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Category: goals

03/29/12 12:58 - ID#56295

Thoughts on switching

Ugly but true.
image

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Category: goals

01/11/12 05:04 - ID#55888

The year ahead.

2012 is going to my best year thus far.

I just decided that it will be so it better be.

Top 10 lessons that I learnt in 2011.

1. Data analyses is 95% data cleaning and variable definition.

2. R is fun and liberating.

3. Perl is even more fun but it's funny and weird and super tough to learn.

4. I have a massive crush on Hadley Wickham. Mostly because he is the ggplot2 creator. And maybe also because he has a website of family recipes and oh, a really informative website manual for ggplot2. Is this as impractical a crush as the Rahm Emanuel phase? Well... slightly less because I might actually get to meet him someday... but on the whole, big check.

5. ggplot2 is a fascinating way to think about data.

6. FlowingData is one of my favourite inspirations. It replaces aldaily (which, unfortunately, I have been steadily ignoring).

7. There is always light at the end of the tunnel. You just need to find the switch - which is often right on the darkly shrouded wall behind you.

8. Linux is not so much a monster as a friendly devil. I prefer linux as my primary OS. Surprise.

9. I love my family. They are the best anyone could ever hope for and of course, the only ones I have.

10. Surprisingly, I like documentaries way more than movies.


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Category: goals

01/01/12 09:24 - ID#55829

Whatever it takes.

That is going to be my philosophy this date onwards.

In the year 2000...
2012...

I will
  1. Work all year in pomodoros and squash as many tomatoes as I can.
  1. Publish. Publish. Publish
  1. Master R and Perl.
  1. Learn how to manipulate and code in Bioconductor
  1. Analyze and publish on least one public dataset in genetics.
  1. Transition into more genetics and bioinformatics.
  1. Write more science. Make future-oriented useful notes.
  1. Be more in contact with my family.
  1. Be less confused, Be more mentally organized
  1. Set priorities and stick with them regardless of what comes in between.
  1. Reach a better place and work on feeling less guilty

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Category: goals

12/23/11 03:38 - ID#55788

Off.

My new deadline is December 31. I am dead serious about this and want to finish it once and for all. Even if lake Erie burst into flames right now and it was a grand public spectacle, I wouldn't want to go see it more than I want to finish my dissertation writing.

So I am taking off the internets and (e:strip) till the next year.

All of you, happy holidays and behave yourselves.

cheerio,
TP

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Category: goals

12/01/11 06:28 - ID#55637

I wish I could learn...

0. R completely and thoroughly
1. Perl well
2. Unix commands well (so commandline becomes second nature)
3. to churn out papers like a maniac (aka postdoc)
4. how to make perfect stovetop popcorn
5. how to make a perfect sourdough bread every single time
6. how to make perfect pancakes or waffles
7. how to make pizza base without a recipe and well.

I intend to get a head start on those resolutions.

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Category: goals

11/15/11 08:32 - ID#55515

The 20 Times Tables: 18

Continuing the "mastering first grade when you are in graduate school" series.
The 18 table.
  1. Starting with 18
  2. 36
  3. 54
  4. 72
  5. 90
  6. 108
  7. 126
  8. 144
  9. 162
  10. 180 -20 + 200
  11. 198
  12. 216
  13. 234
  14. 252
  15. 270
  16. 288
  17. 306
  18. 324
  19. 342
  20. 360
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Category: goals

11/14/11 02:27 - ID#55509

The 20 times tables: 19

I cannot believe just how AWFUL I have become at my 13 through 20 (times 20) tables. Struggling with mental arithmetic is totally unacceptable. It is a sign of mental deterioration that I want to fight against.
  1. Starting with 19
  2. 38
  3. 57
  4. 76
  5. 95
  6. 114
  7. 133
  8. 152
  9. 171
  10. 190 +190
  11. 209
  12. 228
  13. 247
  14. 266
  15. 285
  16. 304
  17. 323
  18. 342
  19. 361
  20. 380

