Morphing Thru Time.

□ Enigma / "Morphing Thru Time"
Official Music Video by Steadycamline Productions.


□ EpiGeneSysFP7:
Best science songs of all time. Fun read :) @SciAm bit.ly/AA7Voa
「科学をテーマにした歌と言えば？」というアンケート。
個人的にはEnigmaの"Morphing Thru Time"が至高。

それで今更知ったんだけど、
Enigma - "MMX"のVideoを手がけたドイツの映像プロダクション、『Steadycamline』が、Enigmaの全楽曲のミュージック・クリップを製作して、Youtubeに次々公開してるみたい。しかも公式に許諾されてるようだ






□ The Scale of Universe Enhanced.

>> http://images.4channel.org/f/src/589217_scale_of_universe_enhanced.swf

いつのまにかパワーアップしてるw
スケールのクラスごとに、どのレベルに「個体群」やネットワークが集積・分布しているか、どんな偏りがあるか調べてみたら面白そう。






□ julientap:
#PLoS: Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics dx.plos.org/10.1371/journa…

We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features…

微生物メタゲノミクス・データ生成確率モデルの為のディリクレ混合多項分布:微生物群集データに有用な機械学習分類アルゴリズム






□ Next Generation Genomics: World Map of High-throughput Sequencers #AGBT

>> http://omicsmaps.com/
>> http://core-genomics.blogspot.com/2012/02/my-agbt-poster.html

There are now over 1800 NGS instruments in 650 labs across 45 countries, which is about 60-70% of installs. Over 150,000 page views suggests that a large number of people using NGS are also curious about who else has one.

There is an interesting graph on my map plotting the growth (and decline) of the major platforms. It is clear Illumina has the most sequencers out there today. However there appears to be a ten to one difference in Ion vs MiSeq, first-to-market is very powerful but will it last?

NGSプラットフォームの世界分布。45カ国650ラボで1800機の約70%稼働

Social Networked Learning

View more PowerPoint from gsiemens

□ Social networked learning in complex information environments
・複雑な情報環境におけるソーシャルネットワーク学習

>> bit.ly/xSFdof

Personalization and adaptive learning at a large scale.

What are the principles that influence education in open settings and social networks?
Learner autonomy
Self-organization
Transparent learning=teaching
Participatory pedagogy
Sensemaking artifacts
Shareable learning paths

□ Network Enabled Research: Maximise scale and connectivity, minimise friction

>> http://t.co/JMEV2xDn

For me, the risk of commercial enclosure is so much smaller than the risk of not building the right networks, or of creating fragmented incompatible networks, of ultimately not being able to solve the crises we face today in time to do any good, that the course of action is clear. Legal tools are useful to assure users of interoperability and their rights, otherwise they just become a source of friction. Social tools are a more viable route for encouraging desirable behavior.

□ DailyNewsGW:
Illumina Reports 4 Percent Revenue Decline for Q4; Rejects Roche Offer Again: read more bit.ly/AlfU72

Illumina reported after the close of the market Tuesday that its fourth-quarter revenues dropped 4 percent year over year, while issuing a separate statement once again rejecting Roche's offer to acquire the company for $44.50 per share, or $5.7 billion.

イルミナ社がロシュの買収案を再び拒否。Q4決算では見込み通りの減益。年度では17%増。Hiseq 2500の出荷もあるし、まだ譲歩するには甘いということか。

Illumina側のコメントは『株主は我々が独立した会社であることを望んでいる』として、買収提案には応じない姿勢を強調しているけれど、具体的な対抗策は講じてあるのかな？実際に現場や業界そのものに、今回のロシュの行動への風当たりが強く窺えるのも事実なので、それを受けての強気かも。

イルミナ社側も、今後2013年にはNIHからの資金調達が8%カットされる可能性があることを示唆しながら、ロシュに『不当な条件』と苦言を呈するなど、上手く牽制して立ち回っている印象。ロシュが主張している買収による遺伝子解析の医療診断・臨床への適応も、イルミナは単独で高成長の見込みとのこと。




□ rnomics:
Roche vs Illumina ? Round 2: Last week, Roche released a plan to take... bit.ly/AxFO9X #News #illumina #rna_sequencing #RNA-seq
Roche disappointed by the actions of Illumina, Inc.’s Board of Directors
>> http://www.roche.com/investors/ir_update/inv-update-2012-02-08b.htm




□ Life Tech Ships Over 700 Ion Torrent PGMs in 2011; Expects $60M Revenue Falloff for SOLiD in 2012

>> http://t.co/9RQykPrv

Life Tech's Genetic Systems division, which includes the Ion Torrent, SOLiD, and capillary electrophoresis platforms, booked $278 million in non-GAAP revenue for the quarter, a 13-percent increase over the year-ago quarter.

