WORLDCOMP'09

WORLDCOMP'09 - Program/Schedule
http://www.worldacademyofscience.org/worldcomp09/ws/program/schedule.pdf

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Metagenomics
http://camera.calit2.net/about-camera/what-is-camera
http://metagenomics.calit2.net/index.php
http://psb.stanford.edu/psb-online/
http://bioinformatics.ucsd.edu/
http://www.jacobsschool.ucsd.edu/news/news_releases/release.sfe?id=499
http://www.hydrocarbonmetagenomics.com/
http://www.genomealberta.ca/research/new_initiatives/oil_sands/default.aspx
http://www.genomealberta.ca/research/projects/
http://www.genomebc.ca/genomics_programs/research-projects.htm
http://www.genomebc.ca/genomics_programs/research_projects/comp1/microbial.htm
http://www.genomebc.ca/genomics_programs/research_projects/environment.htm
http://innovationwatch-archive.com/choiceisyours/choiceisyours-2009-01-15.htm
http://www.nap.edu/openbook.php?record_id=11902&page=47

Committee on Metagenomics: Challenges and Functional Applications

Jo Handelsman (Co-chair), University of Wisconsin-Madison; James M. Tiedje (Co-chair), Michigan State University; Lisa Alvarez-Cohen, University of California, Berkeley; Michael Ashburner, University of Cambridge; Isaac K. O. Cann, University of Illinois, Urbana-Champaign; Edward F. DeLong, Massachusetts Institute of Technology; W. Ford Doolittle, Dalhousie University; Claire M. Fraser-Liggett, The Institute for Genomic Research; Adam Godzik, The Burnham Institute; Jeffrey I. Gordon, Washington University School of Medicine; Margaret Riley, University of Massachusetts, Amherst; Molly B. Schmid, Keck Graduate Institute; Ann H. Reid (Study Director), National Research Council.

This report brief was prepared by the National Research Council based on the committee’s report. For more information, contact the Board on Life Sciences at bls@nas.edu or visit http://nationalacademies.org/bls. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet is available from the National Academies Press, 500 Fifth Street, NW, Washington, D.C. 20001; (800) 624-6242; www.nap.edu. Support for this publication was provided by the Presidents’ Circle Communications Initiative of the National Academies.

top-10-korean-dramas-of-2008

http://starones.wordpress.com/2009/01/01/top-10-korean-dramas-of-2008

http://www.hancinema.net/most_wanted.php

generef ISCB www.bioinformatics.org

http://generef.com/genomics.html

http://www.iscb.org/ismbeccb2011

Bioinformatics for Regulatory Genomics (BioRegSIG)
Special Interest Group (SIG) at ISMB In conjunction with the International Conference on Intelligent Systems for Molecular Biology (ISMB)    
http://light.ece.ohio.edu/bioreg/2011/
http://light.ece.ohio.edu/bioreg/

http://www.bioinformatics.org/

Education: ISCB-Student Council announces undergrad internship w/ Schneider Lab @ EMBL-Heidelberg
Submitted by Abhishek Pratap; posted on Monday, December 07, 2009
The ISCB Student Council is pleased to announce an internship at the Schneider Group at EMBL-Heidelberg. This internship is exclusively arranged by the Student Council in collaboration with Dr Schneider for a student from a developing nation. The goal is to train an undergraduate student in Data Integration and Knowledge Management in Computational Biology.

FUNDING:
Internship will be funded at Euros 400/month for 6 months. Student will be provided with free accommodation during his/her stay at Heidelberg. The cost of the travel to and from the home country to Heidelberg will NOT be covered by the host lab and shall be borne by the student in full.

IMPORTANT DATES:
Last date for Application Submission: Dec 20, 2009
Acceptance Notification: Jan 15, 2010


http://www.craic.com/documents/oreillynet_bioinfo_intro.pdf
What are the Hot Topics in Bioinformatics? (2004)
Comparative Genomics

http://ca.wiley.com/WileyCDA/WileyTitle/productCd-3527313486,descCd-tableOfContents.html (2005)
Cover image for product 3527313486
Larger Image
Handbook of Genome Research: Genomics, Proteomics, Metabolomics, Bioinformatics, Ethical and Legal Issues, Two Volume Set
Christoph W. Sensen (Editor)
ISBN: 978-3-527-31348-8
Hardcover
646 pages
August 2005
1 Genome Projects on Model Organisms (Alfred Pühler, Doris Jording, Jörn Kalinowski, Detlev Buttgereit, Renate Renkawitz-Pohl, Lothar Altschmied, Antoin Danchin, Agnieszka Sekowska, Horst Feldmann, Hans-Peter Klenk, and Manfred Kröger).
2 Environmental Genomics: A Novel Tool for Study of Uncultivated Microorganisms (Alexander H. Treusch and Christa Schleper).
3 Applications of Genomics in Plant Biology (Richard Bourgault, Katherine G. Zulak, and Peter J. Facchini).
4 Human Genetic Diseases (Roger C. Green).
5 Genomic Mapping and Positional Cloning, with Emphasis on Plant Science (Apichart Vanavichit, Somvong Tragoonrung, and Theerayut Toojinda).
6 DNA Sequencing Technology (Lyle R. Middendorf, Patrick G. Humphrey, Narasimhachari Narayanan, and Stephen C. Roemer).
7 Proteomics and Mass Spectrometry for the Biological Researcher (Sheena Lambert and David C. Schriemer).
8 Proteome Analysis by Capillary Electrophoresis (Md Abul Fazal, David Michels, James Kraly, and Norman J. Dovichi).
9 A DNA Microarray Fabrication Strategy for Research Laboratories (Daniel C. Tessier, Mélanie Arbour, François Benoit, Hervé Hogues, and Tracey Rigby).
10 Principles of Application of DNA Microarrays (Mayi Arcellana-Panlilio).
11 Yeast Two-hybrid Technologies (Gregor Jansen, David Y. Thomas, and Stephanie Pollock).
12 Structural Genomics (Aalim M. Weljie, Hans J. Vogel, and Ernst M. Bergmann).
13 Bioinformatics Tools for DNA Technology (Peter Rice).
14 Software Tools for Proteomics Technologies (David S. Wishart).
15 Applied Bioinformatics for Drug Discovery and Development (Jian Chen, ShuJian Wu, and Daniel B. Davison).
16 Genome Data Representation Through Images: The MAGPIE/Bluejay System (Andrei Turinsky, Paul M. K. Gordon, Emily Xu, Julie Stromer, and Christoph W. Sensen).
17 Bioinformatics Tools for Gene-expression Studies (Greg Finak, Michael Hallett, Morag Park, and François Pepin).
18 Protein Interaction Databases (Gary D. Bader and Christopher W. V. Hogue).
19 Bioinformatics Approaches for Metabolic Pathways (Ming Chen, Andreas Freier, and Ralf Hofestädt).
20 Systems Biology (Nathan Goodman).
21 Ethical Aspects of Genome Research and Banking (Bartha Maria Knoppers and Clémentine Sallée).


http://emboss.sourceforge.net/apps/proposed.html

Rice genetic diversity and discovery: meeting the needs of future generations for rice genetic resources

http://beta.irri.org/index.php/Programs/fostering-genetic-diversity/Fostering-genetic-diversity.html

Rice genetic diversity and discovery: meeting the needs of future generations for rice genetic resources

download pdf

Program 5 provides the foundation for applying rice genetic diversity in the implementation of IRRI’s Strategic Plan. It focuses on three themes: characterization and creation of genetic diversity, and gene-function assignment; conservation and documentation of germplasm (seeds and the genetic material they contain); and enabling access to and use of genetic diversity and associated tools. These activities aim to solve production problems by using genetic diversity and by providing a genetic research platform that enables efficient conservation and use of genetic diversity. Thus, Program 5, which represents the interface between understanding and applying genetic diversity, promotes a convergence of approaches and innovations. Although the program’s activities are driven by the problems IRRI seeks to solve, the research also accommodates exploratory work to serve long-term needs.

http://beta.irri.org/index.php/Programs/fostering-genetic-diversity/Output-3-Genetic-pathways-for-select-traits-determined-using-genomics-and-comparative-biology.html

Output 3: Genetic pathways for select traits determined using genomics and comparative biology
Genetic pathways for selected traits determined using genome-wide and comparative biology approaches with priorities on stress tolerance, nutrition and grain quality, and yield established by 2015

download pdf

Users of this knowledge will contribute to the International Rice Functional Genomics Consortium objective of understanding genes controlling target traits, which will enable researchers to develop markers for breeding and lead to, production of prebreeding lines. Acceleration of gene discovery on a genome-wide scale will improve sustainability in intensive pro-duction areas and increase productivity in marginal areas.

Propose in public place

http://www.videojug.com/expertanswer/when-to-propose-3/should-i-propose-in-a-public-place

http://www.japanprobe.com/2006/01/20/generalizations-about-japanese-girls-part-1/
seems like an intersting article ...

http://chibabeat.com/guide_to_dating_japanese_girls
these are some funny and creative tips...

http://www.roadjunky.com/romancepage/412/romance-in-japan-and-dating
For some city girls dating a gaijin is something like having a life-size fashion accessory.
... this sounds a bit harsh ...

http://www.thefrisky.com/post/246-girl-talk-just-not-that-into-him/
. It makes me think of that scene in “The Wedding Planner” when Jennifer Lopez’s father explains that when he first met her mother he had to grow to like her, then lust after her, then love her. But it’s an absurd comparison because (a) her father had a pre-arranged marriage to someone he didn’t know and (b) it’s a J.Lo movie.

It took me 3-4 months to realize I loved him…which is very different from being “in love”. If you want to be “in love”, you should probably look elsewhere, but I feel that fades with time, while “loving” someone is something you can still do when you’re old and gray.

because I had learned you can never create the spark where it has never been.

some guys are too easy

... hmmm ... after reading the comments, it seems to be a 50/50, perfect guy, no spark learned to love after X number of years, and not-so-perfect sparkies ... then ...

A guy who stands up for and is passionate about what he believes in while being civil to those who disagree (and chivalrous/polite in general) is hot.

