Article_Jan.3

□ 生命は複雑系事象の網目を織り成す紐の絡まった結び目のようなもの。解けても何処かに消えるわけでなく、繋がりが変わるだけ。

思考や感情は、発語することで縺れ合う情報繊維を解いて、励起状態から電気的負荷を発散しエントロピーを保つ。では入力を隔絶された孤独な観測者はどうなるか。内部循環と自己摂動。その夢は入れ子の宇宙そのものの姿である。


言語は、現実空間を概念的に可換な発語認識の境界面を規定する。そして言語は共有によってしか発達せず、生物学的空間と共進化する。言語に規定された信号処理ベースの計算は自ずから観測者の行動を制約付きでアフォードし、認知の至る限界を前提している。




□ Sustainability of Bioinformatics Databases: バイオインフォマティクス関連データベースの運用状況。リソースのコストで淘汰傾向。EUはELIXIRに統合を計画 / NAR DB Collecition http://nar.oxfordjournals.org/content/40/D1/D1.full

These recent developments show that the importance of the public database resources, which is obvious to any biologist, needs to be constantly highlighted to the national and international financing bodies.

In Europe, coordination of the bioinformatics infrastructure is planned through the EU-sponsored ELIXIR (European Life Sciences Infrastructure for Biological Information, http://www.elixir-europe.org) project, which aims at guaranteeing seamless access to biological information by integrating data generators and data centers throughout Europe.

□ PLoSCompBiol:
Adjusting Phenotypes by Noise Control dx.plos.org/10.1371/journa…

Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage.

Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks.

This independence was shown to be rooted to a certain network structure satisfying Feinberg's deficiency zero theorem [24]?[26]. We will show that when such species independence occurs, the orthogonal control of mean and noise levels is not possible, but that the application of extrinsic noise or feedback could help achieve orthogonal control.

ノイズ制御による表現型の順応：振動性信号を調節し細胞内蛋白質濃度のノイズレベルを直交制御。意図した表現型を得る確率モデル。欠陥零定理を満たすネットワークでも有用。






□ Amazon Rolls out NoSQL Database Servicein the cloud called DynamoDB

>> http://www.genomeweb.com//node/1016…
>> DynamoDB

Amazon Web Services (AWS) has launched a fully managed NoSQL database service in the cloud called DynamoDB that aims to provide seamless scalability on the fly. AWS is claiming that their new service will offload administrative tasks such as hardware provisioning, setup, configuration, replication, software patching, and cluster scaling.

AWSがDynamoDB上でNoSQLサービス開始。分散システム基盤の超スケーラブル データベース。NoSQLは厳密なスキーマが無く、オミックス分野で有意な計算効率を発揮。

DynamoDBの追加容量、1GBあたり$1か。しかもSSD。NoSQLの顧客層としてゲノミクス分野に訴求するのは間違いないけど（モンサントによるゲノムデータ解析のユースケース有り）、何より昨今の個人研究、ガレージ生物学(Homebrew genomics)普及の一翼も担いそう。

Ion Proton Sequencer+DynamoDBという布陣でLet'sガレージ・ゲノミクス！(※予算一千万円)






□ portablegenomic:
GeneGroove: Portable Genomics is launching tonight the 1st iPhone App to play a unique melody from your genome data bit.ly/xeADvd

昨年も紹介した、自分のDNAデータを音楽に変換するiPhone appがリリース。23andMeにSNPを渡すことが条件。
Genome DataをMusic Fileに置換。iTunesでSync可能。DJ（プログラム？）によるオートアレンジ機能も。GeNumberはゲノム一意性をもちながら不可逆で、デコードされる心配はないらしい。






□ Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

>> http://t.co/noBohY2n

APART, a novel automated computational pipeline, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information.

To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner.

ディープ・シーケンシングデータの解析によるリボソーム関連低分子RNA安定加工種の検出。
新しく提案された自動計算パイプライン『APART』は低メモリに最適化。cDNAライブラリの読み取り実行時間も安定した線形の相関を示すのでローエンドマシンでもいける。






□ MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

>> http://bit.ly/wgRAJp

Ultra-deep RNA sequencing has become a powerful approach for genome-wide analysis of pre-mRNA alternative splicing. We develop MATS (multivariate analysis of transcript splicing), a Bayesian statistical framework for flexible hypothesis testing of differential alternative splicing patterns on RNA-Seq data.

