RiSP-CD.

Plonked Spectral Video from the "RiSP-CD" 2012 from Richard Devine on Vimeo.

□ Richard Devine / "RiSP-CD" 2012 Plonked Spectral Video

>> http://detroitunderground.net/blog/2012/03/28/richard-devine-?-risp-?-cd/

RISP is Richard Devine's algorithm-based exploration of generative time structures for analog synths. Animation by dmas3

With the release of RISP on CD expect to breathe air on distant planets as chaotic, broken machines speak harmonious mutant languages via RD’s human/alien™ sound design and audio activist remixes.

ディヴァイン新譜のlong Video。やばい！！五感が震撼した。重厚かつ鋭利な刃のような構造性ジェネレートミュージック。公式にはリリース日が何処にも明示されてないけど、4月30日らしい(HMV)。ダウンロード版にはBalkansky(= Ivan Shopov)らのリミックスがあるとのことで悩ましい。。






□ Shocking BMW i8 Spyder Concept Hybrid Premiere

>> http://t.co/xMqPeW1b

おお、走ってるw マジでデザインやばい…今世に出ているスポーツカーで最もカッコ良いんじゃないだろうか。値段はIon Proton（次世代シーケンサー）換算で1.5台分かw





(Example layouts for the HPRD network. (A) yFiles Organic layout (ORL). (B) Cytoscape’s Spring-embedded layout (SEL). (C) Cytoscape’s Force-directed layout (FDL). (D) Multilevel layout with the clustering option (MLL-C))

□ BioMedCentral:
Generating network graphs for large datasets http://ow.ly/9TPKG research from #BioDataMining #biology #DataMining

>> http://www.biodatamining.org/content/pdf/1756-0381-5-2.pdf

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

The multilevel approach provided both biologically relevant and visually pleasant layout solutions in most network types, hence complementing the layout options available in Cytoscape. In particular, it could improve drawing of large-scale networks of yeast genetic interactions and human physical interactions. In more general terms, the biological evaluation framework developed here enables one to assess the layout solutions from any existing or future graph drawing algorithm as well as to optimize their performance for a given network type or structure.

大規模データを有する生物学的ネットワークの階層的モジュールを解析するCytoscapeプラグイン。物理・遺伝的相互作用を視覚化するアルゴリズム。

"Semantic similarity in the genetic networks"の項目が興味深い。大規模遺伝子相互作用ネットワークにおける性能評価で、FDLアルゴリズムは物理的遺伝的インタラクションの両方に意味的類似を示す 。






□ isatools:
Case Study: Sage Bionetworks and Amazon SWF - http://goo.gl/5Ml37 - Amazon Simple Workflow Service

>> http://synapse.sagebase.org/

Sage Bionetworks built an on-line environment, called Synapse. Synapse hosts clinical-genomic datasets and provides researchers with a platform for collaborative analyses. Amazon Simple Workflow Service (Amazon SWF) is a key technology leveraged in Synapse. Synapse relies on Amazon SWF to orchestrate complex, heterogeneous scientific workflows.

Open Integrated Workspace

Synapse is different from, and complementary to, other ongoing efforts. It is distinct from the data warehouses (e.g. NCBI, EBI) in that it goes beyond the repository database model to incentivize the creation of active community-based analysis and modeling groups. Synapse will incorporate existing tools such as, GenePattern, Taverna, Galaxy, and geWorkbench.

□ iPlant: Data Store

>> http://www.iplantcollaborative.org/discover/data-store

The iPlant Data Store is accessible by several means. These include iPlant's Discovery Environment, a dedicated web interface called DAVIS, a stand-alone application, command-line tools, and a couple of different application programming interfaces (for those who program).

□ EpiExperts:
Sequencing plant RNA - a tutorial from iPlant Collective, via RNA-Seq Blog http://bit.ly/GRcymK

iPlant Collaborative is a community of researchers, educators, and students working to enrich all plant sciences through the development of cyberinfrastructure ? the physical computing resources, collaborative environment, virtual machine resources, and interoperable analysis software and data services? that are essential components of modern biology.

□ Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

>> http://t.co/HZeJfaVi

Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. Consequently, we show that the new approach is essentially as efficient as and extremely faster than (up to 25 000 times) existing methods, thus paving the way for a systematic survey of substitution process heterogeneity across genes and lineages.

Two improved mapping methods have been proposed: Bayesian Mutational Mapping (BMM, [9]) and Probabilistic Substitution Mapping (PSM). They both use Markov chains to model the substitution process and account for the uncertainty in the ancestral states.

生命の樹：進化過程の時間-異種シーケンス：高速で堅牢な系統分析
Bayesian Mutational MappingとProbabilistic Substitution Mapping






□ The Elements of Bioinformatics

>> eagle genomics

バイオインフォマティクス・ツールの周期表：アセンブラ、Database、ゲノムブラウザ、ワークフローまで、リリース年も示して網羅。Pfam、Biopython等が抜けてるとの指摘。随時アップデート予定




□ Genopole:
World's Largest Dataset on Human Genetic Variation Goes Public http://bit.ly/HyU3xS

>> http://aws.amazon.com/jp/1000genomes/

The White House, for its part, sees the 1000 Genomes Project on cloud as one example of the kind of solutions it is proposing through its Big Data Research and Development Initiative [pdf]. The Office of Science and Technology Policy announced today that more than $200 million will be doled out to six federal agencies in an effort to make the most of the mountains of data being created for scientific discovery, environmental and biomedical research, education, and national security.

□ NIHforHealth:
News: 1000 Genomes Project data available on Amazon Cloud http://1.usa.gov/HnuYbk

The world's largest set of data on human genetic variation ? produced by the international 1000 Genomes Project ? is now publicly available on the Amazon Web Services (AWS) cloud, the National Institutes of Health and AWS jointly announced today.>

□ appliedgenomics:
Obama administration seeking input on human genome sequence data http://bit.ly/HpYBYh. What's your recommendation?




□ OBAMA ADMINISTRATION UNVEILS “BIG DATA” INITIATIVE:
ANNOUNCES $200 MILLION IN NEW R&D INVESTMENTS

>> http://www.whitehouse.gov/sites/default/files/microsites/ostp/big_data_press_release_final_2.pdf

Aiming to make the most of the fast-growing volume of digital data, the Obama Administration today announced a “Big Data Research and Development Initiative.” By improving our ability to extract knowledge and insights from large and complex collections of digital data, the initiative promises to help solve some the Nation’s most pressing challenges.

オバマ政権の『ビッグデータ』運用指針。
NIHは上述の1,000 Genome ProjectのAWSにおける運用。
国防総省は、大規模解析に基づく意思決定の為の防衛アプリーケション開発のワークフロー「XDATAプログラム」に投資

Department of Defense ? Data to Decisions:
National Institutes of Health ? 1000 Genomes Project Data Available on Cloud:
Department of Energy ? Scientific Discovery Through Advanced Computing:
US Geological Survey ? Big Data for Earth System Science:
etc...




□ genetics_blog:
NSF-NIH Interagency Initiative: Core Techniques and Technologies for Advancing Big Data Science and Engineering http://grants.nih.gov/grants/guide/notice-files/NOT-GM-12-109.html




□ ayrrisbio:
The US Government plans to open up their data sets to help advance big data research. http://bit.ly/HazwRY




□ OpenRepository:
Reading: The impact of funding agency #openaccess policies http://bit.ly/HF6PKN #OA #repositories #NIH




□ Roche Raises Bid to Acquire Illumina to $6.6B: an increase of 15%: trade on the Nasdaq, shares of Illumina $52.01 http://t.co/xoBu7lNj




□ Ion AmpliSeq: Highest multiplexed PCR-based solution delivers the fastest and simplest sequencing workflow for analyzing hundreds of genes, with only 10 ng of input DNA

>> http://t.co/kqx6Iyb6

Life Technologies Launches Ion AmpliSeq(TM) Custom Panels, Unlocking Thousands of Disease-Related Research Samples for Analysis