In all relationships the spark fades with time. I’m not saying it won’t ever come back, but the loves that really last are the ones where friendship is the base.

http://socyberty.com/relationships/tips-to-date-a-japanese-girls/

http://www.mynippon.com/romance/jlover.htm

http://www.thefrisky.com/post/246-5-ways-women-try-to-impress-men-and-why-they-dont-work/

http://www.thefrisky.com/post/246-seven-ways-men-try-to-impress-women-and-why-they-dont-work/

http://shine.yahoo.com/channel/sex/7-terrible-ways-to-propose-510672/

http://www.yourtango.com/200684/relationship-red-flags.html

http://www.yourtango.com/helenfisher?alt=3

http://www.yourtango.com/200929208/7-traits-irresistible-men?alt=3

http://www.yourtango.com/200914986/5-things-single-women-hate-hear?alt=3

http://www.yourtango.com/200684/relationship-red-flags.html?page=0%2C2&alt=3

http://www.yourtango.com/helenfisher?page=0%2C3&alt=3

http://www.yourtango.com/200684/relationship-red-flags.html?page=0%2C3&alt=3

Beatles - All My Loving

http://www.youtube.com/watch?v=zJrOjB2UGGQ&NR=1

Big Bang - Let Me Hear Your Voice

http://www.youtube.com/watch?v=yVhHWhePTn4

JUJU and JAY'ed 明日がくるなら - If tomorrow comes

http://www.youtube.com/watch?v=U3B_RTtlq7M

Vi or Vim Colors

set t_Co=0
set t_Co=256

平井堅 – 僕は君に恋をする

http://www.youtube.com/watch?v=xZEM5t3Chcg
Hirai Ken – I’m Falling In Love With You
平井堅 – 僕は君に恋をする
boku wa kimi ni koi wo suru

Lyrics
http://www.quartet4.net/?p=7539

「2009 FNS歌謡祭」 FNS 2009
http://www.fujitv.co.jp/FNS/index2.html

SETLIST
M1 SMAP そっときゅっと M24 AI×ATSUSHI Story（2005）
M2 徳永英明 Hello
Guitar&Chorus：小池徹平 M25 JUJU×徳永英明 やさしさで溢れるように
M3 GIRL NEXT DOOR Infinity M26 甲斐よしひろ×長瀬智也 安奈（1979）
二胡：alan
M4 青山テルマ 忘れないよ
Guitar：村治佳織 M27 SPEED White Love（1997）
Accordion：coba
M5 一青窈×岩崎宏美 思秋期（1977） M28 稲垣潤一×広瀬香美 クリスマスキャロルの頃には（1992）
M6 つるの剛士×欧陽菲菲 ラヴ・イズ・オーヴァー（1979） M29 EXILE Loves Again（2007）
M7 レミオロメン Sakura M30 LOVE PSYCHEDELICO HAPPY XMAS（1971）
M8 KinKi Kids スワンソング M31 倖田來未 Lick me
M9 BIGBANG 声をきかせて M32 Aqua Timez 決意の朝に（2006）
M10 NYC boys NYC M33 森高千里×稲垣潤一 雨（1990）
M11 郷ひろみ 男願Groove！ M34 ヘキサゴンオールスターズ 泣いてもいいですか
M12 槇原敬之×嵐 冬がはじまるよ（1991）
Accordion：coba／Guitar：小倉博和 M35 東方神起×徳永英明 レイニーブルー（1986）
Violin：宮本笑里
M13 槇原敬之×青山テルマ×JUJU×SPEED 北風（1992）
Guitar：小倉博和 M36 東方神起 Stand by U
M14 槇原敬之×SPEED×ヘキサゴン女子 私がオバさんになっても（1992） M37 EXILE ふたつの唇
M15 SPEED×ヘキサゴン女子 17才（1989） M38 嵐 明日の記憶
M16 森高千里 渡良瀬橋（1993） M39 コブクロ I LOVE YOU（1991）
M17 コブクロ STAY M40 倖田來未 いい日旅立ち（1978）
M18 Superfly Alright!! M41 平井堅 僕は君に恋をする
M19 LINDBERG 今すぐKiss Me（1990） M42 一青窈 うんと幸せ
Piano：小林武史
M20 NOKKO フレンズ（1985） M43 ゆず 虹
M21 V6 GUILTY M44 JUJU with JAY'ED 明日がくるなら
Guitar：村治佳織／Violin：宮本笑里
M22 TOKIO 太陽と砂漠のバラ M45 絢香 みんな空の下
M23 絢香×平井堅 Love Love Love（1998） M46 SMAP 世界に一つだけの花
Guitar：小倉博和／Violin：宮本笑里

Japanese vocab 単語 たんご

http://en.bab.la/dictionary/english-japanese/all-you-can-eat.html

all-you-can-eat [ex.] 食べ放題 [たべほうだい] [ex.]

無理 むり
impossible

admission free {noun} 傍聴無料 [ぼうちょうむりょう] {noun}

無料 free
むりょう

料 [りょう] {noun} speak fee fee {noun}

禁　きん
prohibited

danger {adj.} 危険 [きけん] {adj.}

Australia: Research hopeful for fast growing rice

http://www.abc.net.au/rural/news/content/200907/s2621031.htm

http://beta.irri.org/news/index.php/rice-news/australia-research-hopeful-for-fast-growing-rice.html
ABC Radio Australia: A James Cook University researcher is working as part of an international team to develop faster growing rice. Professor Jim Burnell is one of a group of 26 researchers who are working to increase the rice plant's growth rate and reduce the amount of water and fertiliser the plant needs. By changing the biochemistry of rice plants, professor Burnell's team are hoping to enhance the photosynthetic process in rice making it grow up to 50 per cent faster. "If we can introduce what we call the C4 pathway - photosynthetic pathway, into rice, which is a C3 plant, we should also be able to increase it's water use efficiency and it's nitrogen use efficiency, so that you could grow plants using less water and less nitrogen fertilisers," he says.

Sorting dictionary values in Python

Python dictionary value sorting:
http://wiki.python.org/moin/HowTo/Sorting#Sortingbykeys

If the invocation of key returns a tuple, second and subsequent items in the tuple will be treated as sub-keys in the same way that Python generally sorts tuples:

>>> L = [('d', 2), ('a', 4), ('b', 3), ('c', 2)]
>>> sorted(L, key=lambda x:(x[1], x[0]))
[('c', 2), ('d', 2), ('b', 3), ('a', 4)]

Yokozunas - highest rank in sumo

http://en.wikipedia.org/wiki/Asash%C5%8Dry%C5%AB_Akinori
Asashōryū Akinori (朝青龍 明徳?, born September 27, 1980 as Dolgorsürengiin Dagvadorj, Mongolian: Долгорсүрэнгийн Дагвадорж) is a sumo wrestler (rikishi) from Ulan Bator, Mongolia. He is the 68th yokozuna in the history of the sport in Japan and became the first Mongolian to reach sumo's highest rank in January 2003. He is one of the most successful yokozuna ever,[1] and has won 24 top division tournament championships to date, equal third on the all-time list. In 2005 he became the first man to win all six official tournaments (honbasho) in a single year.

http://en.wikipedia.org/wiki/Hakuh%C5%8D_Sh%C5%8D
Hakuhō Shō (白鵬翔?, born March 11, 1985 as Mönkhbatyn Davaajargal, Mongolian: Мөнхбатын Даваажаргал) is a professional sumo wrestler (rikishi) from Ulan Bator, Mongolia. Making his debut in March 2001, he reached the top makuuchi division in May 2004. On May 30, 2007 at the age of 22 he became the second native of Mongolia, and the fourth non-Japanese overall, to be promoted to the highest rank in sumo, yokozuna. He has won eleven yusho or tournament championships to date, second only to his yokozuna rival (and fellow Mongolian) Asashōryū amongst active wrestlers.

Isaac_Asimov - Science Fiction author

http://en.wikipedia.org/wiki/Isaac_Asimov

Isaac Asimov (born Isaac Yudovich Ozimov, Russian: Исаак Юдович Озимов; c. January 2, 1920[1] – April 6, 1992), was a Russian American author and professor of biochemistry at Boston University, best known for his works of science fiction and for his popular science books. Asimov was one of the most prolific writers of all time, having written or edited about 500 books and over 9,000 letters and postcards.[2] His works have been published in nine of the ten major categories of the Dewey Decimal System (the sole exception being the 100s: philosophy and psychology).[3]

Asimov is widely considered a master of the science-fiction genre and, along with Robert A. Heinlein and Arthur C. Clarke, was considered one of the "Big Three" science-fiction writers during his lifetime.[4] Asimov's most famous work is the Foundation Series;[5] his other major series are the Galactic Empire series and the Robot series, both of which he later tied into the same fictional universe as the Foundation Series to create a unified "future history"

igraph - python graph library

http://igraph.sourceforge.net/index.html

Introduction

igraph is a free software package for creating and manipulating undirected and directed graphs. It includes implementations for classic graph theory problems like minimum spanning trees and network flow, and also implements algorithms for some recent network analysis methods, like community structure search.

Features

igraph contains functions for generating regular and random graphs, manipulating graphs, assigning attributes to vertices and edges. It can calculate various structural properties, graph isomorphism, includes heuristics for community structure detection, supports many file formats. The R and Python interfaces support visualization.

Python logging

Python Logging
http://blog.tplus1.com/index.php/2007/09/28/the-python-logging-module-is-much-better-than-print-statements/

import logging

# Log everything, and send it to stderr.
logging.basicConfig(level=logging.DEBUG)

def g():
1/0

def f():
logging.debug("Inside f!")
try:
g()
except Exception, ex:
logging.exception("Something awful happened!")
logging.debug("Finishing f!")

if __name__ == "__main__":
f()

Japanese conjugation

A Japanese Conjugation Builder
http://homepage3.nifty.com/jgrammar/grammar/bldverb/index.htm

Japanese Verb Conjugation Table
http://www.reikialoha.com/raymond/learning-japanese/verbs/

Semantic MediaWiki (SMW)

http://semantic-mediawiki.org/wiki/Semantic_MediaWiki

Semantic MediaWiki (SMW) is a free extension of MediaWiki – the wiki-system powering Wikipedia – that helps to search, organise, tag, browse, evaluate, and share the wiki's content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that let you easily publish Semantic Web content, and allow the wiki to function as a collaborative database.

Perl

http://www.perl.com/pub/a/2002/04/10/mod_perl.html

http://search.cpan.org/~jmm/Heap-0.80/lib/Heap.pm

http://search.cpan.org/CPAN/authors/id/J/JM/JMM/Heap-0.80.tar.gz

% perl Makefile.PL PREFIX=$HOME

% make
% make test
% make install # if you 'su' then to quit su mode
% make clean

export PERL5LIB=$HOME/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/:$HOME/lib/perl5/site_perl/5.8.8

% man stats
% export MANPATH=$HOME/man/:$MANPATH
% man -M $HOME/man Heap
% man --manpath=$HOME/man Heap
% man --manpath=$HOME/man AI::Pathfinding::AStar
% perl -e 'use lib "$ENV{HOME}/lib/site_perl"; use Heap;';
% perl -e 'use lib "$ENV{HOME}/lib/site_perl"; use AI::Pathfinding::AStar;'

http://www.perlhowto.com/extending_the_library_path

% export PERL5LIB=$HOME/lib/site_perl/

Python built-in functions

http://docs.python.org/library/functions.html

I heard they're pretty fast

map - maybe better for parallelization purposes
---
>>> l=[1,2,3,4,5]
>>> def dbl(x):
return x*2

>>> map(dbl, l)
[2, 4, 6, 8, 10]

or just
[x*2 for x in l]

set
---
>>> set([1,1,2,2,3,3])
set([1,2,3])

http://stackoverflow.com/questions/672172/how-to-use-python-map-and-other-functional-tools

PuLP - Linear Programming modules for Python

http://www.purplemath.com/modules/linprog.htm
http://code.google.com/p/pulp-or/wiki/OptimisationWithPuLP

http://mail.python.org/pipermail/python-announce-list/2005-May/003989.html
# Borrowed code from Jean-Sebastien, see link above ...
Example script:
--------------------------------------------------
from pulp import *

prob = LpProblem("test1", LpMinimize)

# Variables
x = LpVariable("x", 0, 4)
y = LpVariable("y", -1, 1)
z = LpVariable("z", 0)

# Objective
prob += x + 4*y + 9*z

# Constraints
prob += x+y <= 5
prob += x+z >= 10
prob += -y+z == 7

GLPK().solve(prob)

# Solution
for v in prob.variables():
print v.name, "=", v.varValue

print "objective=", value(prob.objective)
--------------------------------------------------
http://www.gnu.org/software/glpk/glpk.html

Linear programming is good for maximization or minimization problems or solving Sudoku puzzles! (http://130.216.209.237/engsci392/pulp/SudokuAsAnLP)

Works by incorporating linear equations ie y = mx + b (objective function) and a bunch of constraints eg 3*x - y <= 3 or something
works like magic!