MATS uses a multivariate uniform prior to model the between-sample correlation in exon splicing patterns, and a Markov chain Monte Carlo (MCMC) method coupled with a simulation-based adaptive sampling procedure to calculate the P-value and false discovery rate (FDR) of differential alternative splicing. Importantly, the MATS approach is applicable to almost any type of null hypotheses of interest, providing the flexibility to identify differential alternative splicing events that match a given user-defined pattern.

RNA-seqデータの差動選択的スプライシング識別に有用な多変量解析ベイズ・フレームワーク。ユーザ定義のパターンに対して柔軟性を持ち、ほぼ全てのパターンの帰無仮説に適用可能。




□ DailyNewsGW:
AB Sciex, Indigo to Market Mass Spec Solutions: read more bit.ly/xPGip7

The solutions streamline data acquisition and automate data review and are expected to accelerate the use of mass spec technologies by simplifying the workflows. The partnership is also expected to ensure better results in clinical research, forensic toxicology, and pre-clinical and clinical trials of new drugs

□ rnomics:
Fine-Scale Temporal Dynamics of a Fragmented Lotic Microbial Ecosystem: Microbial ecosystemsbit.ly/ADIwzS

Scaling is an important concept in landscape ecology, where it is usually used in a geographical, rather than temporal perspective34. A lesson from experiment described in this study is that a bacterial community can change drastically and rapidly and yet have an equally rapid recovery. Our data emphasize the need for a re-evaluation of the time scale of microbial sampling experiments beyond diurnal cycles, especially in dynamic environments such as fresh water streams, lakes and irrigated soil.

河川中の断片化された微生物生態系の細密スケール時間ダイナミクス: ヤーコン川上下流における生息状態の変化から従来の流水中の実験サンプリングを再評価する必要性




□ rnomics:
Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in... bit.ly/zM2ZMU #BMC

We have removed globin transcripts from 6 human whole blood RNA samples with a human globin reduction kit and compared them with the same non-reduced samples using deep Serial Analysis of Gene Expression.The reduction of globin transcripts in whole blood samples constitutes a reproducible and reliable method that can enrich data obtained from next generation sequencing-based expression profiling.

□ Differential network biology

>> bit.ly/xVGJYw

Here, we review the technological developments and experimental designs that have enabled differential network mapping at very large scales and highlight biological insight that has been derived from this type of analysis. We argue that differential network mapping, which allows for the interrogation of previously unexplored interaction spaces, will become a standard mode of network analysis in the future, just as differential gene expression and protein phosphorylation studies are already pervasive in genomic and proteomic analysis.

差動ネットワーク生物学：生物システム環境の相互作用マップ。バイオインフォマティクスの大規模データセット差分解析と類似。この手法で蛋白質複合体の摂動時における関数関係の再構成を解明。

生物学的空間に置けるインタラクトーム間の関係性をノードで結索することは、高スループット化の進むデータの機能的解釈の地道なメソッドではある。もっとセマンティックな切り口もありそう。




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□ Merck4Bio:
Single-celled #organism can evolve multicellularity within months bit.ly/zTl26q

The origin of multicellular life, one of the most important developments in Earth’s history, could have occurred with surprising speed, US researchers have shown. In the lab, a single-celled yeast (Saccharomyces cerevisiae) took less than 60 days to evolve into many-celled clusters that behaved as individuals. The clusters even developed a primitive division of labour, with some cells dying so that others could grow and reproduce.

酵母が示唆する多細胞生命の迅速な発生:60日で単細胞生物から『スノーフレーク』状の多細胞生物を培養可能。古代における起源も意外と早い？




□ Sigma-Aldrich to Distribute TriLink's CleanAmp Products

>> http://www.genomeweb.com//node/10166…
>> http://www.trilinkbiotech.com/
>> http://www.sigmaaldrich.com/japan.html

TriLink BioTechnologies today said that Sigma-Aldrich will sell and distribute the firm's CleanAmp dNTPs globally.
The San Diego-based firm said that its CleanAmp dNTPs, which are designed for hot-start PCR, are an "ideal complement to Sigma-Aldrich's product and service offerings." It added that the latest advancement in CleanAMP dNTP chemistry provides "improved amplicon yield in endpoint PCR and earlier Cq values in fast cycling real-time PCR."

