general · science –
After discussing my second PhD year today, and after noticing that not even a single professor from the commitee was there (save my boss and a person that joined later on), I realized that the situation for students like me isn’t really the best.
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general –
Wednesday I got around to assemble a replacement for largo, what used to be my old “main” desktop. I also got a new case and power supply for leon, the other desktop I own, but I need to switch things around from the “old” largo to leon and I didn’t have the time yet.
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science –
I’ve noticed that the journal Science code for Biology and Medicine has finally launched. While some said that would be a journal if someone is desperate for a publication, I think it fills in a gap that’s very felt in bioinformatics: the availability of source code.Perhaps I’m being too naive, but I think that at least academic groups should always release their source code, if they develop a new program or an algorithm, or just give a proof of concept so that others can reproduce their work. This will also help in finding and squashing bugs. Bugs that are sadly much present in a large part of the biological software outlined in publications.
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final fantasy xi –
Last Tuesday I assembled a group and we took on the (only) battle present in the new Treasures of Aht Urhgan update. I had to look for members, but since Besieged was going on I lost a lot of time shouting for members. In the end I managed to get a red mage and a ninja along people I had arranged to meet with.
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general · linux · science –
Finally I cleaned up my code enough to post it here. It’s probably still ugly, but not as ugly as when I wrote it down the first time. It’s all about manipulating text files, to be precise tab-delimited files. All the snippets are published under the GNU GPL v2 (not that I think that anyone would use them, but just in case…).
I started with one file, listing Entrez Gene identifiers for a number of genes coming out of a statistical analysis, along with their SAM scores to see if they were differentially expressed or not. I needed to add information such as gene name and symbol, Gene Ontology, and Uniprot/SwissProt IDs, leaving out the statistical paramters. I tried at first to use the EUtils package of Bioptyhon, but due to both my lack of skill and the total lack of documentation, I dropped the idea and moved to a different plan.
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linux –
I’ve upgraded both leon (one of my computers at home) and quant (my work machine) to Kubuntu Edgy Eft (now in Release Candidate status, screenshots here). Leon’s upgrade went perfectly, while quant gave me some headaches. First of all there was a conflict between packages, then the nvidia module for legacy hardware wouldn’t load:
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general · s.t.e.a.l. –
I haven’t had much time to write here as I’ve been busy fixing and arranging things for the web page on S.T.E.A.L. It appears that thanks to Too’s deviation posting and subsequent journal entry, hits have skyrocketed. This makes me happy but it also means more work and need for refinement. As a matter of fact, I wrote a little more yesterday, and today I’ll be aiming to complete chapter 4. Since I’ve been working on that for the past 3 years, it would be a nice accomplishment.
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