rubbish talk_15.

□ POLAR BEAR BLOG: 『知恵の影を使うということ』を読んで

>> http://akihitok.typepad.jp/blog/2011/05/知恵の影を使うということ.html


とても美しい文章。「知識を使役する」 テクノロジーと、それに対する批判の普遍性。かつてプラトンは現代と全く同じ論調で「文字」の普及を批判していたという内容。

古代の「文字への批判」と現代の知識提供技術への批判を全く同列で語ることは出来ないけれど、両者に共通する構造的普遍性は「持つ者」と「持たざる者」との権力ゲームの軋轢にあるのかもしれない。また、知識体系の基幹を担保するのは、開発過程でインプラントされる学術水準の保証そのものにある。


「知恵のブラックボックス化」は、あらゆるレベルで発生する。だけどそれがテクノロジーの水準を押し下げるかといえば全く逆で、寧ろ知恵のアーカイブを担保する技術こそが、疎隔・細分化する知識体系のバンドギャップを補う要になるのだ。

Controllability of complex networks.

(Control robustness)

□ Controllability of complex networks: 複雑性を手なずける: ネットワーク制御のための数学
? 細胞生物学から携帯電話まで

>> http://www.nature.com/nature/journal/v473/n7346/pdf/nature10011.pdf
>> http://nature.asia/lWkWmT

The ultimate proof of our understanding of natural or technological systems is reflected in our ability to control them. Although control theory offers mathematical tools for steering engineered and natural systems towards a desired state, a framework to control complex self-organized systems is lacking.

Here we develop analytical tools to study the controllability of an arbitrary complex directed network, identifying the set of driver nodes with time-dependent control that can guide the system’s entire dynamics.

制御理論は人工系や自然系を目的とする状態へ向かわせるのに使えるが、複雑な自己組織化した系を制御するための枠組みはまだない。このようなネットワークは制御可能なのだろうか。

生物の調節や神経、代謝にかかわる経路から食物網、携帯電話の動き、社会的相互作用などについて、モデル系と実際の系の両方を使い、任意の複雑な有向ネットワークの制御性を調べる解析手段を開発し、時間に依存した制御を行うと系全体の動態を制御できる最小のドライバーノード群を見いだした。意外なことに、これらは通常ネットワークハブには位置していない。

□ 2011 Sage Bionetworks Commons Congress videos now on iTunes

>> http://bit.ly/jJJsg5 (iTunes)

Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the full agenda is available at www.sagecongress.org.

There are also several excellent podcasts from the January 2011 Symposium on Human Data Interoperability. Upcoming posts will feature presentations and interviews on network biology, genomics, healthcare and open science.

□ アメリカ遺伝学会が、ゲノム研究の出版・評価・データセットを多角的に扱うオープンアクセス・ジャーナル『G3』を発表。

G3 by the Genetics Society of America: Genes|Genomes|Genetics, a new peer-reviewed/peer-edited/fully open access journal g3journal.org/

・Emphasis on data quality and utility, rather than on detailed mechanistic insight or subjective assessment of immediate impact;
・Rapid publication of high-quality, large-scale datasets;
・Emphasis on creating and maintaining links between the data and the associated articles, to enable future access and analyses;
・Fully open access, with a Creative Commons Attribution License.

□ DailyNewsGW: 米政府、過去15年間にヒトゲノム計画に38億ドルの拠出、7960億ドルの経済生産を駆動。
UPDATE: Report Suggests Big Payoff from Human Genome Project: The $3.8 billion investment in the Human Genome Pr... http://bit.ly/kkShGg

The US government's $3.8 billion in spending on the HGP over 15 years has been critical to driving a total of $796 billion in economic output impact through companies in the life sciences using tools and technologies and research funding, the analysis from Battelle Technology Partnership Practice found.

□ DailyNewsGW: 日本法人との連携も行うカナダ・RB社、第一四半期の売上高が前年比67％上昇。大幅なコスト減。R&D 及びSG&Aは非公開。
Response Biomedical's Q1 Revenues Jump 67 Percent: read more http://bit.ly/j4Asg1




□ rnomics: 古細菌キメラRNAの構造的進化と機能。
Archaeal-Bacterial Chimeric RNAse P RNAs: Towards Understanding RNA's Architecture, Function and... http://bit.ly/kcKBwz




□ eurogene:
Special issue of Genetica: Genetics & Origin of Species, not #OA xcpt 4 a couple articles http://bit.ly/m9eAd9




□ AIP_Publishing: グローバル安定性と三角格子反強磁性体の幾何学的フラストレーションの磁気相図
Global stability and the magnetic phase diagram of a geometrically frustrated triangular lattice antiferromagnet http://ow.ly/4SXro