As for applications, one example is with Punyakanok et al. '04 where he applies it to optimizing the best set of argument labels in semantic role labeling (SRL)
http://l2r.cs.uiuc.edu/~danr/Papers/PRYZ04.pdf

Google going global with Apps

http://www.reuters.com/article/technologyNews/idUSTRE59I09A20091019?feedType=RSS&feedName=technologyNews

Cloud computing.

WordNet / VerbNet via Python NLTK

WordNet as thesaurus
>>> from nltk.corpus import wordnet as wn
>>> set([s.name.split('.')[0] for s in wn.synsets('trade') if s.name.find(".v.") != -1])

VerbNet
>>> from nltk.corpus import verbnet
>>> verbnet.classids('drink')
['eat-39.1-2']
>>> v=verbnet.vnclass('39.1-2')
>>> [t.attrib['type'] for t in v.findall('THEMROLES/THEMROLE/SELRESTRS/SELRESTR')]
['comestible', 'solid']
>>> [t.attrib['type'] for t in v.findall('THEMROLES/THEMROLE')]
['Patient']

Clustering
http://docs.huihoo.com/nltk/0.9.5/api/nltk.cluster-module.html
import numpy
from nltk import cluster

vectors = [numpy.array(f) for f in [[3, 3], [1, 2], [4, 2], [4, 0]]]

# initialise the clusterer (will also assign the vectors to clusters)
clusterer = cluster.KMeansClusterer(2, euclidean_distance)
clusterer.cluster(vectors, True)

# classify a new vector
print clusterer.classify(numpy.array([3, 3]))

Named Entities
http://nltk.googlecode.com/svn/trunk/doc/book/ch07.html#named_entity_detection_index_term
>>> import nltk
>>> sent = nltk.corpus.treebank.tagged_sents()[22]
>>> print nltk.ne_chunk(sent)
(S
The/DT
(GPE U.S./NNP)
is/VBZ
one/CD
...
according/VBG
to/TO
(PERSON Brooke/NNP T./NNP Mossman/NNP)
...)

MontyLemmatiser - Strips inflectional morphology, i.e. changes verbs to infinitive form and nouns to singular form eg. eating -> eat
http://web.media.mit.edu/~hugo/montylingua/
>>> from monty.MontyLemmatiser import MontyLemmatiser
>>> lemmatized = MontyLemmatiser().lemmatise_word('eating')

まんが日本昔ばなし (Nippon Manga folklore)

昔　むかし　olden days / former

まんが日本昔ばなし (Nippon Manga folklore)
Bilingual Books

by Sayumi Kawauchi　川内 and Ralph F. McCarthy

http://ja.wikipedia.org/wiki/%E3%81%BE%E3%82%93%E3%81%8C%E6%97%A5%E6%9C%AC%E6%98%94%E3%81%B0%E3%81%AA%E3%81%97

金太郎 きんたろう
桃太郎　ももたろう 桃=peach

太郎　たろう　is common name for healthy boys

吃驚　びっくり　bikkuri　surprise

RPG Games

The World End With You
Suikoden Tierkreis
Kingdom Hearts 358/2 Days***
Valkyrie Profile: Covenant of the Plume
Shin Megami Tensei:Devil Survivor
Dragon Quest V
Black Sigil
FFX12 Revenant Wings

Shin Megami Tensei:Persona 3 and 4 (PS2)

http://ps2.gamezone.com/gzreviews/r29763.htm
http://www.siliconera.com/2009/09/13/ds-rpgs-wheres-my-plot/

***Note: Fix
http://www.romulation.net/forum/index.php?topic=23731
http://www.gbatemp.net/index.php?showtopic=158107
How to manually hex edit KH rom:
1: Google and download a program called XVI32 (hexer for ubuntu). This is the hex editor I used.
2: Open your KH rom.
3: At the top click address, then click goto, then click hexidecimal.
4: Type 010E5DC into the address box and click ok. (or hex value ctrl + f: 01 E2 0C 51 00 0D)
5: The first block should be highlighted and have 0C in it.
6: At the top click edit, click overwrite string, click hex string, in the bottom box type 37 and click ok.
7: Where it said 0C in the first box it should now say 37.
8: Click file, then click save.
9: Put the file you just saved on your flash cart and enjoy :)

semantic role labelling - SRL

www.cs.brandeis.edu/~cs114/slides/SemanticRoleLabeling.ppt

Semantic Role Labeling – Giving Semantic Labels to Phrases
[AGENT Sotheby’s] offered [THEME a money-back guarantee] to [RECIPIENT the Dorrance heirs]

Applications
-----------------
Question Answering
Q: When was Napoleon defeated?
Look for: [PATIENT Napoleon] [PRED defeat-synset] [ARGM-TMP *ANS*]

Machine Translation
English (SVO) Farsi (SOV)
[AGENT The little boy] [AGENT pesar koocholo] boy-little
[PRED kicked] [THEME toop germezi] ball-red
[THEME the red ball] [ARGM-MNR moqtam] hard-adverb
[ARGM-MNR hard] [PRED zaad-e] hit-past

Document Summarization
Predicates and Heads of Roles summarize content

Information Extraction
SRL can be used to construct useful rules for IE

Annotations Used
-----------------
Syntactic Parsers
Collins’, Charniak’s (most systems) CCG parses ([Gildea & Hockenmaier 03],[Pradhan et al. 05]) TAG parses ([Chen & Rambow 03])

Shallow parsers
[NPYesterday] , [NPKristina] [VPhit] [NPScott] [PPwith] [NPa baseball].

Semantic ontologies (WordNet, automatically derived), and named entity classes
(v) hit (cause to move by striking)

propel, impel (cause to move forward with force)


Subtasks
-----------------
Identification:
Very hard task: to separate the argument substrings from the rest in this exponentially sized set
Usually only 1 to 9 (avg. 2.7) substrings have labels ARG and the rest have NONE for a predicate
Classification:
Given the set of substrings that have an ARG label, decide the exact semantic label

http://research.microsoft.com/pubs/101987/SRL-Tutorial-AAAI-07-0723.pdf

Wheesung

http://www.4shared.com/dir/21371251/e1d8c53e/Wheesung_Vol6_-_Vocalate.html

http://www.youtube.com/watch?v=8Vzn8l3Hx2s

Long-term monkey tests back Oxford's gene therapy

http://www.reuters.com/article/scienceNews/idUSTRE59D4DL20091014?feedType=RSS&feedName=scienceNews

ProSavin, which is administered directly to the striatum in the brain, delivers three genes required to convert cells that normally do not produce dopamine into cells that do.

http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml
What factors have kept gene therapy from becoming an effective treatment for genetic disease?

* Short-lived nature of gene therapy - Before gene therapy can become a permanent cure for any condition, the therapeutic DNA introduced into target cells must remain functional and the cells containing the therapeutic DNA must be long-lived and stable. Problems with integrating therapeutic DNA into the genome and the rapidly dividing nature of many cells prevent gene therapy from achieving any long-term benefits. Patients will have to undergo multiple rounds of gene therapy.

* Immune response - Anytime a foreign object is introduced into human tissues, the immune system is designed to attack the invader. The risk of stimulating the immune system in a way that reduces gene therapy effectiveness is always a potential risk. Furthermore, the immune system's enhanced response to invaders it has seen before makes it difficult for gene therapy to be repeated in patients.

* Problems with viral vectors - Viruses, while the carrier of choice in most gene therapy studies, present a variety of potential problems to the patient --toxicity, immune and inflammatory responses, and gene control and targeting issues. In addition, there is always the fear that the viral vector, once inside the patient, may recover its ability to cause disease.

* Multigene disorders - Conditions or disorders that arise from mutations in a single gene are the best candidates for gene therapy. Unfortunately, some the most commonly occurring disorders, such as heart disease, high blood pressure, Alzheimer's disease, arthritis, and diabetes, are caused by the combined effects of variations in many genes. Multigene or multifactorial disorders such as these would be especially difficult to treat effectively using gene therapy. For more information on different types of genetic disease, see Genetic Disease Information.

Somatic cell - Wikipedia, the free encyclopedia
Somatic cells are any cells forming the body of an organism, as opposed to germline cells. In mammals, germline cells (also known as "gametes")

linux changing network info

change hostname
$ sudo hostname new_hostname

change macaddress
$ sudo apt-get install macchanger
$ sudo ifconfig wlan0 down
$ sudo macchanger -r wlan0
$ sudo ifconfig wlan0 up

python best practices

http://www.fantascienza.net/leonardo/ar/python_best_practices.html

# Python profiler:
python -m profile -o stats myscript.py
>>> import pstats
>>> p = pstats.Stats('stats')
>>> p.sort_stats('time').print_stats(15)

# For source code with not 7-bit ASCII
add this on top:
# -*- coding: UTF-8 -*-
# Or just, if you have less memory:
# coding: latin

# Use iter* methods when possible
mapping = {5: "5", 6: "6"}
for key, val in mapping.iteritems(): ...
for key in mapping: ...

a = 5
b = 6
a, b = b, a # swap

a = b = c = 5

if x == 1: y = fun1(x)
elif x == 2: y = fun2(x)
elif x == 3: y = fun3(x)
else: y = None
# But sometimes a dict is better:
funs = {1: fun1, 2: fun2, 3: fun3}
y = funs.get(x, lambda x:None)(x)

def mul(x, y):
return x * y
l = [2, 3]
print mul(*l)

# Generally getters and setters are not used.
# Instance names starting with _ are meant as
# 'to not mess with' by convention.
# Instance names starting with __ are private
# and receive name mangling.
class Foo(object):
def __init__(self, x, y, z):
self.x_public = x
self._y_private = y
self.__z_veryprivate = z
print Foo(1, 2, 3).x_public

finder = re.compile(r"""
^ \s* # start at beginning+ opt spaces
( [\[\]] ) # Group 1: opening bracket
\s* # optional spaces
( [-+]? \d+ ) # Group 2: first number
\s* , \s* # opt spaces+ comma+ opt spaces
( [-+]? \d+ ) # Group 3: second number
\s* # opt spaces
( [\[\]] ) # Group 4: closing bracket
\s* $ # opt spaces+ end at the end
""", flags=re.VERBOSE)
# Sometimes it's positive to indent logically those
# lines just like code.

