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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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Permalink: Learning_to_be_a_software_carpenter.html
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Location: Buffalo, NY
Last Modified: 11/09/11 08:17


Category: eating in

10/19/11 07:20 - ID#55335

Complete Fridge Wipe Out

I am very close to a complete Fridge wipeout.
I currently have
- A wonderful big Cauliflower {needs to be used this weekend}
- 2 frozen bananas
- 1 ripe tomato {priority use this weekend}
- 1 orange
- 1/4th lb okra {super priority use maybe tomorrow}
- Ginger
- Garlic
- Some hot chillies

Well.. maybe not that close but still this is a reflection of workload. I think I might reach the wipout this weekend and give the fridge a scrubdown before I go grocery shopping.
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Permalink: Complete_Fridge_Wipe_Out.html
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Location: Buffalo, NY
Last Modified: 10/19/11 07:21


Category: linux

10/17/11 07:29 - ID#55328

[Solved] External Monitor problems on Fedora 15

Found a nice solution to the crazy external monitor problem in Fedora 15:
Download the latest release of ARandR from here:
Extract to some directory and navigate to that directory:

cd /arandr-0.1.5/



Run arandr.

./arandr



All external display problems SOLVED! Woohoo. Thank you, Christian Amsuess. You simply rock.
I saw they are trying to get this nifty program reviewed to include it in the Fedora yum repository For such a wonderful program that replaces the crap they have in gnome 3, the brutal review process seems somewhat counterproductive.



The Extended monitor display works. However, if I assign the external monitor as the primary display, it doesn't work. It gives me a blank backlit screen. WHYYYY?

I really need one of these counters now.
image
The number matches. I have the exact expression too.

In addition, I feel like I could outshout the incredible hulk anytime after /var/log/messages records an exception that could have well read, "You wouldn't like me when I'm angry normal".

Last few lines from /var/log/Xorg.0.log


[ 2244.948] (II) intel(0): EDID vendor "HWP", prod id 9896
[ 2244.948] (II) intel(0): Using hsync ranges from config file
[ 2244.948] (II) intel(0): Using vrefresh ranges from config file
[ 2244.948] (II) intel(0): Printing DDC gathered Modelines:
[ 2244.948] (II) intel(0): Modeline "1680x1050"x0.0 146.25 1680 1784 1960 2240 1050 1053 1059 1089 -hsync +vsync (65.3 kHz)
[ 2244.948] (II) intel(0): Modeline "800x600"x0.0 40.00 800 840 968 1056 600 601 605 628 +hsync +vsync (37.9 kHz)
[ 2244.948] (II) intel(0): Modeline "640x480"x0.0 31.50 640 656 720 840 480 481 484 500 -hsync -vsync (37.5 kHz)
[ 2244.948] (II) intel(0): Modeline "640x480"x0.0 25.18 640 656 752 800 480 490 492 525 -hsync -vsync (31.5 kHz)
[ 2244.948] (II) intel(0): Modeline "720x400"x0.0 28.32 720 738 846 900 400 412 414 449 -hsync +vsync (31.5 kHz)
[ 2244.948] (II) intel(0): Modeline "1280x1024"x0.0 135.00 1280 1296 1440 1688 1024 1025 1028 1066 +hsync +vsync (80.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1024x768"x0.0 78.75 1024 1040 1136 1312 768 769 772 800 +hsync +vsync (60.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1024x768"x0.0 65.00 1024 1048 1184 1344 768 771 777 806 -hsync -vsync (48.4 kHz)
[ 2244.948] (II) intel(0): Modeline "832x624"x0.0 57.28 832 864 928 1152 624 625 628 667 -hsync -vsync (49.7 kHz)
[ 2244.948] (II) intel(0): Modeline "800x600"x0.0 49.50 800 816 896 1056 600 601 604 625 +hsync +vsync (46.9 kHz)
[ 2244.948] (II) intel(0): Modeline "1152x864"x0.0 108.00 1152 1216 1344 1600 864 865 868 900 +hsync +vsync (67.5 kHz)
[ 2244.948] (II) intel(0): Modeline "1152x720"x60.0 67.32 1152 1208 1328 1504 720 721 724 746 -hsync +vsync (44.8 kHz)
[ 2244.948] (II) intel(0): Modeline "1280x960"x0.0 108.00 1280 1376 1488 1800 960 961 964 1000 +hsync +vsync (60.0 kHz)
[ 2244.948] (II) intel(0): Modeline "1440x900"x0.0 106.50 1440 1520 1672 1904 900 903 909 934 -hsync +vsync (55.9 kHz)
[ 2244.948] (II) intel(0): Modeline "1600x1000"x60.0 133.14 1600 1704 1872 2144 1000 1001 1004 1035 -hsync +vsync (62.1 kHz)
[ 2261.254] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2261.254] (II) intel(0): Printing DDC gathered Modelines:
[ 2261.254] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.258] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2262.258] (II) intel(0): Printing DDC gathered Modelines:
[ 2262.258] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.353] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2262.353] (II) intel(0): Printing DDC gathered Modelines:
[ 2262.353] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2262.467] (II) intel(0): Allocated new frame buffer 1728x1050 stride 7168, tiled
[ 2293.167] (II) intel(0): EDID vendor "SEC", prod id 21825
[ 2293.167] (II) intel(0): Printing DDC gathered Modelines:
[ 2293.167] (II) intel(0): Modeline "1366x768"x0.0 72.33 1366 1414 1446 1526 768 770 775 790 -hsync -vsync (47.4 kHz)
[ 2293.280] (II) intel(0): Allocated new frame buffer 3072x1050 stride 12288, tiled