□ MaliciaRogue:
Introduction à la reconstruction automatique de réseaux métaboliques http://bioinfo-fr.net/reconstruction-automatique-de-reseaux-metaboliques #bioinformatique

Cet article n’est bien évidemment qu’une introduction à la reconstruction automatique de réseaux métaboliques. Pour une vue plus ? globale ? du travail de reconstruction on peut se référer à l’excellent article d’Ines Thiele et Bernhard Ø Palsson qui fait le tour à la fois de la reconstruction initiale mais également des méthodes pour une amélioration ultérieure du réseau. On pourra notamment y découvrir que d’autres outils que Pathway tools existent pour effectuer le type de reconstruction présenté dans l’article. On peut par exemple citer les logiciels metaSHARK ou AUTOGRAPH mais cette liste est, vous vous en doutez, loin d’être exhaustive.

大規模塩基配列データのゲノムアノテーションから、代謝ネットワークを自動再構築、高速シーケンスのリスク予防。




□ jd_mathbio:
"How to Make Epidemiological Training Infectious" in PLoS Biology Education #MMED: http://bit.ly/HcH8qJ




□ miRDeep, miRanalyzer & DSAP:

>> http://t.co/xdYWu1PC

Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation




□ SAGRudd:
Meta-analysis identifies nine new loci associated with rheumatoid arthritis = #GWAS alive and well in Japan! #awesome @ http://bit.ly/HaVfx3



□ SAGRudd:
Inference of modules associated to eQTLs - #awesome permutation of SNP and gene expression data & topological context @ http://bit.ly/HaVVT1




□ Analysis of insertion?deletion from deep-sequencing data:
- software evaluation for optimal detection

>> http://t.co/Pr0eU7Hj






□ Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes
- effect of selection on the extrinsic incubation period of viruses.

>> http://shar.es/pAeBk




□ [氷河期と遺伝変異] Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period

>> http://t.co/cI63IaJy






□ genomigence:
GenomeResearch: RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulat... http://bit.ly/Hc3uTh




□ DailyNewsGW:
Myriad Developing Companion Diagnostic for Cephalon: http://bit.ly/HhvztL

Myriad Genetics and Cephalon have signed an agreement to conduct BRCA1 and BRCA2 mutation testing on patients to be enrolled in a Phase I/II clinical study, Myriad announced after the close of the market Wednesday.

ミリアド・ジェネティクスとセファロン社がBRCAの変異試験を実施。最近、分子診断企業の遺伝学的臨床試験(Genetics/Clinical Trial)の締結が活発な気がする。ミリアドと提携してBRACAnalsysを行う企業は4社目




□ sysbiomed:
New Version of CellNOptR 1.2 available in Bioconductor with significant improvements http://bioconductor.org/packages/release/bioc/html/CellNOptR.html




□ DEXSeq: Detecting differential usage of exons from RNA-Seq data. an R package had more significant hits than cuffdiff. http://www.r-bloggers.com/rna-seq-methods-march-twitter-roundup/
2






□ genomigence:
NAR: SAVoR: a server for sequencing annotation and visualization of RNA structures: RNA secondary structure is r... http://bit.ly/HKk64t




□ druvus:
Semantic Web meets Integrative Biology: a survey http://bit.ly/Hp4jKU #semweb



□ BioQ: tracing experimental origins in public genomic databases using a novel data provenance model http://bit.ly/HlpMmJ #semweb #genomics






□ WIREsSysBioMed:
Systems vaccinology: learning to compute the behavior of vaccine induced immunity http://wires.wiley.com/WileyCDA/WiresArticle/wisId-WSBM163.html




□ BIO-Quantum PHYSICS: DNA/RNA As an Information Energy Catalyst in Life Systems http://www.wbabin.net/science/manzelli.pdf




□ Big Data Counting: How to count a billion distinct objects using only 1.5KB of Memory http://highscalability.com/blog/2012/4/5/big-data-counting-how-to-count-a-billion-distinct-objects-us.html