Life Tech社、Q4決算4%収益成長率。2012年度はProtonの出荷を控え強気。また、競合他社と足並みを揃えるように臨床分野に成長戦略。SOLiDプラットフォームでは大幅な売上高減衰を見込みながらも今後アップグレード予定。
今後PGM Sequencerは"small genomes"への利用を焦点に市場投入していくつもりらしいし、微生物メタゲノム分野での需要を視野に入れてるんだろうね。新車を買うかPGMを買うか。




□ Genaris Omics Club >> 『次世代シーケンサーの未来』

>> http://t.co/UKMqdqb3

"次世代シーケンサーの性能向上は今後鈍化する。上述の酵素利用技術が持つ欠点を解決する質的進化が起こることを期待"

俄然nanoporeシーケンサーのAGBT公開に胸熱。（チップ内の電位差のみを利用する技術）

>> Oxford Nanopore to present DNA 'strand sequencing' technology at AGBT conference
commercialise independently in 2012- http://www.nanoporetech.com/press_releases/detail/122

□ BioInfoLLC:
Oxford Nanopore to Commercialize DNA Strand Sequencing this Year; Illumina not Involved bit.ly/wjTSn2





(コノハズクのL4微生物群集における6年間に渡る永続性をカラースケールで示した図)

□ Defining seasonal marine microbial community dynamics

>> http://www.nature.com/ismej/journal/v6/n2/full/ismej2011107a.html

the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21?130 OTUs were identified by denoising the data.

The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

微生物群集のダイナミクス:季節変化の環境変数が細菌分類群内に強い相関。水流内サンプリング設計がラグランジュである複雑さに堅牢な手法。



□ EurekAlertAAAS:
Ocean microbe communities changing, but long-term environmental impact is unclear. eurekalert.org/e/4dh0



□ BioMedCentral:
Review: #Metagenomics - a guide from sampling to #data analysis ow.ly/8ZyWM #bioinformatics #genomics






□ A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

>> http://nar.oxfordjournals.org/content/early/2012/02/08/nar.gks063.full

古細菌のChIP-seqプロトコル。GaggleからRプログラム等に転送できるよ。

The Pique package, an open-source bioinformatics method, is presented for identification of binding events. Relative to ChIP-Chip and qPCR, this workflow offers a robust catalog of protein?DNA binding events with improved spatial resolution and significantly decreased cost. While this study focuses on the application of ChIP-seq in H. salinarum sp. NRC-1, our workflow can also be adapted for use in other archaea and bacteria with basic genetic tools.

□ The pique package is a high efficiency peak finder for ChIP-seq experiments. (peak calling application) https://github.com/ryneches/pique



□ dritoshi:

TFの ChIP-seq 解析でピークのほうを主役に考えて解析するツールがあるが、履き違えてると思う。あくまでも周辺遺伝子の転写を制御するのだから遺伝子が主役。peak を中心に考えて良いことはあまりに少ない。

□ Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation. http://aem.asm.org/content/78/4/1015.abstract




□ NCBI:
The NCBI Genome Remap service now has an API! 1.usa.gov/zgoQX6 #bioinformatics




□ synt_biology:
The Governance of Synthetic Biology bit.ly/Av9eaA via @addthis




□ euroepinomics:
When exome sequencing and incidental findings meets ethics - genomethics bit.ly/yNxRxB

Whole genome studies have the ability to produce enormous volumes of valuable data for individuals who take part in research. However, as a consequence of analysing all 20,000+ genes, whole genome studies unavoidably involve the discovery of health related information that may have actual clinical significance for the research participant. Some of this will be considered a ‘pertinent finding’, i.e. directly related to the phenotype under study (e.g. the child’s developmental disorder); some of this will be considered an ‘incidental or secondary finding’ in that it is not directly linked to the phenotype under study or the research question that the genomic researchers are trying to answer.

全ゲノム解析によって『偶発的な初見』を得られたときに生じる倫理課題。データ共有と患者の自主性の利害を両立する議論が急務




□ NatureRevGenet:
AOP highlight on using NGS to diagnose mitochondrial diseases (￡):bit.ly/vZgx71

A recent paper discussing the application of next-generation sequencing (NGS) to study mitochondrial disease illustrates the potential and challenges of using NGS in clinical diagnosis. A crucial aspect of the clinical setting is that the aim may be to diagnose a single affected individual with no family history of the disease.