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Permalink: _Solved_External_Monitor_problems_on_Fedora_15.html
Words: 449
Location: Buffalo, NY
Last Modified: 10/23/11 12:36


Category: linux

10/16/11 08:39 - ID#55323

Nvidia and Intel Graphics in Fedora 15

There's something really wrong with my setup here:


01:00.0 VGA compatible controller [0300]: nVidia Corporation Device [10de:0df4] (rev a1) (prog-if 00 [VGA controller])
    Subsystem: Toshiba America Info Systems Device [1179:fc31]
    Flags: bus master, fast devsel, latency 0, IRQ 16
    Memory at f6000000 (32-bit, non-prefetchable) [size=16M]
    Memory at e0000000 (64-bit, prefetchable) [size=256M]
    Memory at f0000000 (64-bit, prefetchable) [size=32M]
    I/O ports at e000 [size=128]
    Expansion ROM at f7000000 [disabled] [size=512K]
    Capabilities: [60] Power Management version 3
    Capabilities: [68] MSI: Enable- Count=1/1 Maskable- 64bit+
    Capabilities: [78] Express Endpoint, MSI 00
    Capabilities: [b4] Vendor Specific Information: Len=14
    Capabilities: [100] Virtual Channel
    Capabilities: [128] Power Budgeting
    Capabilities: [600] Vendor Specific Information: ID=0001 Rev=1 Len=024
    Kernel driver in use: nvidia
    Kernel modules: nvidia, nouveau, nvidiafb



Even though there is now a driver in use (installed from here: ) I still cannot adjust my resolution. I didn't install nVidia's own driver because of this article:

There is only ONE resolution in the display settings (1024X768). Attaching an external monitor results in the computer shutting down on its own. And there is no way to adjust brightness.

Aarrgh. Frustration ++. I am just going to ignore this today. I have too much work piled up.

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Permalink: Nvidia_and_Intel_Graphics_in_Fedora_15.html
Words: 200
Location: Buffalo, NY
Last Modified: 10/16/11 08:41


Category: linux

10/16/11 04:42 - ID#55318

Fedora 15 with XFCE. Some Notes

Remove irritating desktop icons from view.
  • desktop settings > icons > icon type > choose "None"

Getting information about package versions from Yum
  • yum info packagename

Side note to (e:paul): R does pull in the following dependencies:

texlive.x86_64 0:2007-62.fc15
texlive-dvips.x86_64 0:2007-62.fc15
texlive-latex.x86_64 0:2007-62.fc15
texlive-texmf.noarch 0:2007-37.fc15
texlive-texmf-dvips.noarch 0:2007-37.fc15
texlive-texmf-fonts.noarch 0:2007-37.fc15
texlive-texmf-latex.noarch 0:2007-37.fc15
texlive-utils.x86_64 0:2007-62.fc15



It's such a pity the packages it pulls are from 2007! :/

And Gnumeric doesn't even start up now. Something about:

gnumeric: symbol lookup error: /usr/lib64/libspreadsheet-1.10.17.so: undefined symbol: go_direction_get_name



  • In Debian, you can actually, copy the entire /var/apt/cache files into a new installation and have the apt manager pull the .deb files from there without having to download packages over and over. But I don't see any such package repository in Fedora in the /var/cache/yum/ directory. It's all rolled into some sort of a database file. I found from this link that yum *deletes* everything after install. This is kind of wasteful for people who have enough space but not enough bandwidth(ME!). To prevent yum from deleting all the packages after install, apparently, I need to make keepcache=1 in /etc/yum.conf Now I only need to remember this detail next time.

  • These are my detailed specs just for reference...
[txt]1011/toshibaspecs.txt[/txt]

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Permalink: Fedora_15_with_XFCE_Some_Notes.html
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Location: Buffalo, NY
Last Modified: 10/16/11 09:40


Category: linux

10/16/11 07:10 - ID#55314

Making a bootable USB in Linux

Sometimes the simplicity of things across all distributions of linux are most refreshing. To burn an iso into a USB and create a bootable USB, I was glad to find out that I didn't need to hunt for programs as I usually do. I could do it in 4 steps.


