lens, align.

Lang ist Die Zeit, es ereignet sich aber Das Wahre.

Andain / "You Once Told Me"

2012-09-30 12:14:20 | music12
Yotm



□ Andain / "You Once Told Me"

♪ <script type="text/javascript" src="http://mediaplayer.yahoo.com/js"></script>You Once Told Me
After
Forget Your Face

Release Date; 24/09/2012
Label; Black Hole
Cat.No.; none
Format: iTunes LP

>> http://www.facebook.com/andainofficial

>> tracklisting.

01. Turn Up the Sound
02. Like
03. Much Too Much?
04. Ave Maria
05. Promises?
06. After
07. What It's Like
08. Forget Your Face??
09. Find Your Way
10. You Once Told Me
11. Taken Away
12. Summer Calling
13. Beautiful Things (Gabriel & Dresden's Unplugged Mix)
14. Promises (KOAN Sound Remix)
15. Promises (Jaytech Remix)
16. Much Too Much (Zetandel Chill Remix)
17. Much Too Much (Rido Remix)
18. Turn Up the Sound (Gabriel & Dresden Remix)
19. Turn Up the Sound (Stratus Remix)


?Video
??"Promises"
??"Much Too Much"?
??"Turn Up the Sound"



All songs written and produced by Josh Gabriel and Mavie Marcos.
Additional writing by Dave Dresden on tracks 1?3, 5?9, and 11, 13
David Penner on tracks 4, 5 and 10, 12, 13





2000年代初期のEDMシーン黎明期に雷名を轟かせたエレクトロニカ・ダンス・ユニット、Andainが、デビューから凡そ10年目にして解き放つ1st Album。

このブログの設立時にも幾度となく紹介してきた、私にとってもクラブシーンにとっても、おそらく最もリスペクトされた最重要のアーティストでありながら、幻と消えたデビューアルバム、活動休止や再結成、解散を繰り返すなど、紆余曲折を経て伝説となりかけていた。

そんなAndainが2011年、新曲"Promises"を引っさげてターンバックしてきた時の界隈の衝撃と賑わいは、今も記憶に鮮明だ。



2000年代前半にかけて、"Summer Calling"、"Beautiful Things"など、フックの効いたメロディと可憐なヴォーカルがダンス要素の逸材として重用され、主にそのリミックス・タイトルがTiestoなどの主要プレーヤーによって世界のクラブシーンを席巻。


さらにJosh Gabriel自らがGabriel & Dresden名義で発表した"Bloom"に収録した、AndainとしてカヴァーしたDepeche Modeの"Here is the House (Gabriel & Dresden Remix)"がリスナーから好評価を獲得。今は幻となりつつある超名リミックスだが、Andainは確実にクラブ・レジェンドへのステップを踏みながらファン層を広げつつあった、だが、その珠玉のリミックスの題材となった『原曲』への評価については、いや、その存在すら、あまり顧みられて来なかったのだと思う。



当時、シンガーのMavie Marcosは米国代替医療の名門バスティーユ大学で薬学を専攻し、幼いころからクラシック音楽の教育も受け、実演経験も重ねた、まさに才媛と呼ぶに相応しい存在だった。

同じくJosh Gabrielによって才能を見出されたマルチ・インストルゥメンタリストのDavid Pennerは、MITで宇宙航法学を学ぶ天才。現在は学位を取得し、Andainとしての活動からは身を退いているが、このアルバムの幾つかの曲にクレジットされている。



"You Once Told Me"は、表題曲も含め過去にお蔵入りとなったアルバムから数曲をサルベージして大幅にリメイクを行っているものの、大部分は新曲が占める"Reboot"された作品であり、同時にAndainとしての特徴である、耳に残るメロディセンス、ヴォーカル・コラージュ、遊び心に溢れたパーカッション・プログラミング、そして可憐なパフォーマンスには不釣り合いと言えるほどの、ロックスタイルに通じる骨太なベースラインは、Andainが未だ無二の存在感を放つカリスマであることを如実に代弁している。



"Ave Maria"からは原曲にあった合唱サンプリングは省かれてしまったものの、"You Once Told Me"と双璧を為すスタイリッシュなエレクトロ・ヴォーカル作品として息を吹き返しており、当世風のサウンド・コンストラクションによって、よりクールな輪郭を引き締めている。


"Promises"、及び"Taken Away"で聴かれる自作オルゴールの音色や、"Turn Up The Sound"のラーガ調のイントロからパーカス、2000年代同期の北欧Trip Hopを彷彿とさせる"Like"、ニューエイジ色の強い頃のMylène Farmerもかくや、と思わせる"Fordet Your Face"などの変化球にも富んでいる。



EDMというシーン自体の先駆けであったAndainが自ら原点に立ち返り、こうした手作り感を漂わせる、よりアナログでオーガニックな触感の作品を10年目の今にして世に出すことは、未だ代わり映えしない『環の端無きが如し』のようなElectronica/Clubシーンにとり、実際にJosh Gabrielはその前線に身を置いているわけだが、実にポジティブな意味を付与するものでもあると受け止められる。



