch; no one really knows why.

I’ve been spending a lot of time on the App Store seeing what’s available. My choices so far:

• Google Earth
• Shakespeare
• Stanza

Unfortunately, there’s a real paucity of scientific applications.

Boston Drum Center

2008-11-22: I took my brother, who is visiting from Oregon, out to the Boston Drum Center in Acton, where he tried all the cymbals. Great store!

Harvard Square Book Shopping

2008-11-22: @02138now My brother and I bought presents for his kids at Curious George and the Coop. Both stores were packed with people who love books.

@02138now retweets Harvard Square activities; 02138 is the zip code that contains Harvard Square.

Touch Screens

2008-11-22: This afternoon, the touch screen of my cell phone wouldn’t respond. Then I remembered, it doesn’t have a touch screen.

This is iPod touch disease. I use my iPod touch so much more than my cell phone that I forget that I have to use the buttons on my cell phone.

Learning Microsoft Access

2008-11-09: My colleagues use Microsoft Access heavily, so I’ve spent the entire day using Vista + Access 2007 on my MacBook Pro.

2008-11-09: I highly recommend Access Data Analysis Cookbook, by Ken Bluttman and Wayne S. Freeze (O’Reilly). Good examples and code samples.

Vista and Office 2007 run very nicely on my 2.2-GHz MacBook Pro. I’m not very enthusiastic about most Microsoft products, but I think Access is a really great tool for managing data.

Michael Crichton

2008-11-09: This is Audible devoted a show to the recently deceased Michael Crichton, who didn’t think global warming is real. It is real.

I am not a fan of Michael Crichton.

Verizon Store Incompetence

2008-11-10: We went to the Verizon store to combine our accounts and buy new phones. Somehow, Verizon couldn’t get it together to help us out. No go.

We were told that we couldn’t combine our accounts to a family plan until we received and activated our new phones. We spent an hour looking at phones and picking out a model. Then we were told that the store was out of stock on that phone, so we would have to order it. And then it turned out that the phone wasn’t available at the warehouse, either, so we’d have to choose a different phone. These scenarios weren’t helpful, so we left. We plan to order our new phones online.

Paul Krugman: The Conscience of a Liberal

2008-11-10: I just finished listening to the audiobook The Conscience of a Liberal, by Paul Krugman, winner of the Noble Memorial Prize for Economics.

2008-11-10: Paul Krugman got interested in economics after reading Isaac Asimov’s Foundation Trilogy. He writes for the New York Times.

Paul Krugman asserts that conservative Republicans want to destroy the protections created by the New Deal and later enhanced in the 1950’s and 1960’s, when Democrats and Republicans did a better job of working together to promote welfare. Fortunately, people have finally figured this out after the eight disastrous years of the Bush/Cheney administration, but there’s a lot of damage to repair.

Resuscitating a PowerBook G4

2008-11-15: Tonight I installed Debian 4.0r5 on my old PowerBook G4, but I can’t get a wireless connection to my Airport Extreme base station.

My wife is a proud owner of a shiny, new MacBook Pro. I took her to the Apple store on Boylston Street in Boston to look at the new models, but she did not want a model with the glossy screen. We ordered the previous model with a matte screen from MacConnection, which has them for $400 off.

I got my old PowerBook G4 back when the new MacBook Pro arrived. It has been a solid machine with no problems, although the case has a lot of dents and dings. I thought I would install Linux on it for experimentation, since my only Linux computer is an old Toshiba laptop with only 1 GB of RAM.

@agbiotec had good luck with installing Debian on his PowerBook, but no matter what I did, I couldn’t get a connection to my Airport base station using WPA. Another drawback to Debian was that Firefox 2.0.x was the latest version available, and I didn’t really want to have to compile Firefox 3.0.x.

The Election

2008-11-02: @feministchemist Bill Clinton was Arkansas attorney general for 2 yrs and Arkansas governor for 2 and 10 years, way more exp. than Palin.

2008-11-03: I’m sick to damn death of political ads that lie. Politicians will do anything to get into office. It’s no wonder no one respects them.

2008-11-04: @feministchemist I, too, was disappointed that Obama didn’t pick a woman for VP. Granholm, McCaskill, or Gregoire would have been good.

2008-11-04: I’m off to vote. We expect a record turnout in Massachusetts, which was ignored by presidential candidates because we’re solid blue.

2008-11-04: I waited in line for 20 minutes to vote this morning. For once, I have voted for the winner in every race and initiative.