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Category: goals

10/21/11 10:20 - ID#55340

Learning to be a software carpenter

Coding is time consuming. I didn't really consciously think about this till my advisor asked me about the roadblocks to my progress in my dissertation. I thought back and it occurred to me that I was
  • learning a somewhat new language (R)
  • trying to code in it using concepts from statistics that I already have
  • trying to generalize code so that it could be less repetitive and automate chores and processing
  • trying to splice other languages such as latex and perl to interact with R code
  • learning THOSE other languages
  • trying to prevent errors in their interaction
  • trying to write functions that would serve a purpose similar to "macros" on SAS but yet be understandable to me at a somewhat-novice level.
  • debugging to see where it all goes wrong when errors turn up
  • differentiating what is my code's fault, what can be changed in R preferences, and what is inherently the fault of the R build on the particular linux distro I am using.

Why am I doing this when I have a data manager for the data I am dealing with? Because it's insane to go whining to the manager the minute you want some data processing done. He has own Ph.D. to complete and has limited time and innumerable demands. So there is really no option but to power through all of this on my own. Besides, I think population sciences are *really* about statistics and data processing even though population scientists who don't do all this dirty work may persuade themselves that it is just about interpretation. It is as much about quality control in the data and seemingly trivial logical checks as it is about analyzing super-clean data in the end and figuring out what it could mean in the bigger picture of million other studies. I think it's important to acquire this skill so I can use it in my future. Not everyone has a data manager, a software coding bloke and a statistician to always help them.

The process itself is exhausting because it's like learning a completely new language without having ANY experience in how the semantics work. Apparently some people have observed this exhaustion and set up sites like "Software Carpentry": It sets up a formalized framework within which you could learn these skills. I think courses like this should be mandatory to population sciences coursework. At some point, we need to realize that population sciences and bioinformatics are very similar in their scope and application. This is more true than ever as we progress rapidly towards HUGE datasets, complex data structures, multidimensional variables and the necessity of channeling all of this into interpretations simple enough to make sense to health-related and population policy-making.
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Category: goals

10/15/11 10:51 - ID#55304

Diffused Sunlight Simulation

The basic nature of sunlight indoors is that it is never direct most of the times. Almost all sunlight that filters through into rooms is reflected, diffuse and full spectrum (~5500 Kelvin). These three qualities set sunlight apart from artificial light.

The sunlight simulation lamps in the market are mainly high wattage, full spectrum and power consuming lamps. They are targeted at people with SAD - Seasonal Affective Disorders. While I am not convinced I have SAD and need the everyday intensive 1/2 hour to 1 hour therapy that these lamps are regularly recommended for, I am really interested in simulating sunlight at home especially when there is none outside.

I recently went to IKEA and saw this floor lamp, called "Tived".
image
The design is nothing spectacular. In fact, I would call it a bit ugly. But it has flexible arms that can be directed at various parts of the ceiling and walls. It looks like this flexibility could achieve that diffused reflected sunlight feel I want. I almost bought it but it comes with its own set of LED bulbs. I don't like that. I want to be able to readily replace the bulbs if they burn out. The only way to do this would be to get a lamp that holds regular full-spectrum CFLs. None of the more interesting IKEA lamps allow you to put your own bulbs in them.

If it had a few more flexible arms for some more bulbs and it took regular full-spectrum bulbs, it might come close to what I have in mind. IKEA also has a table lamp version of the "Tived" with more arms, but it could be tough to focus the light on the ceiling because of the lack of height. Even if I somehow succeeded in elevating the level of lamp, the bulbs are still the peculiar LED ones. image

I wonder where I can get such a lamp. It would be so cool to have one this winter.

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Category: goals

10/03/11 07:57 - ID#55236

Clueless about regex

What I want to do is match strings with regular expressions.

^ : start of string
[ : beginning of character group
a-z : any lowercase letter
A-Z : any uppercase letter
0-9 : any digit
_ : underscore
] : end of character group
* : zero or more of the given characters
$ : end of string


Now I can't even write code for matching a variable length sentence or phrase in curly brackets for example:

{A quick brown FOX jumps over a sprightly hare}

Hmm... this does not work
(\{)[.*?](\})

This doesn't work
(\\{).*?(\\})

This doesn't work either.
\\{.*?\\}

ARRRGH.
It's funny how it's called regular.

References

1.
2.
3.
4.
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