□ moorejh:
Dynamic Models of Complex Traits are Containers of Missing Heritability http://is.gd/Nzx9tA #genetics #complexity #bioinformatics




□ jeff_hayes:
[World Report] UK announces strategy for regenerative medicine http://bit.ly/HzqFXJ




□ EurekAlertAAAS:
First targeted nanomedicine to enter human clinical studies. http://eurekalert.org/e/4h8Q #SciTM




□ NCBI:
New in dbVar: browse multiple studies at once using the dbVar genome browser, for example: http://1.usa.gov/HgCCbv . #bioinformatics




□ BioMedCentral:
A new analytical tool in biocatalysis http://bit.ly/Hd0Eni #BMCBiotechnology #Catalysis #Chemical engineering

Dual-lifetime referencing (DLR): a powerful method for on-line measurement of internal pH in carrier-bound immobilized biocatalysts

□ Dev_journal:
An sRNA pathway controls megasporogenesis to megagametogenesis transition in female gamete development of Arabidopsis. http://ow.ly/9Ltf4




□ TheACMG:
Record attendance! 2000+ genetics/genomics professionals registered for #ACMG2012 Annual Meeting in Charlotte. http://www.acmgmeeting.net



□ RedGene27:
David Dimmock: to analyze an exome, need 700 hrs to get data - 17,000 variants, 7,000 non-synomymous. And then the work begins! #ACMG2012




□ Wikipedia’s Next Big Thing: >> http://t.co/tVdQBH0X
Wikidata, A Machine-Readable, User-Editable Database Funded By Google, Paul Allen And Others




□ Bigger data, better intelligence for government: OSTP, NSF, NIH, DoE, DoD, DARPA & USGS outline of Big Data research http://t.co/h6ceg4jG

>> http://live.science360.gov/bigdata/




□ OpenRepository:
Excellent #openaccess resource from @EIFLnet http://bit.ly/GXaDef #OA #repositories #opendata




□ Luminex mRNA quantification

>> http://t.co/psQli7ah

Affymetrix gave a talk at our institution today and mentioned that they bought a company called Panomics, which had developed a bead-based test performed on a Luminex instrument for quantifying RNA from crude samples without RNA extraction. They claim sensitivity comparable to qPCR. Has anyone tried this technology? Is it worth the investment?

□ NCBI:
Catch views of NCBI’s RefSeq, Gene, GEO, CCDS and SNP resources in the PBS’s NOVA episode ‘Cracking Your Genetic Code’: http://to.pbs.org/w6YeRI




□ Appistry-powered big-data analysis could help create disease-resistant plants to feed the world's hungry.

>> http://t.co/rajVBDLd

SpringerがAyrris BIOのソリューションを利用、大規模データ解析からデザインした耐性植物で飢餓問題を解決する計画。




□ BioMedCentral:
Biomedical #textmining enhanced by lemmatization tool http://ow.ly/a18Ep research from Journal of Biomedical Semantics

>> http://www.jbiomedsem.com/content/3/1/3/abstract

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

An innovative aspect of the BioLemmatizer is the use of a hierarchical strategy for searching the lexicon, which enables the discovery of the correct lemma even if the input Part-of-Speech information is inaccurate. The BioLemmatizer achieves an accuracy of 97.5% in lemmatizing an evaluation set prepared from the CRAFT corpus, a collection of full-text biomedical articles, and an accuracy of 97.6% on the LLL05 corpus.

□ druau:
PLoS Comp Bio wikification. the article (fixed): http://bit.ly/H4lxND ; The wiki version: http://bit.ly/H4ljWB @ploscompbiol




□ PLoSCompBiol:
Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion http://dx.plos.org/10.1371/journal.pcbi.1002449




□ Trends_Ecol_Evo:
New Cell Press Discussion on ecological neutral theory: useful model or statement of ignorance? http://news.cell.com/discussions/




□ BioMedCentral: Microbiome is now accepting submissions! http://ow.ly/a1Kak #openaccess #oa






□ NatureJapan:
【情報理論】なぜ一部のミームだけが急速に広まるのか （Scientific Reports）http://nature.asia/HzfOSH

The wide adoption of social media has increased the competition among ideas for our finite attention. We employ a parsimonious agent-based model to study whether such a competition may affect the popularity of different memes, the diversity of information we are exposed to, and the fading of our collective interests for specific topics.