Financial and other terms of the agreement were not disclosed.

シグマ＝アルドリッチ社がTriLinkBioの改良ホットスタートPCR、CleanAmp dNTPsの世界発売に向けてディストリビュート。プライマーの温度変化を阻止する製品として非常に優秀な評価があり、miRNA市場での訴求は大きそう




□ genetics_blog:
Interesting results in genomeweb survey: exome arrays > GWAS; RNA-seq, people plan to spend more $ on #bioinformatics genomeweb.com/forward/emailr…
Survey Finds Exome Arrays on the Upswing as GWAS, Gene Expression Apps Decline




□ OxfordJNLsJapan:
【科学・社会】学界におけるリサーチツールの共有：日本でのケーススタディ　oxford.ly/wrr8VH
Sharing research tools in academia: the case of Japan

Although studies in the US have indicated that the trend of academic capitalism or commercialization deters material transfer, our results show limited negative impact in this regard. Second, this study examines the use of central repositories of research tools as a means to the wider dissemination of such tools. The results suggest that entrepreneurial scientists and scientists in public research organizations are more willing to provide their research tools through this publicly accessible system.

日本に学ぶ生命科学・材料科学分野での研究ツール共有・公開システムの中心的なリポジトリの利用。物質移動契約と成果のリターン、米国では商業主義的




□ SAGRudd:
Bioinformatics: Data compression facilitates genome assembly = #awesome; j.mp/yrCGDi

As genome sequence data sets continue to grow, there is a pressing need to develop accurate yet memory-efficient means of assembling genomesde novo. Using new computational tools, the authors assembled a human genome using less than 64 gigabytes of memory.

□ SAGRudd:
BamView: visualizing and interpretation of next-generation sequencing read alignments = #awesome j.mp/zB6kKT

BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user.

□ NatureRevGenet:
Review (in GWAS Series). G. Gibson on 20 arguments for and vs two main models for the genetic basis of complex traits: bit.ly/wKWAOd

Genome-wide association studies have greatly improved our understanding of the genetic basis of disease risk. The fact that they tend not to identify more than a fraction of the specific causal loci has led to divergence of opinion over whether most of the variance is hidden as numerous rare variants of large effect or as common variants of very small effect. Here I review 20 arguments for and against each of these models of the genetic basis of complex traits and conclude that both classes of effect can be readily reconciled.

□ jeff_hayes:
[Editorial] Addiction?a global problem with no global solution bit.ly/zbTYE5

international drug conventions protect public health, or otherwise, and concludes that national policies aligned with risks of different drugs are needed. The authors state: “The cultural positions of different drugs vary enough to preclude universal policies on how to deal with all illicit or indeed licit drugs. From the perspective of public health, we need to move towards a control system that is more aligned with the risks that different drugs pose to users and shows an understanding of the effects of different regulatory approaches on drug use and harm.”

□ NYT uses R to map the 1%
>> http://www.r-bloggers.com/nyt-uses-r-to-map-the-1/

The on-line version of the article included interactive features like this interactive map showing where your household ranks in the country and in local regions. The print edition, however, included some different (and necessarily static) representations of US wealth data, such as this map of where the wealthiest 1% live

□ CODEX: Exploration of semantic changes between ontology versions

>> http://www.izbi.de/codex

２つのオントロジー差分を検知するツール

The CODEX (Complex Ontology Diff Explorer) application allows for determining semantic (complex) changes between two versions of an ontology. The application is based on a general diff algorithm called COntoDiff (Complex Ontology Diff) which applies rules to iteratively compute the most compact (semantically richest) diff between two ontology versions.

□ PLoS:
Analysis of 500 scholarly article tweets 88% discuss it 9% are author/publisher originated 27% use conclusions bit.ly/AEsIwD #scio12




□ Annotating limma Results with Gene Names for Affy Microarrays: r-bloggers.com/annotating-lim…

I could annotate each probeset ID with a gene symbol, gene name, Ensembl ID, and have that Ensembl ID hyperlink out to the Ensembl genome browser.