2008-11-04: John McCain’s good side came out during his concession speech. Too little, too late, after his despicable behavior during the campaign.

2008-11-04: Congratulations, Barack Obama! I wish I were in Chicago to help celebrate. I’m feeling hopeful for the future of the United States.

2008-11-05 12:14 AM: What a great speech Obama is giving. This is such a wonderful change from the horrible Bush years. Counting the days to January 20th….

2008-11-08: “Yes we did!” crows moveon.org (of which I’m a member). But I think moveon is premature; the real work starts now.

That was a good election, even though the counting is dragging on and on. The Bush/Cheney administration caused real, lasting damage to the United States that will take years to heal.

Recreation

2008-11-02: We enjoyed a beautiful autumn day by taking the dogs to Revere Beach. That is the end of vacation; it’s back to work tomorrow morning.

Dogs are allowed on the beach after summer is over. The beach is so empty that we let our dogs off their leashes, and they have a good time sniffing seaweed and chasing their tennis ball.

SQL

2008-11-02: I feel like an idiot. I just learned that you can GROUP BY more than one field in an SQL statement, a solution I couldn’t figure out myself.

2008-11-03: @gotgenes In my opinion, SQL was not well designed. A language should be consistent in its syntax, and it should help, not hinder the user.

2008-11-04: I spent my afternoon taking doses of DayQuil and writing SQL queries. I will probably have to rewrite the drug-addled queries tomorrow.

2008-11-05: I wrote a lot of SQL commands again today. I feel like I’m becoming an SQL master.

I’m getting better at SQL by having to use it daily.

Phishing Example

2008-11-03: I posted a link to a phishing page as an example of what one looks like, but then deleted it because I might be violating the twitter TOS.

2008-11-03: The story about the phishing page is at http://tinyurl.com/6g5sgs. Firefox 3.0 blocks access to the page, but Safari does not.

I thought this was interesting, having never seen a phishing page before. It’s a pretty big giveaway when the page asks for your social security number. What I found interesting was that the phishing site got most of its content directly from the akamai.net servers that support Apple’s site. I made the following comments on the MacInTouch web site:

I examined the HTML source code for the phishing page. It is full of links to authentic apple.com material (style sheets, JavaScript code, and image files) hosted at https://a248.e.akamai.net/. If akamai.net checked the referring host for these requests, it could easily detect that the requesting page is not hosted by apple.com, and it could block the request. This would disable most of what makes the phishing page look authentic. I think akamai.net is making it too easy for the phishers.

For entertainment, without having filled in the form, click the Continue button. A very ugly graphic appears that pretends to process the submission, followed by forwarding to a real apple.com page. Firefox 3.0 blocks access to the phishing page, but Safari does not.

New MacBook Pro

2008-11-05: This morning I ordered a new MacBook Pro, the older matte screen model, which is still available for $400 off from macconnection.com.

This will be my wife’s new laptop, which she uses for her business. We went to the Apple store and looked at the new models, and she doesn’t like the glossy screen on the new model.

TED

2008-11-06: I just learned about TEDTalks. It’s like going to a conference but in the comfort of your own home at no expense.

The only drawback is that I have a backlog of about 70 talks I want to watch; this will take about 35 hours.

What Is That Song?

2008-11-06: I heard a song at Flat Top Johnny’s in Kendall Square this evening that is familiar, but I can’t remember the artist. I need music search!

@neilfws recommended that I try http://www.melodyhound.com/. Unfortunately, by the time I received his tweet, the tune had gone out of my head.

Vote by Mail

2008-10-28: I spent the weekend in Oregon, where they vote by mail. Everyone I talked to has already voted. The election is over, except for counting.

Apparently, many people around the country are voting early by absentee ballot or other early voting mechanisms. Vote by mail has been a huge success in Oregon, which is a state that does not tolerate corruption and fraud. I’d like to see voting by mail in Massachusetts.

Twitter Is Improving

2008-10-28: I spent the last four days without Internet access. I discovered today that Twitter now gives you 40 pages of tweets. I have twitter-glut.

When I visit my parents, I don’t have good access to the Internet. After a four-day visit, I’m pretty behind on Twitter, and it used to be that Twitter would provide access only to the ten most recent pages of tweets (which for me is about one day’s worth). Now Twitter provides at least forty pages of recent tweets, a huge improvement. Their efforts at stabilizing their service are paying off. (Now if they can only figure out how to make money off the service.)

The Beet Queen, by Louise Erdrich

2008-10-28: On the plane to Portland on Friday, I finally read The Beet Queen, by Louise Erdrich. That is a great book, but all the characters are crazy.