# Sometimes it can be positive to compose REs:
spaces = r"\s*" # optional spaces
number = r"( [-+]? \d+ )" # Group
bracket = r"( [\[\]] )" # Group. Closing bracket
parts = ["^", bracket, number, ",", number, bracket, "$"]
finder = re.compile(spaces.join(parts), flags=re.VERBOSE)


# Use doctests (or module tests):
def function(data):
"""A comment

>>> function()
None
>>> function(1)
result1
>>> function("a")
Traceback (most recent call last):
...
TypeError
"""
...implementation...

if __name__ == "__main__":
import doctest
doctest.testmod()
print "Tests done."


x = (1, 2, 6, 55, 63, 96, 125, 256,
301, 456, 958, 1256,
1359, 2568, 3597)
# Too much long lines must be broken with \
# but \ isn't necessary inside () [] {}



# Using psyco array.array of double and
# signed long become very fast
import array
a = array.array("d", [3.56, 2.12])

Streaming Music

http://www.live365.com/listen/recommendations.live
http://kawaii-radio.net/page/listen

eeepc ubuntu firefox flash

$ sudo apt-get remove swfdec-mozilla

$ sudo cp libflashplayer.so /usr/lib/mozilla/plugins/

$ ls /usr/lib/mozilla/plugins/ -l
total 10056
lrwxrwxrwx 1 root root 37 2009-10-09 04:47 flashplugin-alternative.so -> /etc/alternatives/mozilla-flashplugin
-rwxr-xr-x 1 root root 10278616 2009-10-09 17:59 libflashplayer.so

$ ls /etc/alternatives/mozilla-flashplugin
/etc/alternatives/mozilla-flashplugin

YEN to USD

http://www.x-rates.com/d/JPY/USD/graph120.html
http://www.yen-to-dollar.com/

Best place seems to be the Japan Post Office, next are the Japanese banks.

Trio wins chemistry Nobel for solving ribosome riddle

http://www.reuters.com/article/scienceNews/idUSTRE5961NG20091007?feedType=RSS&feedName=scienceNews

The academy said many of today's antibiotics cure various diseases by blocking the function of bacterial ribosomes.

"Fifty percent of all antibiotics target the ribosome, and now we have the tools to begin looking at if there are other substances we can fit into different slots to block and disturb bacteria in our bodies," said Peter Brezinski, a member of the chemistry panel at the Royal Academy of Sciences in Stockholm.

Japanese handwriting IME

http://singularity.agronesia.net/2007/03/31/japanese-kanji-handwriting-recognition-in-windows-xps-ime/

press F5 to activate while typing something in Japanese

Kanjipad for Ubuntu
http://manpages.ubuntu.com/manpages/intrepid/man1/kanjipad.1.html

ラーメン　ramen
醤油　shouyu　 a kind of japanese soy sauce
塩　shouyu　salt
豚骨　tonkotsu　pork
昆布　konbu　kelp / a large seaweed (algae)

New flood-tolerant rice offers relief for world's poorest farmers

New flood-tolerant rice offers relief for world's poorest farmers
August 9, 2006 06:36 PM

http://www.biologynews.net/archives/2006/08/09/new_floodtolerant_rice_offers_relief_for_worlds_poorest_farmers.html

http://rice.genomics.org.cn/rice/index2.jsp
The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis, and biological research of the rice genome. Our Rice Information System (BGI-RIS) is targeted to be the most up-to-date integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops.

http://beta.irri.org/publications/index.php?option=com_content&task=view&id=1&Itemid=24

ubuntu eeepc wifi disabled at boot time

found these while i was looking for a fix ...

http://www.ventanazul.com/webzine/articles/fix-wireless-connection-problem-gutsy-gibbon

hopefully a more standard fix / update comes out soon

Rodrigo_y_Gabriela 11:11 (2009)

http://en.wikipedia.org/wiki/Rodrigo_y_Gabriela
http://en.wikipedia.org/wiki/11:11_(Rodrigo_y_Gabriela_album)

Firefox optimizations

http://www.zolved.com/synapse/view_content/24939/How_to_reduce_the_memory_usage_on_Firefox

Click Privacy. Un-check the "Remember What I've downloaded" check box.
browser.cache.memory.enable=true
browser.cache.memory.capacity=8192
config.trim_on_minimize=true

linux disk utilities

been having problems with my ata 4gb siliconmotion ssd that came with my asus eeepc, just missed the 1yr warranty by 2 months so I'm stuck with it ...

some useful info from my google travels

Linux disk utilities
http://felipecruz.com/linux-disk-utilies.php

TestDisk / PhotoRec -- fine data recovery tool
www.cgsecurity.org/wiki/TestDisk_Download

UltimateBoot CD
www.ultimatebootcd.com/

UNetBootin -- bootable usb images
unetbootin.sourceforge.net/

Damn Small Linux (DSL) ~50mb
http://www.damnsmalllinux.org/wiki/index.php/Install_to_USB_From_within_Linux

Natural Language Processing - NLP

Good summary of current NLP tools that are available

http://torg.media.mit.edu/rob/index.php/NLP_Seminar

MKL and Numpy

http://www.shocksolution.com/2008/09/19/installing-numpy-with-the-intel-math-kernel-library-mkl/

Intel MKL (math kernel library) http://software.intel.com/en-us/intel-mkl/ install with Numpy

1. Unpack the tar file with: tar xfvz numpy-1.0.4.tar.gz
2. cd numpy-1.0.4
3. cp site.cfg.example site.cfg
4. vi site.cfg
5. python setup.py install –home=~

[mkl]
library_dirs = /opt/software/intel/mkl/10.0.1.014/lib/em64t
mkl_libs = mkl, guide
lapack_libs = mkl_lapack
include_dirs = /opt/software/intel/mkl/10.0.1.014/include

http://mail.scipy.org/pipermail/numpy-discussion/2007-November/029881.html
http://www.scipy.org/Installing_SciPy/Linux#head-7ce43956a69ec51c6f2cedd894a4715d5bfff974

Norman Borlaug, 1970 Nobel Peace Prize for developing high-yielding crops

http://www.reuters.com/article/scienceNews/idUSTRE58C0KM20090913?feedType=RSS&feedName=scienceNews

WASHINGTON (Reuters) - Norman Borlaug, the U.S. agricultural scientist who received the 1970 Nobel Peace Prize for developing high-yielding crops to prevent famine in the developing world, has died at age 95, Texas A&M University said.

Borlaug, hailed as a central figure in the "green revolution" that made more food available for the world's hungry, died on Saturday night from cancer complications in Dallas, the university said in a statement.

The "green revolution" -- the development of crops such as wheat that delivered better yields than traditional strains -- is credited with helping avert massive famines that had been predicted in the developing world in the last half of the 20th century.

Dr. Richard Bruskiewich - International Rice Research Institute

http://beta.irri.org/index.php/Home/Welcome/Frontpage.html
International Rice Research Institute - IRRI

http://www.sfu.ca/alumni/our_alumni/outstanding/

Dr. Richard Bruskiewich, BA ’87 - Academic Achievement
Senior Scientist, Bioinformatics, International Rice Research Institute – Manila, Philippines

Dr. Richard Bruskiewich is one of the world leaders in Bioinformatics. After completing his degree at SFU with a minor in Computing, Richard trained in Biological Sciences at UBC and became interested in combining computational analysis with biology. As a PhD student he became renowned for being the first person to transfer the genome database, Acedb, to the PC. This led to post-doctoral research at the Sanger Centre in England, one of the most internationally prestigious centers for computational genetic analysis. During this time he made salient contributions to many important genomic analyses, including the analysis of the human chromosome 22. With several world-class opportunities available to him, he took the road less traveled by choosing to carry out his research in a developing country, joining the International Rice Research Institute in the Philippines. At the IRRI, he is responsible for using bioinformatics to decipher the genetic structure of rice, one of the largest and most important food crops in the world. His work develops both understanding and prediction of those genetic features that are critical to crop yield and environmental and disease resistance under various conditions. Since food – particularly rice – is one of the biggest health determinants in the third-world, Richard’s research impacts the developing world in ways often overlooked by the western world.

How To Format a USB Pen Drive in Linux

http://www.cyberciti.biz/faq/howto-format-usb-pen-drive/

Q. How do I format a USB pen drive under Ubuntu Linux for ext3 file system?
A. You can format USB pen drive with the help of following commands:

[a] fdisk : Partition table manipulator for Linux

[b] mkfs.ext3 : Create an ext2/ext3 filesystem by formatting given partition name (/dev/partition)

[c] e2label : Change the label on an ext2/ext3 filesystem

First make sure USB pen is not mounted. Click on Places > Computer > Select USB pen > Right click > Select Unmount Volume.

Let us assume that /dev/sda1 is your partition name for USB pen. To format type the following command (Open X terminal and type the command)
$ sudo mkfs.ext3 /dev/sda1
Caution: Careful while entering device/partition name; wrong name can wipe out entire hard disk!!!
Now use e2label command to change the filesystem label on the ext3 filesystem located on device /dev/sda1:
$ sudo e2label /dev/sda1 usb-pen
You can also create an MS-DOS/Windows XP file system under Linux, enter:
$ sudo mkfs.vfat /dev/sda1

Now you are ready to use USB pen.

TestDisk: File recovery tool

I thought my pictures were a gonner when my digi cam reported that my memory card is corrupted

fortunately, this handly tool allowed me to recover pictures from my SD, it even recovered pictures that I already removed! wow

testdisk-6.11.3/linux$ sudo ./photorec_static

My micro sd camera card is in /dev/sdb1

http://www.cgsecurity.org/wiki/TestDisk_Download
http://www.cgsecurity.org/wiki/PhotoRec_Step_By_Step

graduate school, research topics

About EBI
http://www.ebi.ac.uk/Information/About_EBI/about_ebi.html


http://www.ebi.ac.uk/Thornton/
* Elucidating and evolution enzyme function through structural analysis
* Deriving principles of protein structure
* Functional annotation of genomes, proteins and structures
* Functional genomics analysis of ageing
* Web tool and resource development

http://www.ebi.ac.uk/Rebholz/
The group focuses on extraction of facts from scientific literature in molecular biology. This is mainly based but not limited to matching of language patterns. In addition we do research on the disambiguation of semantic types, e.g. proteins, genes, species, drugs, and on automatic methods to identify language patterns. Both approaches require machine learning expertise and domain knowledge. The group has strong experience in Natural Language Processing methods (NLP) in the biomedical domain, and has applied its methods to different problems, e.g. identification of protein-protein interactions, extraction of acronyms and identification of mutations. All solutions are implemented as stand-alone modules, which can be combined and used to process text data in a pipeline. Existing modules are made available to the public through EBI's central services ('Whatizit', now as SOAP Web Service).

http://www.ebi.ac.uk/luscombe/
The Luscombe group's research focuses on the genomic analysis of regulatory systems.

We study how the biology of an organism is shaped by regulation of gene expression. We investigate this at various levels of complexity, from single-celled bacteria and yeast to complex mammals. Expression of a gene - i.e. production of a protein - is a complex exercise requiring large, gluttonous protein machines which expend the cell's energy reserves. Hence, the organism needs to be judicious in choosing which proteins to produce when and where. Furthermore, the expression of all genes at all times would be detrimental to the organism. Expression must be rigorously regulated so that the right genes are ‘switched on or off’ in response to changes in the internal and external environments of the cell.

http://www.ebi.ac.uk/chembl/
The ChEMBL group's research focuses on mapping the interactions and functional effects of small molecules binding to their macromolecular targets.