このアルバムにも、ボーナストラックとしてシーンの主要DJたちが素晴らしいリミックスを提供している。"Turn up the Sound (Gabriel & Dresden)"の終盤におけるビート・プログラミングは、"Here is the House"のそれの印象を喚起する懐かしささえあり、このようなリミックスワークに素晴らしい『素材』を提供するAndainとクラブシーンの関係性は、それ自体がシーンから産み落とされたものであるという点において、あたかもリ・プロダクションの入れ子構造を、プロダクトそのもので体現しているようにも見える。



ともあれ、"You Once Told Me"は、往時のTrip Hopの薫り漂うセンチメンタルな気色に溢れた作品であり、Mavie Marcosの湿った感傷性と、Josh Gabrielの乾いた情緒という正反対の要素が、この上なく見事に配合された会心の一作と言えよう。切ない恋心や凛とした心情を謳った、脆いようで芯の通ったセピアのアルバム。胸を締め付ける秋の夜長に、隣に添えておきたい一枚となりそうだ。




********************************************************************************

"You Once Told Me"

You once told me I wouldn't know it enough
Well, let me tell you something Yeah, I do
You once told me I wouldn't feel it enough
Well, let me tell you Baby, I do

Sometimes I find myself in a scene in a dream that's so far away
Sometimes ah, Tell me what's happened to me


Sometimes I see myself falling
Well I don't show it much
Sometimes I'm crazy for you
Well, maybe I'm fine And tell me you're mine but


Tell me, baby, can you hold me now?
You don't have to say it-I feel it, too
maybe I'm falling well maybe but I don't show it much

Tell me, baby can you see me now
and Show me baby
that I don't know how and how
Can I start to see inside the fall but







Article_Sep.2 - β

2012-09-16 10:34:14 | Science News
Eccb12


□ ECCB'12 - the European Conference on Computational Biology 2012 (9-12.Sep)

>> http://www.eccb12.org/  #ECCB12 #uniprot10

ECCB'12 - the European Conference on Computational Biology - is the key European computational biology event in 2012 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, biology, medicine, and systems biology. ECCB'12 will take place 9.-12. September 2012 at the Congress Center Basel, Switzerland.

Participation at ECCB'12 will be the prime opportunity to learn about cutting-edge research in computational biology and bioinformatics and to network with other members of our community. ECCB'12 will be organized in association with the 10th [BC]2 Basel Computational Biology conference - the annual scientific symposium of the SIB Swiss Institute of Bioinformatics.




ECCB12:
#eccb12 conference proceedings papers released as open access special issue at Oxford University Press Bioinformatics http://bioinformatics.oxfordjournals.org/content/28/18.toc



ECCB12:
Download the #eccb12 conference app for your iPhone / iPad to plan your personal conference program (Android soon too) http://eccb12.org/app



□ Chris Sander: Protein 3D Structure Computed from Evolutionary Sequence Variation:

>> http://www.plosone.org/article/info:doi/10.1371/journal.pone.0028766

The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7?4.8 Å Cα-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.



□ EVfold: http://evfold.org #ECCB12

Evolutionary Constraints:
Calculate correlated amino acid changes in protein families across evolution.
Use evolutionary couplings as distance constraints to predict 3D structure.



compbiobryan:
@razoralign Yeah, it's a great method. Be sure to see the sine qua non underlying contact predictor too: "Direct-coupling analysis of residue coevolution captures native contacts across many protein families." http://www.ncbi.nlm.nih.gov/pubmed/22106262





Biovis


GigaScience:
K Neiselt in Bioimaging session presenting on visual eQTL analytics. Some of this from the BioVis challenge: http://www.biomedcentral.com/1471-2105/13/S8/S8/abstract … #ECCB12




Bioxsd


□ BioXSD ? the XML schema for basic bioinformatics data:

>> http://t.co/eb6ipnc4

BioXSD has been developed to fill the niche of missing canonical XML schema-based exchange format for basic bioinformatics data: sequences, alignments, features, references to resources, and identifiers. The canonical format can either be consumed and produced by tools directly, or serve as an intermediate format that the other formats can losslessly be serialized to and from.

バイオインフォマティクス・データに不足している正規なXMLスキーマベース(配列・アラインメント・リソース参照・識別子など)を補完




Ngslogistics


□ NGS-logistics: data infrastructure for efficient analysis of NGS sequence variants

>> http://cdn.f1000.com/posters/docs/250830577

The main goal of NGS-Logis,cs is to deliver processed NGS data to end users. We offer several modules, which each cover one aspect of analysis, either towards research or diagnos,cs. Complexity of algorithms, queries and data structure are covered by a user-friendly web based interface. The structure of NGS-Logis,cs is designed to cover any type of samples. With NGS- Logis,cs you can easily define a data set, assign samples to that data set and make it accessible to authorized researchers.