I have had this book on my bookshelf for nearly twenty years. It is beautifully written, with believable and truly human characters. But because the characters are human, they are all nut cases; I would not want to know any of these people.

Sarah Palin and John McCain

2008-10-28: Here’s a photo, from the Washington Post, in which Sarah Palin and John McCain are flashing gang signs.

My wife found this photo and pointed it out to me, making the comment about gang signs.

Dell Incompatible With Dell

2008-10-29: My stupid Dell laptop, running Windows XP SP2, has forgotten again how to set the correct resolution on my 1680 x 1050 Dell monitor.

This is an on-going battle between my Dell Latitude 610 laptop and my Dell 22-inch monitor. My Apple MacBook Pro never has a problem with this monitor.

The Silent War, by Ben Bova

2008-10-29: Yesterday, I read The Silent War, Book 3 of the Asteroid Wars, by Ben Bova. I like it that Bova doesn’t fall in love with his characters.

These books are not compelling or great literature, but they are intelligent and entertaining. Bova allows things to happen to his characters; some change because of events or stress, and sometimes a main character dies. Many threads in his books are left unresolved and are not picked up in the sequels.

I read somewhere (but I can’t find the reference now) that Bova uses ancient Greek tragedies as a guide to writing his books. I think that sometimes he reaches a point where he has to decide whether a character lives or dies, and he flips a coin.

Learning SQL

2008-10-30: I find SQL hard and counterintuitive. I’m attempting to improve my SQL skills by reading SQL Cookbook and SQL Hacks, two O’Reilly books.

Hallowe’en

2008-11-01: We spent Hallowe’en in New York City at a combined wedding reception and costume party. We went as Nick and Nora Charles (The Thin Man).

2008-11-01: Did anyone dress as an avout last night, wearing a bolt and chord and carrying a sphere?

The first tweet is a reference to The Thin Man series of movies, which star William Powell and Myrna Loy as Nick and Nora Charles. The movies are based on The Thin Man, written by Dashiell Hammett. The “thin man” is actually one of the characters in the book and the first movie who is missing and is suspected of murder. Nick Charles wears a pencil-thin mustache, so I let my mustache grow for two months. Since it was grey, I dyed it and then shaved it down to a pencil-thin mustache for the party. As soon as we got back to our hotel room, I shaved the damn thing off, because it made me look old.

The second tweet is a reference to Anathem, by Neal Stephenson. One comment I received was that I am the only one who has actually finished this book. A common complaint has been that you have to read 250 pages before you can really get into the book. I had the same experience, but having read many very long books, I have learned to persist. My experience reading Anathem was the same as reading Jonathan Strange & Mr Norrell, by Susanna Clarke. Both books were slow going at first, both books were extremely long, but the effort was worth it to reach the end.

Anathem, by Neal Stephenson

2008-10-19: I finished Anathem after a marathon reading session. Stephenson kept me guessing to the end. It was a very good book.

As I wrote last week, Neal Stephenson did a good job of creating a new world, although I don’t think the result was as complete as Dune, by Frank Herbert. There is a twist near the end of Anathem, where Stephenson goes off in a new direction, that I didn’t find entirely convincing. I’m going to have to reread this book soon.

Database Development Using MySQL and Perl

2008-10-20: I spent the day designing a new database and writing Perl code to fill it. I’m applying Perl Best Practices, by Damian Conway.

2008-10-22: 8 solid hours of coding today. By the end of the day, all test data was loading correctly into my new database. Big data load is tomorrow.

2008-10-22: I stayed up late experimenting with creating an ERD of my MySQL database using Visio Pro 2007. The MySQL 5.1 ODBC driver is necessary.

2008-10-22: Microsoft tools such as Visio Pro are the wrong tools to use with MySQL. Tomorrow, I will experiment with MySQL Workbench.

I’ve been doing what I’m good at, creating a database and getting data into it and out of it.

Republican Party Obtuseness

2008-10-23: The Republican Party thought $150,000 in new clothing would fool us into thinking Sarah Palin is qualified for VP. Nope, still not.

I don’t understand why the Republican Party would destroy the image of an “ordinary hockey mom” by buying her $150,000 of clothes. Of course, Sarah Palin and her husband already have an estimated net worth of $1 million, so they aren’t ordinary people. Sarah Palin is dangerously unqualified for vice president; McCain made a mistake choosing her.

