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http://nar.oxfordjournals.org/cgi/reprint/gkm259v1?ijkey=7rAn6VnzAJbPKAO&keytype=ref(please ignore the extra symbols in the following. I just copied and pasted from a different page to give a basic synopsis)
WoLF PSORT: protein localization predictor Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada1, C.J. Adams-Collier and Kenta Nakai, Computational Biology Research Center, AIST, Tokyo, Japan, 2Center for Genome Science, National Institute of Health, Korea Center for Disease Control & Prevention, 5 Nokbeon-Dong, Eunpyung-Gu, Seoul 122-701 Korea, 3Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan and 4Collier Technologies, Everett, WA, USA *To whom correspondence should be addressed. Tel: + 81-3-5449-5131; Fax: + 81-3-5449-5133; Email: knakai@ims.u-tokyo.ac.jp Received January 30, 2007. Revised March 26, 2007. Accepted April 8, 2007. WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting signals, amino acid composition and functional motifs such as DNA-binding motifs. After conversion, a simple k-nearest neighbor classifier is used for prediction. Using html, the evidence for each prediction is shown in two ways: (i) a list of proteins of known localization with the most similar localization features to the query, and (ii) tables with detailed information about individual localization features. For convenience, sequence alignments of the query to similar proteins and links to UniProt and Gene Ontology are provided. Taken together, this information allows a user to understand the evidence (or lack thereof) behind the predictions made for particular proteins. WoLF PSORT is available at wolfpsort.org
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Neat. I found the following in my drafts. I thought I had lost it...
I need to re-build my entire system. Someone broke in to colliertech.org and used the system to send huge amounts of spam. This cost my upstream provider a ton of money. I then misplaced my USB disk which contains a(n admittedly obscure) filesystem with my PGP key, colliertech.org's private root x.509 key and the same for my family. I could assume that whoever found my usb disk would pass it on to a lost-and-found location without having torn it apart, figured out how to mount the filesystem, brute-forced the password out of the pgp key and x.509 keys, etc, etc. But I won't. I will now admit defeat and start over. But first, I'm going to read chapter 19.34 of teh RCW, some books on intrusion detection and prevention, some docs on MAC, specifically SELinux as it pertains to Debian. My mentor and owner/operator of the largest ISPs on the Kitsap Peninsula during the late 1990s said something about the incident that made me think. He said something to the tune of "you were trained better than that." I don't know that I had ever been trained in security, other than during my stint at Security Portal... But I only worked on writing Perl code there... I was only tangentally associated with any security stuff... So now I'm going to edumacate myself :)
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So, I changed my blog name to something more catchy. "C.J.'s Journal of Studlyness" was fun for a while, but it's time to try something new. The new name ("The Pædantic Programmer's LiveJournal") is a play on The Pragmatic Programmer, but using the word "pædant" instead of "pragrmatic." I changed the title to this in particular because:
- everyone else has a more mature and catchy blog name than me
- I'm re-building colliertech.org, after the most recent hacking attack, and it seems like a good time to make some major changes
- I find myself being being more and more pædantic in my code, my work, and my life these days
- because my wordpress blog (currently down) is my primary blog, but this one is important, too</lil>
Thoughts? I didn't find any other hits on Google for "pedantic programmer," so I don't think I'm stepping on anybody's toes... Whee! :) Tags: blog, pædantic, web 2.0
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Oh well. Anyway... I went to LinuxFest Northwest yesterday with ![[info]](http://p-stat.livejournal.com/img/userinfo.gif) fuzzyredmittens and scarletwilde. I hung out at the Mono Project table and gave away some books and t-shirts that Miguel sent over for the occasion. Coincidentally, the Mono Project booth was set up right next to the MySQL booth, which was manned by none other than Gerry and a couple of his kiddos. Gerry and I manned the MySQL booth together in 2006, and it was good to be sitting next to him again this year. Tim Maher, retired president for life of the Seattle Perl Users' Group and recipient of the White Camel, was selling copies of his Minimal Perl in the exhibition hall. I bought a copy and Tim even signed it for me. Whee! This is the first book that I've got an acknowledgement in, so I had to have a copy. Quite a few fun folks stopped by the booth including Paul Bartell, brad, Allison, chromatic and lots of folks with questions, comments, rants and concerns about the Mono project. We've got a shower for baby Zelda today, so we're not going to be attending the second day of the conference. I hope I'm forgiven... :) Although Hannah offered to let me sleep in this morning, I couldn't fall back asleep after about 5:15. So I'm writing down some the thoughts that kept me up... 1) Moose helps perl devs create classes that are nearly CLS compliant. It would be nice to either patch Moose to fully implement CLS compliant classes or create a CLI:: namespace with classes that are CLS compliant. OMG! Strongly typed Perl!!! 2) It would be nice to target Perl to the CIL virtual machine. What is the process of adding another architecture to Perl's vast target suite? 3) Module::Starter::Moose, Module::Starter::DotNet, Class::Mop, Class::CLS ECMA335::* blah blah blah :) Tags: linux, linuxfestnw, livejournal, mono, mysql, o'reilly, perl, spug
Current Location: Everett, WA
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