Quantum Forest logs are written by Luis A. Apiolaza in Christchurch, New Zealand and powered by TextPattern.

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I do run ASReml in a mac
Published Thursday January 18, 2007 · Permalink

For quantitative geneticists and breeders out there: ASReml runs OK in any mac with Intel processor and Parallels. You can find some comments on using it in the ASReml Cookbook.

Incidentally, SAS works OK in a mac using Parallels too. However, I am enjoying R a lot more.

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Slowing down for a while
Published Sunday November 12, 2006 · Permalink

Parochialisms—almost cute—of the month:

Nice , actually really useful, pieces of software that I find myself relying more and more upon:

Personal issues have taken a toll on me, so I will devote very little time to update this blog. Most likely though, I will update the wiki side of the side a bit more frequently, particularly the pages corresponding to research: my work on breeding and wood quality has acquired a sense of urgency.

See you again, once in a while.

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The effect of community
Published Saturday October 7, 2006 · Permalink

(Or why do I prefer software where I do have a say)

Recently I was commenting on some software that I use for writing. I think that one of the main reasons non-strictly related to software usefulness is the quality of the community around the software. This has two elements:

As an example, I like using Journler to keep track of odd ends in my mac computer. I also like using Writeroom when starting to write, because I can focus on my ideas only. Both programs have relatively active groups of users (here and here) and receptive developers, who are looking for feedback. The feeling is of people who care about a product, which in general is a necessary (although not sufficient) condition for good programs. By comparison, I struggle with Copywrite, because there is no public feedback mechanism: I do not know what other users think or what are the projects of the developer for this software. Is he (or she) still developing it or now he is moving to live in Vanuatu to enjoy the rest of his life?

An interesting element is that both Writeroom and Journler are free (sensu gratis)—although the developers ask for donations—while Copywrite costs US$30 or so. There is a psychological element on paying for software; one thinks that the programmers must be working on the product. However, there is no feedback to confirm this assumption in Copywrite. In addition, I expect more activity from smaller companies: they are supossed to be more agile than, say, Microsoft.

Thus, if you are a small company I expect you to show some changes here and there. If you are a small company and charge for your product I better should have a say on what is going on. If you are a large company, most likely I will buy your software only if I need to, because most probably you are developing not very interesting products (there are exceptions1 of course).

1 Wolfram’s Mathematica is an example. Insightful’s Splus is not: R is much more active, there is plenty of feedback and it is free.

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First casualty: Macbook Pro
Published Friday September 22, 2006 · Permalink

It all started last week with problems coming back from sleep mode. The MBP would wake up for a few seconds and then shutdown completely. It was an annoyance, but given that I was still teaching and preparing lectures using the laptop, I just kept going. Last Monday 19th September it was happening often enough that I sent an email to the University’s IT support, for which I received an automatic reply on Tuesday saying ‘we got your message’.

Yesterday, Wednesday 21th September, the computer just ‘died’ four hours before my last lecture for STAT220. I would turn on and then shutdown almost immediately. I had prepared the last lecture at home, without a chance for the automatic network backup that I get at work. Therefore, I spent the last few hours franctically trying to recreate the lecture (in PowerPoint rather than Keynote) in a borrowed HP laptop. Not the best final lecture, but at least a decent end for my participation on the course.

Marcela dropped the laptop at MagnumMac, the authorised Mac reseller in Christchurch. We were presented with the following options: for normal guarantee work (which certainly was this case) I would need to wait until next week so the technicians had a look at the computer. That is, waiting at least from Wednesday until Monday so someone would touch the computer, not even repair it. The option: spend NZ$75 so the technicians would put my computer at the front of the queue—skipping another 14 computers—and start diagnosing the problem. Not having the computer is certainly worth much more than $75 per day for me, so I decided to pay, but the whole system sounds wrong:

Apple has not found the problem yet: I was told—after I called a couple of times—that they have reproduced the problem but that they are still trying to figure out what is its cause. Once that happens, it will take several days for me to get back my computer (tomorrow is Friday already): normally they order the parts from Australia, which may take several days, even weeks.

This is the second time that my computer goes back to Apple: the first time was a battery problem (before the big battery recall). It has been very disappointing to have these problems, particularly when they seem to be so common place.