The group studies the interactions of pharmacologically active molecules and their receptors. In particular the group builds and maintains a series of drug discovery databases that are components of ChEMBL.

http://www.ebi.ac.uk/goldman/
Our main interests are in methods for the analysis of DNA and amino acid sequences to study evolution. Past work has been on the theoretical basis of phylogenetic analyses of this data, aiming to understand and improve methods, and on the development of statistical methods that test the accuracy of current mathematical models. More recent work has concentrated on devising new, better, mathematical models and the application of these models and methods to comparative genomic data.

http://www.ebi.ac.uk/panda/
The Protein and Nucleotide Database Group (PANDA) is a large group providing all the sequence resources at the EBI, from DNA through to Protein and encompassing the associated databases, such as genome databases (eg, Ensembl), protein families (eg, InterPro), protein function (eg, UniProtKB), proteomics (eg, IntAct) ontologies (eg, GOA), and pathways (eg, Reactome).

http://www.ebi.ac.uk/compneur-srv/
The interests of the group Computational Neurobiology revolve around signal transduction in neurons, ranging from the molecular structure of membrane proteins involved in neurotransmission to modelling signalling pathways. A strong focus is the molecular and cellular basis of neuroadaptation in neurons of the basal ganglia. We also provide services that facilitate our research, including database production and software development.

http://www.ebi.ac.uk/bertone/
The Bertone Group analyses genetic and biochemical mechanisms underlying cellular differentiation events, particularly in human and mouse embryonic stem (ES) cell lines.

SFU Bioinformatics Program
http://compbio.cs.sfu.ca/bio_graduate.htm

UBC Bioinformatics Program
http://www.bioinformatics.ubc.ca/

Bioinformatics at Boston University
http://bioinformatics.bu.edu/

July 15 deadline
http://www.embl.de/training/eipp/application/index.html

research groups
http://www.embl.de/training/eipp/application/recruiting_gl/index.html

research topics
http://www.embl.de/training/eipp/application/research_topics/index.html

Data integration / structural biology
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

********** Data integration - disease mechanism
http://www.embl.de/research/units/scb/schneider_reinhard/index.html

******* Protein interactions and complexes - disease mechanism
http://www.embl.de/research/units/scb/russell/index.html

*** Gavin
http://www.embl.de/research/units/scb/gavin/awards/index.html

shared applicant questionnaire
https://www-db.embl.de/jss/servlet/de.embl.ml.phdProgramme.PhdApplicationExternalViewer?m=handleRequestExtView

Structural and Computational Biology:

Bork Group - Deciphering function and evolution of biological systems
Briggs Group - How proteins manipulate membranes - cryo-electron microscopy and tomography
Russell Group - Structural bioinformatics
Scheffzek Team - Signal transduction – disease proteins
Schneider (Reinhard) Group - Data integration and knowledge management

http://www.icapture.ubc.ca/who/who_mark_wilkinson.shtml
He then worked as a freelance bioinformatics consultant for one year, after which he joined the iCAPTURE Team, and now continues working in the area of bioinformatics, with a particular focus on data integration and machine-readable knowledge representation.

Visit the Wilkinson Lab Homepage (http://wilkinsonlab.ca) for up-to-date information on our research activities. The Wilkinson Laboratory is
interested in the problem of facilitating the interaction between a biologist and the data and analytical tools they require each day to make new discoveries. Our laboratory focuses on four main themes: Annotation, Interrogation, Integration, and Visualization.
http://www.biomoby.org/

CardioSHARE
http://cardioshare.icapture.ubc.ca/
CardioSHARE will use the knowledge of biologists, encoded in "Ontologies" to help interpret these kinds of questions, and automate the discovery and retrieval of the answers. When completed, CardioSHARE will be sufficiently powerful to answer questions for which the answer IS NOT KNOWN - putting it well beyond the power of keyword-style searches like Google and Entrez. CardioSHARE will accomplish this by having sufficient
understanding of biological/bioinformatics analyses that it can automatically construct and execute the pipeline of analytical tools necessary to answer the question being asked, thus finally bringing the power of in silico research into the hands of biomedical bench scientists.
- semantic web


http://www.stat.ubc.ca/~jenny/research.html
* High-throughput phenotypic experiments, genome-wide reverse genetic studies
* Finding informative sets and clusters of genes. Novel forms of meta-analysis. Using concepts from graph theory and survival analysis in the context of cluster analysis.

eeebuntu home key

eeepc eeebuntu keyboard shortcuts is under system/control centre/keyboard shortcuts

super L = home = window key

very helpful tip, can't see the ok or cancel buttons in dialog boxes because they are below the screen?

> If you hold down the alt key and drag (double tap on touchpad) (anywhere in) the window up you should be able to see those buttons.

http://www.sizlopedia.com/2008/10/09/install-ubuntu-on-eee-pc/

what to pack for japan

http://www.realgap.co.uk/What-to-pack-for-Japan

bags, sturdy backpack
documents
warm clothes and rain coats - weather http://www.japan-guide.com/e/e2273.html, june = rain (tsuyu), 31-5 degrees
shoes
towel
camera
toiletries, toilet paper, toothpaste, floss, sunscreen, deodorant,
first aid kit
guide books, phrase book, form book
pen and paper
gift
padlock
alarm clock
money - atm and visa on post offices (http://www.japan-guide.com/e/e2208.html) (yuubinkyoku 郵便局 http://www.yuubinkyoku.com/index.html) and 7-eleven
ear plug
entertainment - ds


http://www.japan-guide.com/e/e2063.html
July
Kyoto Gion Matsuri (more details)
Kyoto
The festival of Yasaka Shrine, Gion Matsuri is ranked as one of Japan's three best festivals, featuring over 20 meter tall festival floats. The highlight of the festival takes place on July 17.

Format USB drive in linux

http://www.cyberciti.biz/faq/howto-format-usb-pen-drive/

$ sudo mkfs.ext3 /dev/sda1

To see the list of mounted drives, do
$ mount | grep /media
/dev/sdb1 on /media/disk type vfat (rw,nosuid,nodev,uhelper=hal,shortname=mixed,uid=1000,utf8,umask=077,flush)

To unmount do
$ umount /dev/sdb1

http://www.pgts.com.au/cgi-bin/psql?blog=0808&ndx=b002

Finally create a folder called "games" in the root of the Micro SD disk. You can copy .NDS games into here. While I was about it I created some additional folders, called "pictures", "music" and documents. This enabled the kids to use the Micro SD as memory stick when it wasn't being used as part of the R4DS. Here is a summary of the commands to use for Linux. Take Note: This example uses the values of /dev/sdb1 and the mount point of /media/disk -- As stated earlier, This may vary according to the version and hardware -- Substitute the appropriate device name and/or mount points, for your system, in the commands below:

1. umount /media/disk
2. sudo mkfs.vfat -I -F 32 -v /dev/sdb1
3. Mount the device again (just unplug it and plug it again -- if you have automount, or use "mount" if you know the command)
4. Change directory to the location where you downloaded the RAR file, and enter this command:
unrar x English-1.18.rar
5. chdir English
6. cp -rp * /media/disk/
7. mkdir /media/disk/games /media/disk/pictures /media/disk/music
8. You can now copy games to the /media/disk/games folder.
9. umount /media/disk
(or use "Safely Remove" option).

If you are a windoze user, (what are you doing reading this blog?), these commands should work:

1. Use WinZip to upack the RAR, make sure that you preserve the Folders. Copy it to a separate folder (eg. C:\FOO)
2. Insert the USB stick (with the Micro SD in it). Determine which drive it has mounted as. (Check with Windoze Explorer). I'll assume that it is drive E:. Substitute the appropriate drive.
3. format e: /fs:fat32
4. e:
5. xcopy /s c:\foo\English\*
6. mkdir games
7. mkdir pictures
8. mkdir music

dbsk-tohoshinki-doshite-kimi-wo-suki-ni-natte-shimattan-daro

http://sapphirebluelove.wordpress.com/2008/06/14/mp3-updates-dbsk-tohoshinki-doshite-kimi-wo-suki-ni-natte-shimattan-daro-cddvds/

passing away

good friend for 2 yrs has passed away, blame it all on the weather and the heater ...

PictoDS

http://cbds.free.fr/Softwares/PictoDS/?language=en

It didn't run for amd64 so I ripped the swt.jar from Vuse (Azureus) and replaced the one in lib/swt.jar and it worked!
http://www.megaupload.com/?d=PWGU052H

http://ubuntuforums.org/showthread.php?t=154852
Originally Posted by art View Post
apt-get install imagemagick
On the command line type
convert file.pdf file.jpg

Then I did `convert book.pdf book.jpg` and I got all my jpgs w00t. I also needed to create this dir manually ` $ mkdir -p /home/foo/PictoDS_linux_2.1.0/bin/pictodstmp`

Now I can view PDFs in ComicDS


http://www.r4ds-forums.com/viewtopic.php?f=38&t=705
Soft reset on NDS
Where can I find it?

The soft reset is represented by a little R circle (either green or red) at the top right of the bottom screen when you are in the folders.

Green = soft reset function is enabled.
While in a game, press L+R+A+B+X+Y (i.e. the front two shoulder buttons and the four buttons next to the bottom screen of the NDS)

http://www.r4ds.cn/r4ds.html

http://colors.collectingsmiles.com/faq.php#43
Colors! for drawing stuff on a NintendoDS

Homebrew Apps
http://dshb.50webs.com/pages/hb.htm

http://en.wikipedia.org/wiki/List_of_Nintendo_DS_Homebrew

Project JDS -- learning hiragana, katakana
http://dl.qj.net/Homebrew-Applications/pg/12/fid/14919/catid/220

raikachan and other japanese learning tools

Raikachan mozilla jap translation plugin

http://rikaichan.mozdev.org/installation.html

BabelFish Instant Translation 1.84
by NettiCat

https://addons.mozilla.org/en-US/firefox/addon/7004

Learn Japanese with NintendoDS
http://learn-japanese-ds.blogspot.com/2008/06/anpaman-toasobo-i-u-e-o-kyoushitsu.html

Comic DS [convert PDF to JPG] ... slow?
http://cbds.free.fr/Softwares/ComicBookDS/?language=en#download

offline maps
http://sdesmedt.wordpress.com/offline-maps/

japanese nouns

学生寮　がくせいりょう　student dorm
地図　ちず　map

job applicant qualities

We would like to know who you are and how you think. Incorporate the following into your application:

* Your information
o Name, email, and website(optional)
o Brief background: education and relevant work experience
* Your programming interests and strengths
o What are your languages of choice?
o Any prior experience with open source development?
o What do you want to learn this summer?
* Your interest and background in biology or bioinformatics
o Any prior exposure to biology or bioinformatics?
o Any interest in learning a bit of biology this summer?
* Your ideas for a project (an original idea or one expanded from our Ideas Page)
o Provide as much detail as possible
o Strong applicants include an implementation plan and timeline (hint!)
o Refer to and link to other projects or products that illustrate your ideas
o Identify possible hurdles and questions that will require more research/planning
* What can you bring to the team?
o Are you enthusiastic?

eeepc screen brightness

to remember the screen brightness level on every startup

BRIGHTNESS

When the computer gets idle, the screen becomes darker. Unfortunately, when it wakes up, the brightness is restored to 100 %. To suppress this behavior, I went to System > Preferences > Power management and unchecked boxes called "Dim display when Idle", "Reduce backlight brightness" and moved the cursor on the bar called "set display brightness to". This is probably redundant, but this solved my problem.