HONK! Festival

2008-10-12: HONK! festival was a huge success yesterday. Today’s parade from Davis Square to Harvard Square starts at noon. http://www.honkfest.org/

2008-10-12: The HONK! Festival parade today reclaimed the streets for horns, bikes, and feet. A good crowd followed the parade down Mass. Ave.

I wish I knew how to play a musical instrument, so I could participate.

The Rock Rats, by Ben Bova

2008-10-12: Another audio book from audible.com finished: The Rock Rats (The Asteroid Wars, Part 2), by Ben Bova. Excellent production, good story.

Ben Bova’s novels contain lots of interesting ideas and pretty good characters. The audio books make them even better, because they use multiple readers. This gives the listener a better sense of the different characters.

Columbus Day

2008-10-13: Today is Columbus Day in the United States — probably our most stupid holiday — celebrating a man who didn’t know what he’d found.

Code Documentation

2008-10-13: I struggled all day with badly-documented code. I just cannot figure out how some things are done. It might be faster to rewrite the code.

It’s a dilemma whether to use the existing code or write new code. Sometimes there is no good answer, but there is always pain.

New MacBook Pro Models

2008-10-14: I’m disappointed by the new MacBook Pros. I consider the new keyboard and the glossy screen two steps backward. I have no urge to buy.

2008-10-16: We’re going to the Apple store on Boylston tomorrow evening to test the new MacBook Pro. If we don’t like it, we’ll order the old model.

2008-10-17: We’re back from looking at the new MacBook Pros. The keyboard is better than I thought, but we dislike the glossy screen.

The glossy screen becomes an ergonomics issue when the user has to cope with bright reflections. It is disappointing how sometimes Apple makes a bad decision based solely on design and Steve Jobs’s whims.

Group Meeting

2008-10-17: I stayed up until 1:00 am last night working on a presentation I gave at group meeting today. Presentation provoked lots of discussion.

2008-10-17: I was so tired, I fell asleep on the sofa at 8:30 pm while reading Anathem. It wasn’t the book that made me sleepy, it was lack of sleep.

It’s disappointing that sometimes I have to work so hard that I don’t have time for my personal life.

Ringo Starr

2008-10-17: I dreamed last night that Ringo Starr was playing drums brilliantly, dynamically, in a live show. When I woke up, I burst out laughing.

My father plays drums and my brother plays drums, so I know what good drumming sounds like. Ringo plays adequate drums on many early Beatles tunes, but his later work is abysmal.

Anathem, by Neal Stephenson

2008-10-18: I’ve devoted my day to reading Anathem. Stephenson has created a new world — not as rich and complex as, say, Dune, but very good.

I’m really enjoying this book, and I’m so emotionally involved that it brought me to tears in a couple of places.

Current Bioinformatics Projects

2008-10-05: I spent the morning applying graphical residual analysis to my data. My model isn’t as good as I thought.

2008-10-05: I analyzed some different data this evening. My model is the best of the three I’m testing — w00t!

2008-10-06: I wrote some good Perl code today, but I’m in a hurry and haven’t written the tests yet. I will pay for this later.

2008-10-08: I’m close to finishing another project, but only by working long hours. I won’t be completely caught up by vacation the last week of Oct.

I’ve been working hard and (sometimes) having fun.

The Election

2008-10-07: John McCain, one of the few Republicans I have respected, has lost my respect by making stupid decisions (Palin), lying, going negative.

2008-10-10: Palin’s chief qualification for office: She has experience abusing authority. She is just another conservative hypocrite.

I’m not a Republican.

I’m an Apple Fanboy

2008-10-07: I’m working at home early this morning using my year-old MacBook Pro, which is still an outstanding laptop.

FireFox Doesn’t Support the <nobr> Tag

2008-10-08: A web page at work loaded fine in IE6 but not in Firefox; programmer had used the <nobr> tag, which is not standard HTML. I asked for a fix.

This is what happens when you test only with Internet Explorer 6.

Nobel Prizes

2008-10-08: @easternblot I agree about Nobel prizes. Physics was the premier science of the 20th century; biology is the premier science of the 21st.

In my opinion, the biggest challenges of the 21st century will be solved with biology.

HONK! Festival

2008-10-09: HONK! is coming to Davis Square and Harvard Square this weekend — so fun last year, I watched the parade twice. http://www.honkfest.org/.

The Picture of Dorian Gray, by Oscar Wilde

2008-10-11: I finished an audio book today from audible.com: The Picture of Dorian Gray, by Oscar Wilde, read by Edward Petherbridge. It was excellent.