By the way, I am still waiting to receive an email written by humans from the University’s IT support.

PS. 2006-09-27: I received my laptop back on Monday 25th. Apple’s technician explained to me that they were able to replicate the problem but not to pinpoint the cause. They replaced 512MB of third party RAM for Apple brand and that seems to have temporarily fixed the problem. Today I had a shutdown when running on battery (with supposedly 67% of charge). It may be that the battery needs calibration; however, it may also be the same problem coming back. We’ll see.
PS. 2006-09-28. Random shutdowns are back. Called tech support and they will order the next potentially problematic part.
PS. 2006-10-05. The left I/O board was replaced on Monday 2nd October, got the computer back yesterday and it failed again tonight. I am returning it tomorrow and will ask for a replacement computer. The issue is now how to get a bit over 10GB of data backed up (mostly the multimedia part, the rest—around 2GB—is already safely stored in our network), while the computer is working. If it is not possible, we will need to access the hard drive from somewhere else.
PS. 2006-10-10. I received a new Macbook Pro, which did not present any of the problems of the previous one. Annoyances aside, I received a faster computer (2GHz instead of 1.86GHz) and I used the opportunity to upgrade RAM from 1Gb to 1.5GB. All in all, I am a lot happier with the new computer. Apple was not very keen on exchanging the computer, but I refused to accept back the old one. At least some times it pays to be a real pain in the butt.

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Doing simple things simple
Published Tuesday August 29, 2006 · Permalink

Following my Another mac update post I will cover a few small applications that have made a big difference on the way I do things.

DigitalColor Meter: One of the common tasks that I perform when updating my web sites is to change the CSS files. I keep the same templates, but I do play a fair amount with the design; particularly colours. When I was using mostly a PC I would find a nice colour in a page, take a screenshot (with Shift-Print Screen), open the screenshot in The Gimp and use the color picker to get the hexadecimal representation of the colour. Moving to the mac I had the temptation of doing the same, but using Grab (which comes by default under Applications, Utilities, Grab.app) and The Gimp for mac or—a simplified version of it—Seashore. Then I discovered that the mac ships by default with Digital ColorMeter (under Applications, Utilities, DigitalColor Meter.app) a small piece of software that lets you hover above any screen and get the hexadecimal color. One can even modify the aperture size, to change the number of pixels being included in the average colour measurement. Now it is simply ‘Hover with my mouse, Shift-Command-C’ and I get the hexadecimal values.

Dictionary: The other one is simply Dictionary. Yes, I have a problem, I like dictionaries and related books. I do own a copy of ‘Webster’s New World’, ‘Oxford Advanced Learners’, ‘Roget’s International Thesaurus’, ‘Brewer’s Dictionary of Phrase & Fable’ and ‘Fowler’s Dictionary of Modern English Usage’. This is covering English only. I do have a similar set of books in Spanish, starting with ‘Diccionario del Español Actual’ by Manuel Seco, Olimpia Andrés and Gabino Ramos (4,666 pages), followed by a large number of smaller dictionaries and books on the use of Spanish. I used to go and look for words all the time, but now there is Command-Spacebar Di (in Quicksilver) and the word. That’s it and I love it. I now only need something like that for Spanish.

Still trying on writing tools

Writeroom keeps growing on me, but I need to store all the bits and pieces that I am writing for different reasons. Although I tried Mori (from the same makers as Writeroom), I still do not feel quite comfortable with it. Journler, on the other hand, it is a nice journaling application, although its full screen mode is still a bit clunky.

So, I wrote my first ever piece of Applescript:

tell application "WriteRoom"
set docName to the name of front document
set docContent to the text of front document
end tell
tell application "Journler"
set newEntry to (make new entry with properties {name:docName, plain text:docContent})
end tell

Writeroom assigns automatically the content of the first line as document name. Thus, the script grabs the name and content of a WriteRoom window and creates a new entry in Journler with that title and content.

Yes, I did buy a copy of Copywrite before (I mentioned it here), but I can not make it fit in my workflow yet. I will keep trying it for a while, and see if it ‘just clicks’ with me in the near future.

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