Do this for both AC and Battery Power. Adjust the brightness level and then check the boxes again if you like.

http://forum.eeebuntu.org/viewtopic.php?f=28&t=2331

japanese phrase book

http://wikitravel.org/en/Japanese_phrasebook

Please speak slowly.
ゆっくり話してください。 Yukkuri hanashite kudasai. (YOO-kuree hanash-teh koo-dah-sah-ee)
Please say it again.
もう一度言ってください。 Mō ichido itte kudasai. (mo EE-chee-doh ee-te koo-dah-sah-ee)
Please help!
助けて！ Tasukete! (tahs-keh-teh!)

いいです。 結構です。
Ii desu. Kekkō desu.
"It's good/excellent." Used when you don't want more beer, don't want your bentō lunch microwaved, and generally are happy to keep things as they are. Accompany with teeth-sucking and handwaving to be sure to get your point across - both of these expressions may be interpreted as positive responses if you don't include enough nonverbal indications to the contrary.

I need a doctor.
医者に見てもらいたいです。 Isha ni mite moraitai desu.

I don't feel well.
気分がわるいです。 Kibun ga warui desu.

I need your help.
たすけてください。 Tasukete kudasai.

... hurts.
… が痛い。... ga itai.

What?
何？ Nani? (nah-nee)
Where?
どこ？ Doko? (doh-koh)
Who?
誰？ Dare? (dah-reh)
When?
いつ？ Itsu? (it-soo)
Which?
どれ？ Dore? (doh-reh)
Why?
どうして Dōshite (doh-sh'teh)
How?
どうやって？ Dōyatte (dohh-yah-teh)
How much?
いくら？ Ikura? (ee-koo-rah)
What type of?
どんな？ Donna? (dohn-nah)

Earthquake
地震 (jishin)

now
今 (ima)
later
後で (atode)
before
前に (mae ni)

six o'clock AM
朝6時 (asa rokuji)

today
今日(kyō)
yesterday
昨日(kinō)
tomorrow
明日(ashita)

Sunday
日曜日 (nichiyōbi)
Monday
月曜日 (getsuyōbi)

January
１月 (ichigatsu)
February
２月 (nigatsu)

a word on good posture

http://www.wikihow.com/Improve-Your-Posture

# A great side benefit of keeping your head straight, and your ears/shoulders/hips aligned is an improvement in your self-esteem and attitude. If you walk with your head up, you appear more confident, and feel more confident, which improves your attitude and mood, making it easier to walk with your head up.
# Try these steps to get in alignment: push your shoulders forward, then bring them straight up, then bring them straight back, then bring them straight down. Feel good? If your shoulders feel slightly stiff or tense you may have unnecessary muscle tension.
# If you need help remembering to keep your posture, think of a unique object or color. Every time you think of that object, check your posture.
# Try focusing on your calves. Let your posture and balance rely more on your calves. Try to feel an at ease attitude, and put a bounce in your step. You'll find that it will free up the rest of your upper body to relax and assume a more upright posture that takes pressure from your back, shoulders and neck, and works on your ab muscles. This is awesome, since strong calves and abs rock!

eeepc webcam

wxCam website: http://wxcam.sourceforge.net/
wxCam .deb direct link: http://downloads.sourceforge.net/wxcam/wxcam_1.0_i386.deb?modtime=1201617043&big_mirror=0

$ sudo gdebi wxcam_1.0_i386.deb

eeepc battery life

https://answers.launchpad.net/netbook-remix/+question/69228

$ sudo apt-get install eee-control eee-applet

eeepc sound recording

1. System->Preferences->Sound
Set all auto detect, except
SoundCapture=HDA Intel ALC622 Analog (ALSA)
Device=HDA Intel (Alsa Mixer)



2. Click the Volume Control icon in the task bar
Device=HDA Intel (Alsa Mixer)
Preferences->Check everything
Playback->Disable all e-Mic* (external microphone) and i-Mic* (internal microphone)
Recording->Capture set to 100% and Enable Microphone icon and Speaker icons
Options->i-Mic



3. Use Sound Recorder for testing
Applications->Sound and Video->Sound Recorder

4. For Skype 2.0.0.72
Options->Sound devices
Sound In=HDA Intel (hw:Intel,0)
Sound Out=pulse
Ringing=pulse
(optional) Uncheck Allow Skype to adjust volume




http://forum.eeebuntu.org/viewtopic.php?f=41&t=3655

$ cat /proc/version
Linux version 2.6.29-1-netbook (root@adamm-laptop) (gcc version 4.3.2 (Ubuntu 4.3.2-1ubuntu12) ) #0array1 SMP Mon Feb 23 15:02:03 MST 2009

$ alsamixer

$ lspci | grep Audio
00:1b.0 Audio device: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) High Definition Audio Controller (rev 04)

eeepc webcam

http://forum.eeebuntu.org/viewtopic.php?f=3&t=71&start=15

1)
Enable Webcam in BIOS.

When the EeePC is starting up, before POST you will see the Asus logo and a line telling you to press F2 to enter the BIOS.

Press F2, enter the BIOS settings screen and make sure that the webcam (and everything else you need) is enabled. Then press F10 to save your settings and continue through the boot sequence. You only need do this once, the EeePC will then remember your settings.

2)
Make sure you have the resolution of your webcam set correctly.

You can test this using Cheese, the webcam software that is available via the Add/Remove Software menu option. Use Add/Remove to install Cheese, run Cheese and in the preferences reduce the webcam resolution from 640x480 to 320x240 (or lower). You should get an image in Cheese to confirm your webcam is working. (This may only be a problem for the 701 but it's worth trying anyway.)

eeebuntu medibuntu

http://forum.eeebuntu.org/viewtopic.php?f=28&p=6542

$ sudo wget http://www.medibuntu.org/sources.list.d/intrepid.list --output-document=/etc/apt/sources.list.d/medibuntu.list

$ sudo apt-get update && sudo apt-get install medibuntu-keyring && sudo apt-get update

$ sudo apt-get install skype-static-oss

(the skype install by itself has problems with audio)

ubuntu japanese software

kanjipad - hand writing recognition
gjiten - dictionary http://gjiten.sourceforge.net/
https://help.ubuntu.com/community/Japanese_Input_and_Fonts_in_Ubuntu_7.04
im-ja - japanese input http://im-ja.sourceforge.net/

sudo apt-get install kanjipad gjiten

NintendoDS: Kanji Sono Mama Rakubiki Jiten

http://www.youtube.com/watch?v=F2McMUatkYM

NintendoDS: Kanji Sono Mama Rakubiki Jiten

Translator

http://www.megaupload.com/?d=ITK4107G
http://freakshare.net/files/751912/0405_-_Kanji_Sonomama_Rakubiki_Jiten_J.rar

http://www.romulation.net/NDS/0096_-_DS_Rakubiki_Jiten_(J)(WRG)(0A918F04).rar.html

http://en.wikipedia.org/wiki/DS_Rakubiki_Jiten#DS_Rakubiki_Jiten

http://sizer99.com/rakubiki/

http://www.physics.ucla.edu/~grosenth/manual.html

screen isn't composited

https://bugs.launchpad.net/ubuntu/+source/avant-window-navigator/+bug/359061

warning: Screen isn't composited. Please run compiz (fusion) or another compositing manager

fix:To enable the compositing manager, you need to use the "Configuration Editor", AKA gconf-editor, to set the key /apps/metacity/general/compositing_manager to true (i.e., the box must be checked). "

$ sudo apt-get install simple-ccsm compiz-fusion-plugins-extra compiz-fusion-plugins-main compiz-plugins emerald

Compiz hotkeys
Super E
Super A
Super D

Opacify

eeebuntu on eee-pc broke SD card?

Got these errors after installing eeebuntu on my eeepc-701. After half-a day of research and trying out some digicam SDs, I finally found the fix! And all you need to do is go to the BIOS and set OS Installation to Finished. Voila!

$ dmesg

279.985638] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 279.985706] end_request: I/O error, dev sdb, sector 0
[ 279.995145] sd 2:0:0:0: [sdb] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK
[ 279.995219] sd 2:0:0:0: [sdb] Sense Key : Hardware Error [current]
[ 279.995277] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 279.995350] end_request: I/O error, dev sdb, sector 0
[ 279.995493] unable to read partition table
[ 280.148599] sd 2:0:0:0: [sdb] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK
[ 280.148696] sd 2:0:0:0: [sdb] Sense Key : Hardware Error [current]
[ 280.148759] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 280.148834] end_request: I/O error, dev sdb, sector 0
[ 280.157893] sd 2:0:0:0: [sdb] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK
[ 280.157967] sd 2:0:0:0: [sdb] Sense Key : Hardware Error [current]
[ 280.158029] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 280.158093] end_request: I/O error, dev sdb, sector 8
[ 280.166022] sd 2:0:0:0: [sdb] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK
[ 280.166036] sd 2:0:0:0: [sdb] Sense Key : Hardware Error [current]
[ 280.166047] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 280.166058] end_request: I/O error, dev sdb, sector 16
[ 280.173770] sd 2:0:0:0: [sdb] Result: hostbyte=DID_OK driverbyte=DRIVER_SENSE,SUGGEST_OK
[ 280.173786] sd 2:0:0:0: [sdb] Sense Key : Hardware Error [current]
[ 280.173797] sd 2:0:0:0: [sdb] Add. Sense: Unrecovered read error
[ 280.173808] end_request: I/O error, dev sdb, sector 0

Ubuntu-eee, sdhc 16GB, eeepc 4G

easypeasy aka Eee-Ubuntu aka eeebuntu

easypeasy
http://www.geteasypeasy.com/index.php?menu=download
http://sourceforge.net/project/downloading.php?group_id=213463&filename=easypeasy-1.1.iso

eeebuntu
http://www.eeebuntu.org/index.php?page=download

ISO Image to bootable USB disk
http://unetbootin.sourceforge.net/#other

Steps
# Download and choose Save File. Help?
# When it's done, download the helper application (unetbootin) for Windows or Ubuntu / Linux. Help?
# Insert a usb stick (2 GB or more) and run the helper application. Help?
# Insert the usb stick into the netbook and boot from the stick. Help?
# Run Install found under Administration. Help?
# You're running Easy Peasy! Help?

Biwako

http://www.kandou10.jp/en/emotion/e07_5.html

Biwako Lake Festival, 40km circumference!

heartbreak

http://www.mysoju.com/heartbreak-library/

Nice movie, Eugene and dude from My Girl ... Librarian meets sushi dude.

... pg 198 ...

Goethe's Faust

German poet, novelist, playwright, courtier, and natural philosopher, one of the greatest figures in Western literature. In literature Goethe gained early fame with The Sorrows of Young Werther (1774), but his most famous work is the poetic drama in two parts, FAUST. Like the famous character of this poem, Goethe was interested in alchemy. He also made important discoveries in connection with plant and animal life, and evolved a non-Newtonian and unorthodox theory of the character of light and color, which has influenced such abstract painters as Kandinsky and Mondrian.