□ AIP_Publishing: 線形-非線形組み合わせ回路の温度推定・逆問題
An inverse problem of temperature estimation for the combination of the linear and nonlinear resistances http://ow.ly/4SfsI




□ NCBI:
BLAST DB changes: Transcriptome Shotgun Assembly sequences in "NT" db have been moved to a new "TSA" db. More info: http://1.usa.gov/1zl6qe




□ bioperl: BioPerl Project
GMOD is now on Github github.com/gmod/ see GBrowse and Bio-Graphics /jason




□ tri_iro: Lost Melody Theorem とは：
メロディを聴けば「ああ、この曲か～」と認識できるけれど、自力でそのメロディを思い出すことは絶対に出来ない『ロスト・メロディ』の存在を言う定理である……というのは比喩で、正確にはITTMで認識可能だが記述不可能な実数の存在を言う定理。




□ wakuteka: 牧場の朝

5月14日（土）14時～17時 みんな来てね！（明日かよ / Japanese Society for Bioinformatics - JSBi :: 5大学大学院研究室合同説明会 ─お台場の連携大学院CBRCで学ぶバイオインフォマティクス http://htn.to/FBPRcF

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□ Cold Spring Harbor Laboratory: The Biology of Genomes 2011.

>> http://meetings.cshl.edu/meetings/genome11.shtml
>> lens.align,: The Biology of Genomes 2011. (Day-1)


□ kbradnam: CSHL "Biology of Genomes" トーキングセッション概要。
Copy of my CSHL #bg2011 talk is available as a PDF with notes: korflab.ucdavis.edu/Datasets/Assem…




□ bmahersciwriter: 三大ゲノムアセンブリ評価プロジェクト
Good questions about @assemblathon's use of synthetic data. For more assembly competitions see http://bit.ly/iILFbw #bg2011




□ lukejostins:
KB: Which assembly was best? Everyone is a winner, but SOAPdenovo, ALLPATHS and SGA were more winners than most #BG2011




□ assemblathon:
#bg2011 MS: 'The curse of deep sequencing' ? higher coverage leads to discovery of more systematic errors



□ assemblathon:
#bg2011 MS: at 7x coverage SysCall correctly calls SNPs vs errors ~50% of time. Higher coverages (35x) = ~70% correct




□ genome_gov:
Soodyall: works with National Genographic Project https://genographic.nationalgeographic.com/genographic/index.html . #bg2011




□ larry_parnell:
Population Genomic Variation is the morning theme @ #BG2011 w/ archaic humans, admixture, recomb in African Ams,evol of great apes, more




□ genetics_blog: システム生物学: 異種間Omics-データへの統合的アプローチ
Tip of the hat to @larry_parnell for suggesting refs and examples for systems biology approaches to omics data http://b.qr.ae/iysroe




□ lukejostins: Luke Jostins
RP-R: Take 70 HapMap individuals, measure DNase1 peaks in 100bp windows, look for chromatin accessibility SNPs (caQTLs) #BG2011






□ cshperspectives: CSH Perspectives Ed. : DNAシーケシングの顕著な低コスト高効率化傾向。ムーアの法則を打ち破る。
Plummeting costs of DNA sequencing put Moore's Law to shame http://onforb.es/jIkfAy #bg2011

The cost of getting DNA data is dropping faster than the cost of processing data on computers. The potential to change not just medicine but other industries is huge. At the Cold Spring Harbor meeting, there were literally hundreds of genomes or exomes (that’s just the genes, which are small fraction of DNA) presented.

□ Fourth day of Biology of Genomes blogging. #BG2011 Geography and recent human evolution http://bit.ly/lcm5KC

One theme of the day was the complexity of selection in humans; you do not see very many of the clean, classical selective sweeps that you see in Drosophila. Graham Coop has tied this observation to another complexity of human diversity, that of allelic heterogeneity.

□ michaelhoffman:
#bg2011 TMB discusses a continuum of genomic variation from single substitutions/indels/mobile elements to rearrangements/c'somal variation




□ cshperspectives: CSH Perspectives Ed.
CSH Genomes meeting creating a buzz on Wall St? $ILMN share price up 4% ($PACB unchanged...) #bg2011



□ CSHで行われたBiology of Genomesミーティングの効果でIllumina社の株価が4%上昇したというウワサだけど、ちょうど開催直前の先週火曜日（日本時間）に、ILMN Genome Networkの大幅な低価格化を発表して以来、NASDAQは右肩上がりだったよね。




□ GenomeBiology:
Several speakers announced for GB's Beyond The Genome 2011 conference & Genome Informatics Workshop http://ow.ly/4WnYA #genomics #btg2011