Listening to audio books has greatly increased my ability to “read”, since I can listen while walking to and from work, 90 minutes a day. I picked the version read by Edward Petherbridge because I have enjoyed him in various television series and audiobooks.

Safari Books

2008-09-28: I subscribed today to Safari Books. I’ve started with Learning JavaScript and jQuery in Action. I will expand to 10-book limit soon.

2008-09-28: @mndoci I’m paying for Safari Books out of my own pocket, but it’s only $23 a month. I buy ~20 technical books a year, so I’ll save money.

I thought for many months before subscribing, but I think a subscription will save me money in the long run. There are many books that I want to read only a few chapters of, so they’re not worth purchasing.

Learning JavaScript

2008-09-30: I’m reaching the point in my JavaScript reading that I’m about to begin applying jQuery to my project.

Current Bioinformatics Projects

2008-09-30: I had a tedious day of making scatter plots in Excel and transferring them to PowerPoint for a presentation I’m giving. I wish I’d used R.

2008-10-02: Hierarchical data is not easy to store in a relational database. Today I learned a good way to store hierarchical data in MySQL.

2008-10-03: @agbiotec I’m trying to master this approach for storing hierarchical data in a relational database.

I Know Way Too Much About My Neighbors

2008-10-01: I’m listening to a neighbor — a smoker — attempt to cough up a lung. It’s not a pleasant sound.

Houses in my neighborhood (Spring Hill, Somerville, Massachusetts) are very close together.

New MacBook Pro Models Soon?

2008-10-01: Another sign new MacBook Pro models are imminent: latest MacConnection catalog is offering $150 rebate on current models through October 31.

Lots of rumors about when new MacBook Pro models are coming out. This is a clue that it will be soon.

Circus Ponies NoteBook 3.0

2008-10-01: I just upgraded Circus Ponies NoteBook to version 3.0. This is one of my favorite applications, and I use it daily.

I have a notebook file in which I save everything I need to remember. I store it in an encrypted disk image.

Apple’s Software Update

2008-10-03: Is anyone else annoyed by Apple’s Software Update? Once it has installed the new software, it still says there is new software to install.

5k Race in Davis Square

2008-10-03: We’re cleaning house tonight because we’re holding a brunch after tomorrow’s 5k race in Davis Square. The only time we clean is for guests.

2008-10-04: Beautiful day for the 5k this morning. My competitive juices kicked in, and I finished strong. But a 5k is too short; I prefer a marathon.

This was the Somerville Homeless Coalition 5k, held in Davis Square, Somerville, Massachusetts. About eight of us from work ran the race and them came over for brunch. During the race, I was holding back for the first two miles, saving my legs. Then I realized I only had a mile left to run, so I picked up the pace.

The Fountainhead, by Ayn Rand

2008-09-21: I finally finished listening to an audio book of The FountainHead, by Ayn Rand. I just can’t buy into Rand’s fatuous philosophy.

This was a long book, actually written pretty well. But nobody acts like that, and nobody should.

Current Bioinformatics Projects

2008-09-21: I worked 68 hours this week and managed to finish a BIG project. Now I’m only four weeks behind in my work. Postponing vacation….

I’m Too Close to My Neighbors

2008-09-22: At 4:30 AM, the next door neighbor is puking in his bathroom with the window open, waking up the entire neighborhood. So delightful….

Was it something he ate? Or was it something he drank? I still don’t know.

Autumn Running

2008-09-22: I did a good three-mile run this morning, my first run in three weeks. Autumn is perfect running weather.

I’ve been working too much lately to have time for running. Work-life balance has been difficult lately.

I’ll Always Be A Graduate Student

2008-09-23: Pizza for lunch today at work, provided by the company. My graduate student training — free food! — kicked in, so I’m still full.

When I was in graduate school at Berkeley, our lab was just down the hall from the seminar reception room. I never missed coffee and cookies at 3:30 PM on Wednesday afternoons.

Don’t Try To Do Your Own Bioinformatics Or Statistics

2008-09-24: @tharris @neilfws Too many research groups try to do their own bioinformatics and statistics without really knowing what they’re doing.

Printing Problems At Home

2008-09-24: Printing at home has become a disaster. Old HP 6MP AppleTalk printer won’t connect to network, and newer LaserJet has become unreliable.

2008-09-27: I got my old HP 6MP AppleTalk printer back on the network today by sacrificing two goats to the AsanteTalk Ethernet to LocalTalk adaptor.