Noble be man,
Helpful and good!
For that alone
Sets him apart
From every other creature
On earth.
(from The Divine, 1783)

... heard Goethe from Siga's site http://www.trappedinspace.com/numerology

Stuff Stuff

Stuff

- hiked the Chief http://www.stawamuschiefpark.ca/
- X-Men Origins: Wolverine http://www.youtube.com/watch?v=k6cRSvyC3Ws
- Swine Flu outbreak in Mexico http://health.asiaone.com/Health/News/Story/A1Story20090427-137660.html
- A rescuer's / scientist dream ... http://www.news1130.com/more.jsp?content=20090424_103647_5396
- Canucks defeats St. Louis Columbus BlueJackets http://www.vancouversun.com/health/Gallery+Canucks+Blue+Jackets/1342909/story.html

Can't and Can Quotes

You can't decide the length of life, but you can control how you want to live it.
You can't control the weather, but you can control your mood.
You can't change your look, but you can smile.
You can't control others, but you can control yourself.
You can't foresee tomorrow, but you can utilize today wisely.
You can't win everything, but you can try your very best to achieve that.

Hannes ...

http://www.cbc.ca/canada/british-columbia/story/2009/04/24/bc-north-shore-rescue-glacier-death.html?ref=rss

http://communities.canada.com/theprovince/blogs/newsroom/archive/2009/04/24/north-shore-search-and-rescue-member-dies-in-fall.aspx

http://www.chem.ubc.ca/personnel/faculty/withers/group/group/muelleger/muellegger_main.htm

http://zymeworks.com/about/management/

Improvisation

http://en.wikipedia.org/wiki/Improvisation

Improvisation is the practice of acting, singing, talking and reacting, of making and creating, in the moment and in response to the stimulus of one's immediate environment and inner feelings. This can result in the invention of new thought patterns, new practices, new structures or symbols, and/or new ways to act. This invention cycle occurs most effectively when the practitioner has a thorough intuitive and technical understanding of the necessary skills and concerns within the improvised domain. Improvisation can be thought of as an "on the spot" or "off the cuff" spontaneous activity.

Life's not written with a pencil

Life's not written with a pencil

Nice quote from the movie, 'Call for Love'

http://en.wikipedia.org/wiki/Call_for_Love

katakana

http://thejapanesepage.com/node/gif/katakana.gif

http://thejapanesepage.com/beginners/katakana/page01

~ tara （～たら）expresses condition.

Ken kara dattara inaitte itte.
ケンからだったらいないって言って。

I'm not here if it's from Ken.

少し (すこし) sukoshi ... a bit

かれは少しおそいですね。[kare ha sukoshi osoi desu ne.] [ex #869]
He's a bit late isn't he?

Korean Movie - Romantic Island

This was a pretty good movie with a happy ending ;p

http://www.hancinema.net/korean_movie_Romantic_Island.php

http://www.mysoju.com/romantic-island/

There's actually 3 couples but they only show the two youngest ones -o-

Methanogens -- oxygen producing bacteria

http://en.wikipedia.org/wiki/Methanogen

Methanogens are archaea that produce methane as a metabolic byproduct in anoxic conditions. They are common in wetlands, where they are responsible for marsh gas, and in the guts of animals such as ruminants and humans, where they are responsible for the methane content of flatulence.[1] In marine sediments biomethanation is generally confined to where sulfates are depleted, below the top layers.[2] Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of the Earth's crust, kilometers below the surface.

Methanogens play the vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. Methanogens typically thrive in environments in which all other electron acceptors (such as oxygen, nitrate, sulfate, and trivalent iron) have been depleted. In the deep rock they obtain their hydrogen from the thermal and radioactive breakdown of water.

Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate.[10] Most methanogens are autotrophic producers, but those which oxidize CH3COO- are classed as chemoheterotrophs instead.


http://www.canada.com/Technology/Thank+oxygen+producing+bacteria+your+existence/1478323/story.html

oxygen-producing microbes, which transformed the oceans and the atmosphere and fuelled evolution of creatures that eventually crawled out of the sea, a Canadian-led team reports Thursday in the journal Nature.

"If the oxygen-producing bacteria had never taken over, we wouldn't be here right now," says lead author Kurt Konhauser, a geomicrobiologist at the University of Alberta.

The nickel-poor waters would, however, have been very hospitable to oxygen-producing microbes. And they soon took over as the dominant microbes, pumping oxygen into the oceans and air.

Marine scientist Mak Saito, of the Woods Hole Oceanographic Institution, describes the findings as both "exciting" and "sobering." It suggests "a single geological change can starve a major oceanic microbial community and thereby change the trajectory of life on Earth," Saito notes in a Nature commentary.

As the methanogen microbes died off, there would have been a big drop in atmospheric levels of methane gas, a potent greenhouse gas. This could have cooled the atmosphere, triggering the glaciation.

http://www.space.com/searchforlife/mars_conditions_020819.html
Kral led the experiment and presented it to colleagues during a bioastronomy conference in Australia last month.

"Our goal is first to get the organisms to grow well, then systematically experiment with conditions found on Mars," Kral said last week.

Mars' atmosphere contains large amounts of carbon dioxide with almost no oxygen. Assuming that hydrogen and some water are present under the surface, the basic requirements for methanogen growth are met on Mars. And even if hydrogen is not present, carbon monoxide is, and some methanogens can use this instead of hydrogen.

Since methane is a "greenhouse gas" that traps heat near a planets surface, methanogens could theoretically be used to raise Mars surface temperature, eventually "terraforming" the planet so that it could support life and provide a potential refuge for humanity.

http://zipcodezoo.com/Key/Archaea/Archaea_Kingdom.asp
Achaea kingdom, consists of crenarchaeota, nanoarchaeota, euryarchaeota
- single-celled microorganisms
- prokaryotes - have no cell nucleus or any other organelles within their cells
- Classifying the Archaea is still difficult, since the vast majority of these organisms have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment.
- Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes: notably the enzymes involved in transcription and translation. Other aspects of archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. The archaea exploit a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to using ammonia, metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; in contrast to bacteria and eukaryotes, no species of archaea are known that form spores.
- archaea in plankton may be one of the most abundant groups of organisms on the planet
- One example are the methanogenic archaea that inhabit the gut of humans and ruminants, where they are present in vast numbers and aid in the digestion of food. Archaea have some importance in technology, with methanogens used to produce biogas and as part of sewage treatment, and enzymes from extremophile archaea that can resist high temperatures and organic solvents are exploited in biotechnology.

Metagenomics

dels.nas.edu/dels/rpt_briefs/metagenomics_final.pdf
dels.nas.edu/metagenomics/

"Metagenomics provides a new lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual microbial species. This new approach will bring to light the many abilities of the microbial communities that drive Earth’s energy and nutrient cycles and support the health of its inhabitants. Metagenomics will vastly enhance our knowl-edge of microbial communities and can lead to major advancements in many areas, includ-ing human health, agriculture, energy production, and environmental remediation."

unculturable - nothing grows on the plate, why? one reason could be that it lacks nutrients, what better way to find this? observe the organism in its natural environment -- see 1911 paper of Twort and G. Ingram [Proc. Roy. Soc.LXXXIV, pp. 517-542], Mycobacterium pseudotuberculosis which needed a form of Vit K obtained from dead cells of Mycobacterium phlei

lots of potential in this field, ranging from harvesting energy (Dr. Stephen Larter: Canada Research Chair in Petroleum Geology; microbes to convert athabasca oil sands back to good methane http://en.wikipedia.org/wiki/Athabasca_Oil_Sands), global climate change (eg oxygen minimal water zone, Dr. Steven Hallam UBC MBB), microbes in mouth and gut -> antibiotics Dr. Fergus Shanahan: Director, Alimentary Pharmabiotic Centre and the BioSciences Institute
--topics covered from Genomics Forum 2009
http://www.genomebc.ca/whatnew_press/upcoming_events/2009/genomics_forum_apr09.htm

Introduction to biology

http://themedicalbiochemistrypage.org/
http://research.cs.queensu.ca/~shatkay/490papers/HunterIntroMolecularBiology.pdf
http://www.ebi.ac.uk/microarray/biology_intro.html

Poster tips

http://www2.lut.fi/~jkamarai/misc/poster/latexhelp.html
http://www.swarthmore.edu/NatSci/cpurrin1//posteradvice.htm

I would say that in general, the posters that did the best were very clear and required little explanation. They had good leading headers above all figures, basically outlining in a few words what the figures showed. They had summaries or conclusions that were very clear, and it was clear from the verbal exchange what the presenter had contributed to the research and that the presenter was an expert in their field.

the Pimp My Poster group icon
Pimp My Poster
http://www.flickr.com/groups/688685@N24/

Dr. Miller and Dr. Borchers

My two judges at the poster competition

http://www.pac.dfo-mpo.gc.ca/sci/mgl/staff_profiles/miller_e.htm#Area
Dr. Kristi Miller (Saunders)
Primary work on Marine Ecological Genomics and Adaptation Group (MEGA)

http://www.genomebc.ca/research_tech/researcher_profiles/c_borchers.htm
Dr. Christoph Borchers
Genome BC Platform Leader

Too bad I didn't win, but it was a good experience!

Biomarkers

http://en.wikipedia.org/wiki/Biomarker

A biomarker is a substance used as an indicator of a biologic state. It is a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.

It can also be a substance whose detection indicates a particular disease state, for example, the presence of an antibody may indicate an infection (see biomarker (medicine)). More specifically, a biomarker indicates a change in expression or state of a protein that correlates with the risk or progression of a disease, or with the susceptibility of the disease to a given treatment. Once a proposed biomarker has been validated, it can be used to diagnose disease risk, presence of disease in an individual, or to tailor treatments for the disease in an individual (choices of drug treatment or administration regimes). In evaluating potential drug therapies, a biomarker may be used as a surrogate for a natural endpoint such as survival or irreversible morbidity. If a treatment alters the biomarker, which has a direct connection to improved health, the biomarker serves as a surrogate endpoint for evaluating clinical benefit.

An NIH study group committed to the following definition in 1998: "a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention." [1]

In the past, biomarkers were primarily physiological indicators such as blood pressure or heart rate. More recently, biomarker is becoming a synonym for molecular biomarker, such as elevated prostate specific antigen as a molecular biomarker for prostate cancer, or using enzyme assays as liver function tests. Biomarkers also cover the use of molecular indicators of environmental exposure in epidemiologic studies such as human papilloma virus or certain markers of tobacco exposure such as 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK).