Agents share messages on a social network but can only pay attention to a portion of the information they receive. In the emerging dynamics of information diffusion, a few memes go viral while most do not. The predictions of our model are consistent with empirical data from Twitter, a popular microblogging platform. Surprisingly, we can explain the massive heterogeneity in the popularity and persistence of memes as deriving from a combination of the competition for our limited attention and the structure of the social network, without the need to assume different intrinsic values among ideas.

任意のトピックに言及した＃タグの拡大をノードで可視化。
震災時のJapanタグは偏依に結晶化している。




□ Spinor representation for loop quantum gravity

>> http://t.co/N9qB4kVf

ARBITRARY GRAPHS AND CONTINUUM
"a framework to describe the behavior of gravitational dynamics at the Planck scale."

a quantization of the loop gravity phase space purely in terms of spinorial variables, which have recently been shown to provide a direct link between spin network states and simplicial geometries. The natural Hilbert space to represent these spinors is the Bargmann space of holomorphic square-integrable functions over complex numbers.

We show the unitary equivalence between the resulting generalized Bargmann space and the standard loop quantum gravity Hilbert space by explicitly constructing the unitary map. The latter maps SU(2)-holonomies, when written as a function of spinors, to their holomorphic part. We analyze the properties of this map in detail. We show that the subspace of gauge invariant states can be characterized particularly easy in this representation of loop gravity. Furthermore, this map provides a tool to efficiently calculate physical quantities since integrals over the group are exchanged for straightforward integrals over the complex plane.

□ glynmoody:
Opposition to biotech giant #Monsanto growing worldwide, new report shows - http://bit.ly/HmoKs6 if confirmed, important




□ AliAbunimah:
Remembering Adrienne Rich: poet, activist and supporter of Palestinian liberation | @bangpound on @intifada http://ow.ly/9Y5St




□ Sex Tech: http://t.co/1oF8UOiN
Egyptian Porn Censorship, UK Filesharing Travesty, Wikipedia Sex Wars: "All happens where tech meets sex."






□ Chembl:
Amazing visualisation of ocean currents http://youtu.be/xusdWPuWAoU

This visualization was produced using NASA/JPL's computational model called Estimating the Circulation and Climate of the Ocean, Phase II or ECCO2.

地球上の表面海流の変化を可視化した動画。
音楽が凄い好み。プロユース音源なのが残念。。




□ AIP_Publishing:
Does calling the climate controversy a "war" accelerate civic polarization? http://ow.ly/9SEnD #AIP_PT
気候変動論争は、温暖化の科学的検証とは遠い所でイデオロギーの対立となっている。
主流パブリッシャーからは、温暖化に関して、これを裏付けるような研究や観察事象の更新が日々報告されているのだけど、否定派の論拠は、いつまでも古いソースや陰謀論、政治対立にすがり続ける構図。それを煽動する市民運動家の声ばかりが大きいのも、否定論自身の首を絞めているのかも。

天動説の時代とは違うけれど、気候変動論が「十分に疑わしい」もので、温暖化を否定するデータや解釈が「平等に公表されているのなら」、その二項対立には量的拮抗がみられるはずである。だけどそうなっていない理由として考えられるのは3つだけ。『大多数のメソッドが誤っている』『出版界と学会の圧力』そして『気候変動が起こっている』






□ jricole:
Climate change speeding up & = drought, famine, war in Mideast, Africa http://t.co/VmXO2sBH

In 1951-1980, it was only at most 0.2 percent of the globe’s land area that you had extremely hot summers. Now it is ten percent of global land area. And the change will be costly, even in North America. In 2011, the US was struck by 14 extreme weather events that caused more than $1 billion each in damages. That just isn’t normal, the paper argues.