We own an old HP 6MP printer that has an AppleTalk network interface. When my last Mac with an AppleTalk port died, I bought an AsanteTalk Ethernet to LocalTalk adaptor so I could plug it into the network. The adaptor is flaky and often won’t initialize itself correctly.

The solution was to disconnect the adaptor from the network and connect it directly to my MacBook Pro via the ethernet port. This let me initialize the adaptor by setting up the printer on the AppleTalk network, after which I plugged the adaptor back into the main network.

Housing Prices

2008-09-25: Housing prices are falling nationwide, but zillow.com‘s model says houses in Somerville and Cambridge, Mass., are holding their value.

Anathem, By Neal Stephenson

2008-09-25: I’m the last nerd in my neighborhood to buy Anathem, written by Neal Stephenson. I’ve read 18 pages, and it’s as good as everyone says.

Somehow Leo Laporte got a copy before the publication date. Some of us just have to wait.

Registration Fees For Races

26-Sep-2008: active.com is unpleasantly greedy. They increased their processing fee when I made an extra contribution while registering for a race.

I registered for the Somerville Homeless Coalition 5k, and I decided to contribute an extra $100. active.com increased the registration fee for the contribution; they must work on a percentage basis.

Beer As A Cure

2008-09-26: I felt crummy all day at work. Tonight we went out for beers and now I feel fine. If only I could have had a beer at 10:00 a.m….

Learning JavaScript

2008-09-27: I need to learn JavaScript for a project I’m working on. The question is, which JavaScript library to use? jQuery looks promising.

Brideshead Revisited, by Evelyn Waugh

2008-09-14: I’m reading Brideshead Revisited before I watch the PBS miniseries. Next is Primo Levi’s The Periodic Table, recommended by my wife.

The reviews I read for the new movie of Brideshead Revisited recommended that we watch the PBS miniseries instead. Somehow, I never saw it when it first came out, so I recently bought the series on DVD.

iTunes Genius

2008-09-14: The iTunes 8 Genius feature is going to cost me a lot of money. It keeps finding good songs I’m surprised I don’t already own.

I’m sure that’s the idea.

Slashdot Notices Stack Overflow

2008-09-16: slashdot.org finally noticed stackoverflow.com today, but the original poster didn’t even have the courtesy to get the story correct.

Two-Finger Scrolling

2008-09-18: I’m a Mac, not a PC. I keep trying to scroll my Windows PC with two fingers on the touch pad, but it never works.

And it never will….

Richard Owczarzy

2008-09-18: I spent the day reading papers about how to calculate the Tm of DNA oligos. Richard Owczarzy et al. at IDT do really nice science.

Twitter Has Changed

2008-09-18: Twitter just changed its format. I thought it was bugs until I saw the box that says, “Notice something different? Read about the changes.”

EMBOSS Site Is Hosed

2008-09-19: What’s going on with EMBOSS at sourceforge.net? The site is serving text/x-server-parsed-html files; Firefox chokes on these.

60-Hour Weeks

2008-09-19: So two weeks ago, my manager said he didn’t want me working 60-hour weeks. Since then, it has been, yes, 60-hour weeks.

I’m trying to finish a big project.

Steal This Idea

2008-09-20: GUI windows need a button that maximizes the height of the window without maximizing the width of the window, to enhance readability.

Sometimes I want taller but not wider windows.

Gloria

2008-09-20: I’m listening to 14 different versions of Gloria. Best is by Popa Chubby, but other covers are excellent, too.

I went on a binge and bought these a few months ago on iTunes. But somehow I don’t have the original by Van Morrison.

Tropical Storm Hannah

2008-09-07: We had lots of rain (although not as much as originally predicted) but no damage from the passing of tropical storm Hannah.

Programming With R

2008-09-07: I’ve been reading Software for Data Analysis: Programming With R. At last, I understand functional programming as implemented by R.

2008-09-08: More systems administration today on our Linux box. I compiled and installed R 2.7.2 after compiling and installing external prerequisites.

Software for Data Analysis: Programming With R was written by John M. Chambers, the principal designer of the S programming language, of which R is a dialect. For me, at least, this book replaces the old S Programming by W. N. Venables and B. D. Ripley, which did not cover R adequately. Chambers provides a good explanation of how functional programming works, and this made it instantly clear to me why I was writing some of my code incorrectly; I was not following the functional programming paradigm.

Star Stryder Banned By Google

2008-09-08: I can’t find Star Stryder’s web site using Google, but Yahoo has it. For once, Yahoo has a better search engine than Google.