□ GeneticAlliance:
Calling all social science researchers! Improve your genetics literacy with a new online course from NCHPEG & NIH: ow.ly/8wKJb

The nature/nurture debate has confounded research on social and behavioral phenotypes since the late nineteenth century. This program takes the position that the debate is unhelpful and misleading, because no gene operates outside of an environment - beginning with the environment of the cell and extending to the influences of the external world.

社会科学者の為の遺伝学教育とリソース：社会的行動表現型の古典的研究の混乱から、ゲノミクスが社会・行動科学に齎す影響を正しく評価する為の教育プログラム




□ Big Data Bibliography: http://t.co/Vw27vELg

business intelligence to data mining and machine learning, to cloud services and NoSql Data Stores to data visualization.

□ WBLifeSci:
Computational Approaches in Cheminformatics and Bioinformatics ow.ly/1gQfN5




□ sFFT: Sparse Fast Fourier Transform

>> http://groups.csail.mit.edu/netmit/sFFT/

We consider the sparse Fourier transform problem: given a complex vector x of length n, and a parameter k, estimate the k largest (in magnitude) coefficients of the Fourier transform of x. The problem is of key interest in several areas, including signal processing, audio/image/video compression, and learning theory.

We propose a new algorithm for this problem. The algorithm leverages techniques from digital signal pro- cessing, notably Gaussian and Dolph-Chebyshev filters. The resulting algorithm is structurally simpler than its predecessors. As a consequence, we are able to extend considerably the range of sparsity, k, for which the algorithm is faster than FFT, both in theory and practice.

□ Trends_Endo_Met:
“Article of the Future” video showing an improved, intuitive and interactive interfacethe Science Direct redesign! articleofthefuture.com

The Article of the Future project- an ongoing initiative aiming to revolutionize the traditional format of the academic paper in regard to three key elements: presentation, content and context.

エルゼビアの『未来のアーティクル』科学出版プラットフォームの過去と展望について振り返る動画。紙媒体とインタラクティブ・データとの比較など。謎の感動。音楽のメロディがeRaっぽい




□ dgmacarthur:
Longevity genetics paper retracted by Science reappears - this time in PLoS ONE: retractionwatch.wordpress.com/2012/01/18/seb…




□ the_Node:
We've made a Twitter list of labs and institutes. twitter.com/#!/the_Node/la… Is your lab on Twitter?




□ BrainCosmos:
Learning and Generalization under Ambiguity: An fMRI Study :PLoS Computational Biology bit.ly/yICzp2




□ F1000:
Figshare, the science data-sharing site has released a shiny new website cot.ag/Ai1jxh @figshare #opendata #openscience




□ betterbio:
Still a necessary discussion RT @GCPworks: Resveratrol researcher faked data, report says; what drives academic fraud? lat.ms/zv0IAA




□ DiscoverMag:
Science finds better way to teach science: getting rid of the hallowed (& stultifying) classroom lecture bit.ly/zXsL5d by @dhfreedman




□ BioMedCentral:
RT @bmcmatt: Springer permits commercial use for its hybrid #openaccess program bit.ly/zHqmhS Great move by Springer! NC licenses...




□ creativecommons:
Springer's Open Choice to publish all its #openaccess content under #CC BY: bit.ly/AnNsg9




□ ca_tweet:
Springer社が全てのオープンアクセスコンテンツでCC-BYライセンスを採用し商用利用が可能に current.ndl.go.jp/node/19963




□ FutureProofNSW:
Future Proof: System migrations to archives (a research paper from the digital archives team) bit.ly/xL0fzj #archives

This research paper discusses three problems with using the term transfer to describe the processes that precede ingest into the digital archives and recommends instead the adoption of a project-based, system migration approach.