気候変動が招く中東、アフリカの飢饉と戦争。中長期的な温暖化の過程で、突発的な異常気象のリスクが増大する。

気候変動論の中で温暖化を語るとき、「n年後までに平均気温が○℃上昇～」とか言うけれど、地球の気候環境は全てリンクした事象だから、ゆるやかな変化を続けることで、何処かで本質的に予測不可能性を持つ相転移が起こることも否めない。そのシステムの負荷となる「入力」が人為性かどうかという問題。

「人為も自然だから何しても良いんじゃね」という虚無主義的な気候変動否定論さえいるけれど、人為とは「己の為す」ことで、コントローラブルな事象を指すのだから、人為を捨てたそれはもはや人為じゃねーよw　お前は自然の中の石ころじゃないだろ、とw




□ 32nm:

4/19 からの Sage Bionetworks の Commons Congress がおもしろそう http://sagecongress.org/WP/2012agenda/ George Church, David Haussler, Lessig らがキーノート

□ n0rr:

@jyasuda1 配列情報と長さや数などの測定値は価値が違うってことでしょうか？生物学が一種のリバースエンジニアリングであるという考え方は納得できるので、ボトムアップで理論を作って行くのが難しいというのはもっともだと考えています。

□ hoxo_m:

すげえ！このような有用な電子書籍が無料とな！

“お家でできるMac Bookでやる次世代シーケンスデータ解析(科学・テクノロジー) - iPadZine（電子書籍）” http://t.co/smdfZPlT




□ hinaichigo:

#bioinfo velvet assemblerで、read量、1read長さ、推定ゲノムサイズ等を入力するとお勧めk-mer length設定を教えてくれるchi velvet advisor http://dna.med.monash.edu.au/~torsten/velvet_advisor/

□ synobu:
Biocuration2012は17の国から300人以上. うちわけは, 53の大学, 51の研究所, 11の企業. #isb2012




□ Speed and Retention ? Are e-Readers Slower and More Forgetful? http://t.co/6DpqlN3f
電子書籍で得た情報は忘れやすいのか？という議論。
ラピッド・ラーニングと引き換えにローカルメモリを犠牲にしている？

ネットで得た情報はすぐに忘れるとかいうけど、実感としてそのようなことは皆無だなぁ。何年も前に一瞥しただけの記事を急に思い出すとかデイリーチャメシだし。細部の欠損が多いかというと、書籍も同程度だと思う。学習空間と、そこに至る過程が省略されることで記憶のソートが曖昧にってのはありそう




□ rubbish_talk.

□ ヒトは考えても考えなくても、作為的にしても無為的にしても、考えてないし、考えている。無為にして、作為である。



□ アインシュタインは「真実は経験に耐えうるもの」と言ったけれど、これを転じれば「経験が真実を炙り出す」のだ。そして「時の歩みは悠遠なれど、いずれ眞実なるものは現れいでる」とはヘルダーリンの詩。経験は時として過つ。嘘を吐く。遠回りする。だけど真実は、何万光年も超えて輝く夜空の星なのだ。




□ 批判や言及の対象って、「同じ言葉」を指向していても、Mentionする主観と対象の間にある集合の内包・外在関係で力学的作用が全く異なってくる。それは論理的に正しいとか誤謬があるとか、そういう次元で白黒のつく問題じゃない。


言葉は力だけど、力でしかない。
真実じゃない。

上の否定形の言葉の外側に反乱した意味的作用素の振る舞い。「真実じゃないもの」の外側にあるもの、その全てが真実ではないように、Mentionの対象を一意的に連鎖的な解釈で括ることは出来ないし、意味が無い。あらゆる言葉は真実を捕縛する為ではなく、作用を齎すために発語される。


アンオブザーバブルな作用素には「行間」も含まれる。発語されている意味量は観測者の主観に因って互い違いの値を取る。ところが誤謬の要因たる行間を埋めることはできない。発語量を補って意味を密にしても、行間は等しく増大するからだ。