It turned out that Star Stryder’s site had been hacked, and Google had banned her site because of the keywords present in the hacked material. Now that she has cleaned up her site, she has to wait for Google to review it and re-enter it into their indexes, which could take weeks.

I enjoy Star Stryder’s blog, podcasts, and tweets.

BBEdit Upgrade

2008-09-09: 9 days after paying $30 to upgrade BBEdit to 9.0, I got an email saying that since I was a recent buyer of 8.5, my free upgrade was ready.

Well, BBEdit is still worth it.

iPod touch or iPod nano?

2008-09-09: Decisions, decisions…. Do I buy the new iPod touch or the new iPod nano? I’m disappointed, though, that there’s no new MacBook Pro.

I need a new iPod once my iPod mini dies (and its battery lasts only about six hours now), and my wife needs a new MacBook Pro for her business.

Documentation for RPM Package Management

2008-09-10: Neighbors woke me up by being noisy, so I’m reading documentation about the RPM package management software. Good documentation is sparse.

It’s easier for me to compile from the source code than it is to use RPM. I need to figure this out so I can save time.

Scary Intersection in Cambridge

2008-09-10: The intersection of Sidney St. and Mass. Ave. in Cambridge is scary now that the reconfiguration is finished. Someone is going to get hurt.

I was watching this intersection while sitting outside with friends at The Asgard. Many drivers were running red lights and making illegal turns or going straight ahead in the right turn only lane. This is not to mention the foolhardy bicyclists, who typically break every traffic law while riding.

I Live Too Close To My Neighbors

2008-09-13: It’s 3:49 am. Who are all these people driving up our street, parking, slamming car doors, and talking loudly? Hey! I know where you live!

Get off my lawn!

Jobs at 454

2008-09-13: Received from a friend who just started a new bioinformatics job at 454: A list of 40 open positions there. I already have a good job….

Beatles on iTunes — When?

2008-09-13: What happened to all those rumors about the Beatles’ catalogue becoming available on iTunes? Still not there…. It’s OK — I own the CDs.

I’ve owned the Beatles on vinyl, cassette tapes, and now CDs.

Berkeley Alumni

2008-09-13: I went for a long walk in the city today wearing my Berkeley T-shirt. I was greeted by two strangers, Berkeley alumni. “Go Bears!” indeed.

The Berkeley Alumni Association is really big on the football games. I hated the football games because on game day students couldn’t park on campus. Since I worked in lab every Saturday, on game day I’d have to take BART instead of drive.

Data Visualization

2008-08-31: NY Times article about IBM’s many-eyes data visualization site.

The human brain can pick out patterns from visual data that a computer can’t see yet. But we’re limited to three dimensions. Eventually, computers will “visualize” multidimensional data in ways that we can’t. I predict this will lead to scientific breakthroughs.

Moving Day in Boston

2008-08-31: This is the weekend everyone in Boston moves. It’s a shame that I’m so “busy” that I don’t have time to help my friends and relatives.

Hurricane Gustav Disrupts Republican National Convention

2008-09-01: The silver lining in Gustav’s cloud and big break for McCain: Speeches by Bush and Cheney at Republican National Convention are canceled.

I despise Bush and Cheney and everything they stand for.

Perl Programming

2008-09-01: It’s a holiday, so of course I’m working. Today I’ve been writing three new Perl modules from scratch. It’s boring writing accessor methods.

2008-09-02: w00t! I solved a programming problem today using recursion. Some days I wish I had more formal training in software engineering.

Lights Out In Boston

2008-09-03: It’s about time we quit wasting energy lighting the interiors of skyscrapers at night. Lights out in Boston.

Light pollution is horrible here; I can see only the brightest stars at night.

Journal Club

2008-09-03: I just finished getting ready for tomorrow’s journal club. I read several extra papers for background, and I prepared 26 slides.

I like to provide lots of background before I get to the hard stuff.

Systems Administration

2008-09-05: I’ve been doing systems administration this week. I installed EMBOSS 6.0.1 yesterday; today I set up a subversion server.

A bioinformatician wears many hats.

Twitter Is Improving

2008-09-05: Twitter is improving. I have seen no fail whales for many weeks now. And today I could read 14 pages of tweets instead of 10.

Traumatized by Education

2008-09-06: Early this morning I had one of those recurring dreams where I’m taking a final exam but I don’t know most of the answers.

Programming with R

2008-09-06: Today I purchased Software for Data Analysis: Programming with R, by John M. Chambers. This book is an up-to-date guide to R programming.