Immunology

- b-cells (bone marrow) has antibodies that bind antigens, then it makes clones of these b-cell types and the clones secrete antibodies into the blood stream, eg IgG, IgM (pentamer) (Y structure)
- t-cells 'killer' (thymus) has t-cell receptors which also has immnuglobulin (antibody) folds that recognizes antigens that are bound to mhc complex of infected cells (U structure only)

IgG (humoral, B-cell antibodies):
- immunoglobulin fold has 4 chains, 2 light and 2 heavy chains, 2 anti-parallel beta sheets packed against each other forming a barrel
- fc = crystalizable fragment, fab - antigen binding fragment
- fc and fab connected together by hinge region / flexible linker
- constant domain (ch1, cl) - 4+3 beta strand connected by short loops, linked by disulfide bonds, sheets are 90 degrees, hydrophobic interactions, 4 strands (longest sheet) in the middle, 3 strands in the outside
- variable domain (vh and vl) - 4+3+2 beta strand, long loops for antigen binding, cdr1-3 (complementarityy determining region) or hypervariable region on the same side, c' and c'' forms cdr2, cdr1 connects sheet 1 and 2 (crossover turn), cdr3 has the most variability, 5 strands in the middle (longest sheet) and 4 strands on the outside, c" not involved in packing (outside the barrel)
- epitope (Antigenic determinants) - part of antigen recognized by antibody (vs paratope - part of antibody recognize epitope)

T-Cell Receptors:

Protein crystallography

crystallography
- shine x-ray (1.5A = 1x10^-10 wavelength) on crystals (protein + h2o)
- treat reflections as summation waves (constructive interference = intensity)
- Bragg's Law: n(x-ray wavelength) = 2dsin(theta), d=lattice plane separation distance=resolution, theta is the incidence=reflection angle bouncing off the lattice plane, n=integral number of wavelengths in path length (extra distance travelled by beam on the 2nd lattice plane)
- structure factors (F) - wave equations that describe the reflections
- recombine structure factors to get an image of the molecular structure in the unit cell
- fourier transform - transforms reflections (diffraction patterns in reciprocal space) to electron density function in real space (and vice-versa)
- need to measure intensity and position (+ angle of reflection) of dots (miller indices hkl - name of reflections) in diffraction patterns, not errors (sigma)
- large unit crystals (proteins) produce reflections closer together (inverse relationship of theta and d in Bragg's Law)
- For a unit cell edge of 40 Å, and data collected to 2 Å resolution (d spacing)
40/2 = 20 planes = 20 spots along that direction
- For a unit cell edge of 80 Å, you now have 40 spots in the"same space"
so the reflections are twice as close together
- "as cell gets bigger, diffraction info is more + more compressed"
- phase problem - phase information is lost in the experiment, work arounds:
- MAD (multiple anomalous dispersion) - use SeMet, estimate Se atom phase from difference in Friedel mates, need to collect lots of data to find extent of error
- MIR (multiple isomorphous replacement) - soak crystals in heavy atoms (HA) while keeping the protein (P) isomorphic (same form), then we take the difference in structure factors, F(HA+P) - F(HA) = F(P), distance shown in Patterson map
- MR (molecular replacement) - homology, need at least 35% sequence identity, performs rotational and translational operations to match model with unknown
Methods for phase improvement:
- solvent flattening - ignore solvent envelope from e- density and mask it out
- histogram matching
- non-crystallographic symmetry (NCS) averaging

scavenger hunt

Did some scavenger hunt on campus wih the club, about 12 ppl, 6 groups, 2 ppl each with an escort.

came down on 2nd place, just barely missed one riddle, if we only moved forward a bit more .... so close!

〜ね isn't it?

”ね”(ne) goes at the END of a sentence

これはいいですね。[kore ha ii desu ne.] [ex #698]
Isn't this nice !
ええと、映画館は駅の近くにありますね。[eeto, eigakan ha eki no chikaku ni arimasune.] [ex #699]
Er, the cinema is near the station, right?

風 (ふう) (みたい) ??? style

This also means wind ...

# 日本風のマンションでいいです。 [ex #710]
A Japanese style apartment is fine.
# たまにタイ風焼きうどんを食べます。 [ex #4787]
I sometimes eat Thai-style stir-fried noodles.
# 露天風呂のある純和風旅館に泊まった。 [ex #4788]
We stayed at a purely Japanese-style hotel with an open-air bath.
# どんな風に卵を作れますか？ [ex #5523]
In what kind of style can you cook eggs?

右 migi right
左 hidari left

昨日 kinou yesterday
明日 ashita tomorrow
本日 honjitsu today
来週 raishuu next week

食べる taberu eat
飲む nomu drink
書く kaku write

悪い warui bad
良い yoi good
新しい atarashi new
安 an relax

空の下 sora no shita Under the sky
空の上 sora no ue Above the sky

員 イン in employee
駅 エキ eki station
馬 うま uma horse
引 hiki pull
危 キ ki dangerous
過 カ ka excess, past
簡 カン kan simple

不 ふ fu negative
可 カ ka can

Pattern: subject (彼女 kanojo) wa, with (Tommy トミー) to, time ni, transportation (車 kuruma ) de, destination (駅 eki) ni, verb (itakimasu)
彼女はトミーとの駅まで車で行った ???
kanojo ha tomi^ to no eki made kuruma de itta
she went to the station with Tommy by car

eee pc optimizations

1. Circular Scrolling

all you need to do is edit your /etc/X11/xorg.conf file

under "Input Device" of your touchpad edit to look like the following:

Section "InputDevice"
Identifier "Synaptics Touchpad"
Driver "synaptics"
Option "SendCoreEvents" "true"
Option "Device" "/dev/psaux"
Option "Protocol" "auto-dev"
Option "CircularScrolling" "1"
Option "Emulate3Buttons" "true"
Option "SHMConfig" "true"
EndSection

in firefox
mousewheel.horizscroll.withnokey.action - Set this to '1'
mousewheel.horizscroll.withnokey.numlines - Set this to '1'

http://wiki.eeeuser.com/howto:touchpad_in_advanced
run 'gsynaptics'

2. Firefox addons:
Download plug-ins for Firefox designed for compact computers and easier navigation. Some names to look for include: "Grab and Drag" and the theme "Tiny Menu."
https://addons.mozilla.org/en-US/firefox/addon/1250
https://addons.mozilla.org/en-US/firefox/addon/1455

3. Use RAMDISK in FireFox (check internet connection)
It turns out that there is a hidden setting in firefox called browser.cache.disk.parent_directory and all you need to do is set it's value to /dev/shm and restart firefox and then you are on your way to speedier surfing. so how do you set this, well it is simple

1) open firefox and type about:config in the address bar
2) accept the terms and click the "i'll be carefull" button
3) right click on any of the values on the screen to bring up the context menu and click new->string
4) the first prompt wants the name of the string enter "browser.cache.disk.parent_directory" without the quotes
5) the next prompt is the value set it to "/dev/shm/" without the quotes
6) restart firefox
7) type about:cache in the browser bar and it should tell you it is using /dev/shm under "Disk Cache Device" if you don't see a "Disk Cache Device" section you did something wrong.


4. Disable LAN and Webcam in the BIOS (Hit F2 upon starting the system) if these are not in use.

5. http://wiki.eeeuser.com/howto:maximize_screen_space

6. *some* of the boot process splash screens can be tweaked straight 'out of the box' via Control Center > Display > Theme > Splash Screen.

7. eee pc restore
http://sourceforge.net/project/showfiles.php?group_id=215613
http://www.glenscott.net/2008/11/12/restore-an-eee-pc-701-back-to-factory-xandros-from-a-usb-stick-with-no-asus-support-dvd/

8. flashplayer 10
http://forum.eeeuser.com/viewtopic.php?id=48308
http://download.macromedia.com/pub/labs/flashplayer10/flashplayer10_install_linux_081108.tar.gz

***********************************************
http://gadgetmix.com/index/?p=4102
http://forum.eeebuntu.org/viewtopic.php?t=294&reeedirected=yes

A lot of us have switched to EEEbuntu on our EEE PCs. If you are like me, who likes to keep his netbook clutter free, you will want to set up RAMdisk. And if you thought that setting up RAMdisk in Windows XP was easy (see this article), then in EEEbuntu, it is even easier.

* RAMdisk is located at “/dev/shm”
* Open firefox and type in about:config in the address bar
* Click on “I’ll be careful”
* make a new string browser.cache.disk.parent_directory
* give it a value /dev/shm
* restart firefox

Usual warning about RAMdisk: you will loose all the data upon restart. That is why, it is only recommended for web browsers


http://www.answerbag.com/articles/How-to-Optimize-an-ASUS-EEE-PC/aee034bf-bbb7-73f7-bb6b-826e0204caa0

http://www.callum-macdonald.com/2007/08/24/circular-scrolling/
For the techies, here’s the relevant section of my xorg.conf (see man synaptics for more info):

Section "ServerLayout"
Identifier "Default Server Layout"
Screen "Default Screen"
InputDevice "Generic Keyboard" "Core Keyboard"
InputDevice "Synaptics Touchpad" "Core Pointer"
EndSection

Section "InputDevice"
Identifier "Synaptics Touchpad"
Driver "synaptics"
Option "SendCoreEvents" "true"
Option "Device" "/dev/input/mice"
Option "Protocol" "auto-dev"
Option "CircularScrolling" "1"
Option "Emulate3Buttons" "true"
Option "SHMConfig" "true"
EndSection

Section "Extensions"
Option "Composite" "Enable"
EndSection

たい - I want

# 日本に行きたいです。 [ex #6442] (nippon ni iki taidesu)
(I) want to go to Japan.

# 君のところへ行きたいよ。 [ex #6458] (kun notokorohe iki taiyo)
(I) want to go to where you are.

# 日本で英語をおしえたいです。 [ex #6671] (nippon de eigo wooshietaidesu)
I want to teach English in Japan.

金 kin gold
魚 [さかな] (n) fish [K] [D]

Confusing Katakana

shi シ　tsu ツ　so　ソ

Protein translocation and translation

Protein translocation and translation, signal peptidase complex (spc), ribosome,
http://www.rockefeller.edu/pubinfo/proteintarget.html

Mechanistic Basis of Enzyme-Targeted Drugs

Most often, subtle changes occur in the side
chain and main chain positions of the enzyme in order to
bind the substrates transition state optimally.
(Pauling).


http://pubs.acs.org/doi/full/10.1021/bi050247e

James G. Robertson*
Softzymics, Inc., Princeton, New Jersey 08540
Biochemistry, 2005, 44 (15), pp 5561–5571
DOI: 10.1021/bi050247e
Publication Date (Web): March 22, 2005

Some interesting paragraphs from the paper ...

Thus, it should be stated again. Enzymes are catalysts,
and the catalytic event is at least as important if not more
important than the binding event. Enzyme catalysis progresses
through binding events, conformational changes, one or more
transition states, or reaction intermediates, and product
release, and all of these steps occur with defined rate
constants. The rate constants define a thermodynamic profile
that can be used for drug design, and this differentiates
enzymes from all other target classes.

the larger the increase in replication time, the more toxic the drug

In
addition, purely kinetic information can be used to predict
potential drug toxicity. As an example, a detailed pre-steady-
state kinetic analysis of human mitochondrial DNA poly-
merase has been used to predict the potential toxicity of
marketed antiviral drugs.

One
of the major lessons to be learned from marketed drugs is
that nature has designed enzymes to perform a selective
chemical reaction, and therefore, it is likely that the most
potent drugs to be discovered or designed will be related to
the substrate structure, reactivity, or electrostatic potential
surface of intermediate(s) or transition state(s).