□ sgivan:
BGI Develops BGI-BOX, a Cloud in a Box for Faster Analysis of Genomic Data via @genomeweb ow.ly/8VCu2
BGIのクラウドベースのゲノム解析プラットフォームBGI-BOX、バイオインフォマティクス分野での普及とデータ共有促進により低コスト化の狙い。 世界50箇所以上にターミナルサーバ構築を計画。




□ DailyNewsGW:
Affymetrix Q4 Revenues Drop 23 Percent; Misses Analysts' Estimates: read more bit.ly/wruSTp

The genetic analysis and clinical diagnostics business unit, meanwhile, is Affy's "most robust growth opportunities," and is projected to grow at least 20 percent in 2012, Witney said.The third business unit is life science reagents, which has seen mid-single digit growth and now makes up about 12 percent of product sales.

The company is "aggressively attacking market segments where our technologies bring significant value, such as clinical validation," Witney said in a statement. "In addition, we are pleased with the progress of our clinical program, particularly our CytoScan [research-use only] cytogenetics product."

Affymetrix Q4決算が23%下落と推定値を下回る。eBioscience社との契約履行の遅延が影響。今年は遺伝子解析と臨床診断市場における成長に強気。Rocheが焦るのはここか




□ Erika_Check:
More evidence against "widespread" RNA editing bit.ly/yiBplg (for background: bit.ly/pjoz4r)
Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ~767 million sequencing reads from poly(A)+, poly(A)－ and small RNA samples. We developed a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual.

We found 44 editing sites in microRNAs (miRNAs), suggesting a potential link between RNA editing and miRNA-mediated regulation. Our approach facilitates large-scale studies to profile and compare editomes across a wide range of samples.

□ sinanaral:
Big Data's Impact in the World: nyti.ms/w0XbV6. 1.5M additional data literate managers needed in the US alone. #digitalstrategy #oswc
Big Data・大規模情報って本質的に量的意味を表すものじゃなくて、処理系の制御可能性・可干渉性の単位との乖離の程度を示す。将来的にはBig DataはSmall Dataになるわけだけれど、その処理能力の限界はリソースの持続可能性の他、解析要員のロボ化などに依存していくのかも




□ Sagebio:
"Increased public access accelerates progress in science" CED report on research says it all bit.ly/ybblZk #openscience #OA

CED has released The Future of Taxpayer-Funded Research: Who Will Control Access to the Results? ? a new report that examines how scientific researchers and members of the public will access government-funded research in the expanding digital age.

Digital economy expert Elliot Maxwell, the author of The Future of Taxpayer-Funded Research, notes "public policy that increases access to taxpayer-funded research allows greater use of today's technologies to support more rapid scientific progress, more innovation, and higher economic growth."

□ yas_matsu:

デンマークのOpen Data blog.goo.ne.jp/eabus/e/92cad9…

Datakataloget http://data.digitaliser.dk/
Open Data, Open government Innovation of Denmark:
デンマーク政府のオープン・プラットフォーム戦略。
法律立案、エネルギー使用分布解析などに民間公募のアプリが稼働



□ usdatagov:
@digiphile Agreed--more #opendata=good: +45K new geo datasets last week, +80 to Business.Data.gov, +156 new raw data this year #opengov
...more non-GIS #opendata in Health http://1.usa.gov/zbUCrM and Education http://1.usa.gov/ysFUP9 #opengov



□ eqpaho:
Bridging Technology and Sustainable Development - US Rio+2.0 Conference bit.ly/z0uxUE




□ uurquiza:
New England Biolabs Signs Agreement with Synthetic Genomics Inc. to Launch Gibson Assembly(TM) for synbio applications bit.ly/y9HPRt

"The Gibson Assembly method is a powerful tool that we believe will enable synthetic biology researchers to make rapid advances leading to new discoveries and products," said J. Craig Venter, Ph.D., Founder and CEO, SGI. "SGI is pleased to work with industry leader NEB in commercializing this product."

The Gibson Assembly Master Mix includes protocols for primer design, and can be used for assembly of multiple DNA fragments, including linearized vector and insert. For more information about the Gibson Assembly Master Mix, visit www.neb.com/gibsonassembly

合成生物学のDNA構築物設計ツール、『ギブソン・アセンブリ』のライセンスが、Synthetic Genomics社からNEBに供与。MasterMixとして、DNA断片の結合技術により広汎な可用性を提供。近年NEBは日本法人も設立したばかりだし、アライアンスによる市場リーチに着目。




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