デジタルアーカイブに関するプロジェクトベースでのシステム移行の問題『転送でなく移行』『ファイルレベルでアプローチしない』 『線形モデルでの保全プロセス』『管理権の制御システム』




□ ageimo:

sciencedirect.com/science/articl… 有限時間の軌道断片の軌道安定/不安定性指数の提案。この分解の仕方は面白い。分解は共変的になるようになっているし。有限時間だと、分解は空間計量の取り方によるので、なかなかファイナルアンサーはないけど、共変性は分解が持つべきいい性質だと思う。

□ NatureJapan:
Nature Cover Story: 研究への寄付 民間からの資金提供で落とし穴を避けつつ恩恵を得るための方法 nature.asia/zWmncq




□ 4pdf:
an introduction to systems biology design principles of biological circuits: bit.ly/xzpWR9




□ elsevierjp:
RT @Luke0629 これ面白そう。愛情と誠実に関する生物学的心理学研究の総論。"Love is more than just a kiss: A neurobiological perspective of love … bit.ly/xaowhm






□ thinkgeek:
Physics paper finds Death Star could destroy Earth, but not Jupiter: j.mp/w0R1xo Good to know. #science
デス・スターは地球を破壊出来るけど、木星は無理？惑星の重力結合エネルギーを上回るジュール量から試算。地球では2.25x10^32J、木星ではその千倍必要




□ DBCLS: LinkedData Study Meeting.



□ dbcls:
第3回LinkedData勉強会 の中継を開始します (Broadcasting live at ustre.am/fg0g)

□ Metadata of Microbial Metagenome
・微生物メタゲノムのメタデータ：サンプル採取の環境情報をオントロジーと紐付ける。
・Metagenome Environmental Ontology (MEO): バイオーム・環境情報を辞書や気温推移等の外部の様々なデータと関連づける
・MEOの問題点：オントロジーのライセンス。作業が労働集約的。

上述したヤーコン川での上下流の環境状態における微生物の生息状態の時間的ダイナミクスの論文といい、サンプル採取のメタデータも今後見直されていく必要もあるだろうな。オントロジー自体が柔軟にデータの変化に同期できるシステムであることも大事。




□ yayamamo:

メタゲノムのメタデータ。昨年行ったハッカソンの記録で概要が分かります。wiki.lifesciencedb.jp/mw/index.php/B…ヒト・環境メタゲノムメタデータのオントロジー整備とRDF化 #lodjp

オントロジーのライセンスは厄介。なるべく既存のオントロジーを利用しよう、という考えと対立しかねない。ScienceCommonsの見解としてCC0が推奨されている。 sciencecommons.org/resources/read… #lodjp

□ wintermelon:
MicrobeDB.jp microbedb.jp/MDB/index.html #lodjp




□ Occupy Nigeria: Photos From Abuja | Nigerian Entertainment Today http://t.co/pj0Cwx32




□ Nigeria's First Forensic DNA Laboratory http://t.co/sviZJzpE

Utah-based Sorenson Forensics is designing and implementing the first professional law enforcement DNA laboratory in Nigeria.

ナイジェリアに初の法医学DNAラボを設立。米ソレンソン社：アフリカには未だ法医学的遺伝子検査を行う素地が殆どないという現実。




□ rubbish_talk.

□ 脱原発問題は、エネルギー資源を運用（特にサプライ側）するのに必須な冗長性システムを、どのように移行して行くかという論点に切り換わろうとしている。消費形態を変えるという視点での議論は頭打ちで、供給の冗長性において原発の破綻リスクを評価し代替エネルギーに置換する経済的利点の計量が急務




□ 情報拡散が記憶に与える時間感覚への影響を検証したい。例えばメディアで共有されたトピックについて、2002年に10年前を想起する事柄の印象と、2012年に10年前を想起した事柄の経過時間（懐かしさスコア）の感覚と、年代ごとの分布。情報端末普及により共有が密になった部分と疎になる部分






□ iBooks Authorでブログのレビュー記事全部まとめてみようかな～♪ 権利関係が気になる。電子書籍形態ではなく、電子書籍になるのだろうか。その辺の公開設定出来るのかな




□ iTunesUのファイリング機能クソ便利。今まではiTunes経由で動画にアクセスするだけだったけど、管理が出来るように。これからMendeleyみたく共有とかソーシャルサービスとかアノテーション機能（動画内でも）も充実して行くんだろうか。その先にはiPaper（論文版）が？




□ 特定のトピックに関連する市場の動向に対して、例えば「日本で○○が普及しない理由」は、とかの説明に「価格が高いままだから」「ライセンスの扱い方が違うから」と、表層の現象面のみをあげつらった記事は本当に価値が無いなと。要素に還元してはならない。要素間の力学的関係に踏み込まないとダメ。