The title will already give an idea of what happened to my laptop two days ago. Due to a bus problem and a forced reboot, my root partition got corrupted. Luckily no data was lost as I keep /usr and /home separated from the rest. However reinstalling proved to be a very difficult task.
First of all, my DVD drive has some problems, and so it wouldn’t read the Kubuntu Feisty install disk I had brought from work. I tried then using a thumb drive but no luck, this buggy BIOS does not allow USB boot. I then copied the disk over to a DVD-RW I had, following my brother’s suggestion. So I was able to boot.
Problems didn’t end here as the DVD had trouble reading, so I had to try about three times, then jumping into expert mode to install the base system. When I tried to install the rest, some packages wouldn’t install. I had to make sure I could boot via HD, then I used the Ethernet connection to download and fix the broken packages. It took me three hours or so yesterday.
Then I still had some odd hangs or the kernel log filled with “drive not ready for command”. It came to me that I was using laptop-mode, which my HD did not like. As soon as I disabled it, the kernel messages stopped. I’ll be monitoring the situation and see.
UPDATE: Today I found out that J Brooks (the corresponding author of Zhao’s paper) has agreed to send the data I needed. Thanks a lot!
When you do bioinformatics, you often test your own procedures not only on your data, but also on datasets provided by other people and publicly available. As I stated previously, that’s what meta-analysis is. I’m doing a bit of that for my thesis and recently I noticed that some datasets, while being public, are far from complete.
I was looking at the data published by Zhao et al. today and while it’s a rather interesting dataset (177 samples of renal cell carcinoma compared to Human Universal Reference RNA), there is little or no information regarding the samples themselves. As I’m running analyses comparing different tumor grades, this is essential for me. However neither the supplementary materials nor the paper give any information. Basically this makes the whole dataset a lot less useful than what it could be.
On the same note, evaluating results by Jones et al. presented different problems, because of the aging annotation of the Affymetrix HG-U133A chip. Dai et al. have shown an interesting approach to reannotation for several Affymetrix chips, so I thought I could use that. However, while the supplementary materials give raw normalized data, there are no CEL files, needed for such a procedure.
Personally I think that all journals should make the submission to databases such as Array Express mandatory. MIAME was meant to be a way to give enough information about a microarray experiment, and it’s a shame that there are still so many hurdles when someone wants to make use of someone else’s data.
When starting a run in Dynamis-Beaucedine, some person in charge of my brother’s Dynamis linkshell stated that over a whole Dynamis run (approximately four hours) you should not leave or be away. This statement is misguided at best, and personally I found it rather offensive for a series of reasons:
- Not everyone is in the same timezone: if you have other commitments that force you to stay away for a longer period (such as meals with other people) you should not be blamed for it, after all real life takes serious precedence over gaming;
- Four hours is a long time. While FFXI tries to keep you online as much as possible, there should be no forced requirement at all. Otherwise you are disrespectful of other people’s lives, which again take precedence over anything that goes in-game.
- Last but not least, acting bad towards people that take an effort despite the limited time is a sign of short-sightedness and again lack of respect.
AFv2DoesntExist apparently is run by people who ignore those points. Either they are lifeless people (as the title suggests) or they just ignore anything that doesn’t benefit them.
Today I made a simple sed script that converts a tab-delimited text file to a format that can be pasted into a DokuWiki wiki. There is a plugin that permits to read CSV files directly, however:
- It doesn’t support tab-delimited text files;
- It’s incompatible with some plugins (one being DokuTexit, which I need).
Hence the need for this script. To use it, just copy and paste the code (see below) into a new file, make it executable (chmod +x) and then invoke it with
[code lang="bash"]
tab2wiki inputfile
[/code]
Note that it outputs the result on stdout, so you’ll need to redirect it if you want to save.
Without further ado, here’s the script (syntax may be off regarding colors):
#!/bin/sed -f
# tab2wiki - converts any tab-delimited file into a DokuWiki table
# First line is treated as header (^)
{
s/\t/| /g
s/$/ |/g
s/^/| /g
s/| / | /g
1s/|/\^/g
s/^\s\s//g
}