(e:Paul) would like to remind everyone that this method completely gets rid of all the existing data on the USB drive so do it on an expendable one not somewhere you have all your backup files.



Pull up a terminal.
Pull up the system messages by


tail -f /var/log/messages


This records the realtime happenings on your system

Plug in your USB, you'll see it coming up on the messages window
Let's say its /dev/sdb


At this point (e:uncutsaniflush) would like to say:
You should also note that this only works if your usb drive is "/dev/sdb." If a box has multiple hard drives, it is unlikely that "/dev/sdb" would be your usb drive. If someone had for example two hard drives, "dev/sdb" would be the second one. And thus, all data on the second hard drive would be destroyed. "dd" is a wonderful tool but rather easy to misuse if one isn't absolutely clear which drive is which.


On the terminal again, umount it first


umount /dev/sdb



Go to the directory containing the iso image


cd /directory/that/contains/iso



Then give the simple command to burn the iso into the USB


dd if=file.iso of=/dev/sdb



This will take a while to finish, but yes, it's that simple.
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Permalink: Making_a_bootable_USB_in_Linux.html
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Last Modified: 10/16/11 07:52


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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Permalink: Diffused_Sunlight_Simulation.html
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Last Modified: 10/15/11 11:16


Category: the odes

10/15/11 02:40 - ID#55302

Why go minimal?

And I thought.

What is the meaning of life? Why are we here anyway? Banal questions and the themes of several works of literary merit (or not). But unanswered nevertheless. Where do we go after this life is over? Heaven and Hell and "the great consciousness" seem rather medieval with all this technology surrounding us. It's hard to believe that anyone even gets punished or rewarded for what they do in life here. That sounds like the words of an atheist. But I am not an atheist. I have a TON of faith. Perhaps not in religion, but in people themselves.

I sincerely believe Science cannot exist without this faith in people, in methods, in what we do, faith in our spirit as humans, faith in a better but unknown future, faith that our work is making things better, faith that we are finding meaning in our lives, faith that we will someday be in a better place and faith that we are making progress.

But in the middle of all this hope, what if some of us give out? Sink into death, into the unknown oblivion? Will anyone care? Yeah, maybe. If you are Steve Jobs, people might even cover the walls of the nearest Apple store with post-its. But what if you are not Steve Jobs? What if you are one of the millions who feel impelled to write one of those post-its? Will someone write post-its for you? How many post-its will you get when you leave this life of yours? Will they be enough to cover a wall? Does it even matter?

The pain you will give people by leaving them behind will matter. How will they cope with this pain? Will it be tough for them to see things you lived with when you were... well alive? Was your life so complicated that along with the pain, you leave them with the tough ordeal of going through the complications and the sheer volume of personal effects you lived with. That each little belonging collects the grief and plunges it back into them as they remember you and then realize that you are now gone?

I am not sure what the point of all these morbid musings are. But I don't want people to suffer after I am gone. I want them to know that I lived happily and tried to do my part. It doesn't matter whether I got anywhere or not. It just matters that I lived most moments happily. I don't want so many belongings that people drown in them and need to hold an estate sale because they don't want any of it. I don't want trivial stuffed toys, knick knacks, I don't want heavily highlighted books and notes with the dried flowers and leaves in them, I don't want anything remotely sentimental and pain-inducing. I don't even want a bed. It does sound pretty clinical and detached but I want to wrap up this life as cleanly as possible, as minimally as possible and when its time to leave, I want leave quietly and completely at ease, and smiling. Because I am not sure I know entirely what the meaning of all this existence is, I just don't think it's worth the drama and pain we bring to people when we let it all go.

And no, I am not sad. I just want to break this chain linux based whingeing that I have been indulging in for the past so many posts with some free-writing on a very non-specific stream of thoughts that just came over and needed written expression.

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Permalink: Why_go_minimal_.html
Words: 600
Location: Buffalo, NY
Last Modified: 10/15/11 03:41


Category: i-tech

10/14/11 10:19 - ID#55298

Gadgety Goodness

Woo Hoo!!
image
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Permalink: Gadgety_Goodness.html
Words: 4
Location: Buffalo, NY
Last Modified: 10/14/11 10:19


Category: linux

10/14/11 06:30 - ID#55297

Fedora missing fonts for Gnumeric?

Why are the row and column numbers displaying as numeric placeholder skeletons in Gnumeric??

image

Does Gnumeric use some proprietary fonts that the mighty forces at Fedora have decided to outcast from the distro??

Aaargh. Can one thing be hitch-free for a change??! Apparently not.
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Permalink: Fedora_missing_fonts_for_Gnumeric_.html
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Last Modified: 10/14/11 06:32


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