My Name Is Red, by Orhan Pamuk

2008-08-17: I spent the day traveling from Boston to St. Louis via Chicago. I didn’t mind, because I’m reading My Name Is Red, by Orhan Pamuk.

Orhan Pamuk is a Turkish writer who was awarded the Nobel Prize for Literature in 2006. This is a brilliant novel.

Running in St. Louis County

2008-08-18: I ran three dangerous miles before sunrise in West St. Louis County, where the rich can’t afford sidewalks or even shoulders on the roads.

I don’t understand why the wealthy suburbs of St. Louis can’t afford infrastructure for pedestrians.

Learning Perl, 5th Edition

2008-08-10: I’m steadily reading Learning Perl, 5th edition, and I’m finding many useful nuggets of information, including the new 5.10 features.

This is a good, clear book, although I think it doesn’t have the reader start writing code early enough. It has been a good review for me to read this book, because Perl is a large language, and I’ve missed learning some parts of it.

I Generate Most of My Traffic

2008-08-10: How I double traffic to my web site: I work on my blog. My multiple saves account for nearly all traffic on Sundays.

That is, hardly anyone reads this blog. That’s OK, because it’s more of a memory jogging device for me than a means of communicating to the outer world. I would blog a lot more if I had the free time.

Pillars of the Earth

2008-08-12: @LionEyes What is your opinion of Pillars of the Earth? I hated it, and I gave up 2/5 of the way through. The characters had no depth.

I don’t recommend Pillars of the Earth, by Ken Follett.

Dell Not Compatible With Dell

2008-08-12: New Dell display just worked with MacBook Pro. But with Dell laptop, I had to install a driver to set correct resolution. I hate Windows.

My new display is a Dell 22-inch Ultrasharp E207WFP, which has 1680 x 1050 resolution. My work-provided Dell Latitude 610 laptop, which is only 2 years 4 months old and which runs Windows XP with Service Pack 2, wouldn’t recognize the full resolution of the display until I updated the video driver and installed the display driver. On the other hand, my Apple MacBook Pro, which is 9 months old, and my Apple PowerBook G4, which is 3 years 7 months old, both had no trouble using the full resolution of the display as soon as I plugged it in.

In addition, both my MacBook Pro and my PowerBook G4 have digital video ports, whereas my Dell Latitude 610 has only a VGA video port. People complain that Apple’s computers cost more, but these are two examples where the extra money is worth it to me.

My Beddian Year

2008-08-13: Yesterday I reached my Beddian year. Given that, you can figure out how old I am and what year I was born.

Your Beddian year is the year in which your age matches the last two digits of the year you were born.

Searching for “C”, “R”, “C#”, “C++”

2008-08-14: @codinghorror complains that supporting searches for “C#” and “C++” at stackoverflow.com is hard. It’s even harder for “C” (and “R”).

I really hate it when I have to perform a google search for some R code. Searching with a key word that is a single letter long doesn’t work very well.

A Send-Off

2008-08-14: We had beers this evening at the Asgard in Cambridge to send off a co-worker who is leaving tomorrow for India to get married.

We find an excuse to go to the Asgard about twice a month for beer and appetizers.

idle.slashdot.org

2008-08-14: More amusement from slashdot: http://idle.slashdot.org/. I always thought everything posted on slashdot was from idle people.

Doing Battle With Perl

2008-08-15: I spent the day trying to make some badly documented Perl modules do what I needed, but without success. I battle again tomorrow.

The code is allegedly “self-documenting,” but I still can’t figure it out. When I encounter code like this, I add POD, and I always provide examples of how to use the code. In my experience, a good example is sometimes all the documentation that is needed.

Google Ad Confusion

2008-08-15: More google ad confusion. faceyourmanga.com: “Turn your face soon in [sic] a work of art.” Ads by Google: “Brick face for your home.”

If I were the advertiser, I would ask for some of my money back for improper placement of my ads.

Redbones Barbecue

2008-08-16: I ran six miles this morning, which is good because we’re meeting friends at Redbones (Davis Square in Somerville) tonight for dinner. BBQ!

Great food, great beer, great atmosphere. It’s always fun to go to Redbones.

Congratulations to Constantina Tomescu

2008-08-16: Great performance by Romania’s Constantina Tomescu in winning the women’s marathon at the 2008 Olympics. Very poor viewing for spectators.

Ms. Tomescu ran a great race in warm weather. The course was designed so that the spectators were often 50 feet or more from the course, which meant they couldn’t really cheer the runners on.