□ GigaScience:
Edouard Pauwels next on identifying chemogenomic features from drug-target interaction networks (with a focus on interpretability) #eccb12




GenomicsIo:
#eccb12 Denis Noble & Christoph Denot "It's the proportions that matter not the absolutes - both in music and biology"


#eccb12 IBM targeting the pub security market with Watson - visions of a future of total surveillance made possible by cognitive computing





ISMBECCB:
Are you sad to leave #ECCB12? Us too. However, we have a new look. Time to get excited for ISMB/ECCB 2013 in Berlin! http://bit.ly/RRKfaT




F1000Research:
We’ve had 20 poster submissions already from #eccb12 Why not share yours as well? View & submit #Posters here http://ht.ly/dEOCL




Brainatlas


appliedgenomics:
V. excited about Allen human brain atlas. Not excited another "Rosetta stone" ref. Guardian: http://www.guardian.co.uk/science/2012/sep/19/scientists-create-atlas-of-human-brain …. Abs: http://www.nature.com/nature/journal/v489/n7416/full/nature11405.html





illumina:
Introducing TruSeq Stranded mRNA & Total RNA Sample Prep kits for superior data quality, even from FFPE smpls. http://bit.ly/SXBcrC




EurekAlertAAAS:
BGI Tech develops whole exome sequencing analysis of FFPE DNA samples to boost biomedicine : http://eurekalert.org/e/4qws




Chicken_embryo


the_Node:
Vincent Pasque's developmental biology images were among the winners of this year's Wellcome Image Awards. http://fb.me/1h2cTyMEH




Fretmatrx


□ FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids

>> http://nar.oxfordjournals.org/content/early/2012/09/11/nar.gks856.full

a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base?base FRET).

These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.

核酸内のフェルスター共鳴エネルギー転移ナノダイナミクスの解析および設計ソフト




□ Transcriptome Sequencing ? U.S. Army RFQ:

>> https://www.fbo.gov/?s=opportunity&mode=form&id=719a4dd675ae7d5e8dc6351544b24674&tab=core&_cview=0

This is a Request for Quote (RFQ). This procurement is conducted unrestricted with full and open competition, open to both large and small businesses. The associated North American Industry Classification System (NAICS) code for the procurement is 541380 and the Small Business size standard is $12.0 Million.

The US Army Corps of Engineers, Engineer Research and Development Center Contracting Office, has a requirement for contractor support to assess the chemical stress effects of munitions constituents (MCs) and intensive munitions (IMs) on global gene expression networks in highly sensitive Leopard Frog tadpoles of the species Rana pipien.

アメリカ陸軍工兵隊による軍需的トランスクリプトーム見積依頼。 ある種のオタマジャクシのグローバル遺伝子発現ネットワークと、軍需品の化学的ストレス影響評価




□ Complete Genomics to be bought by Chinese firm for $117.6 million:

>> http://mobile.reuters.com/article/idUSBRE88G0LP20120917?irpc=932


bioitworld:
BGI acquires Complete Genomics ($GNOM) for $3.15/share (last close $2.67). Deal worth $117M. Move into clinical genomics space continues.


DailyNewsGW:
Complete Genomics, BGI Agree to $117.6M Merger http://bit.ly/Uf45gU

Complete GenomicsとBGIの合併については、個人的に思う所アリアリなのだけど、初夏の人員削減からハプロタイピングにおける『LFR技術』論文(株価を50%改善)、高精度の解析。アジア太平洋地域で締結したばかりの代理店供給が、BGIに統括されて水準を保てるかどうか




□ siRNA as a tool to delineate pathway channelization in H2O2 induced apoptosis of primary Leydig cells in vitro:

>> http://www.springerlink.com/content/h3n42w780245618m/




ENCODE_NIH:
Annotation of functional variants: RegulomeDB http://genome.cshlp.org/content/22/9/1790 … #ENCODE




caseybergman:
Many parallels btwn. computational biologists & "data scientists" (http://bit.ly/Pr05qI ) >> #bioinformatics is good training for "sexy" jobs




Chem_Central:
New software in #JCheminf 'OMG: open molecule generator' http://goo.gl/vf9t4 #cheminformatics




PaulLikeMe:
Medicine 2.0 takes Harvard Medical School by Storm http://soc.li/Cjn6WXc




BiologyOpen:
BiO has passed the scientific and technical evaluation stages for inclusion in PMC and PubMed. Contracts to sign... http://fb.me/29y8AjCL0




□ Efficient experimental design and analysis strategies: DESeq algorithm performs more conservatively than edgeR & NBPSeq

>> http://www.biomedcentral.com/1471-2164/13/484/abstract




moorejh:
Big #science, #bigdata, and a big role for biomedical #informatics JAMIA special issue http://jamia.bmj.com/content/19/e1/e1.full … #bioinformatics #datascience





□ PBL awarded two US patents on RNAi: US Patent No. 8,258,285. / No. 8,263,569:

>> http://www.bionity.com/en/news/139697/pbl-awarded-two-us-patents-on-rnai.html?WT.mc_id=ca0067




Bayesianpredict


TrendsCognSci:
Do you think that probabilistic, Bayesian, and optimal computation are synonyms? If yes, you must read this TiCS review http://bit.ly/RQjZO8

Probability has played a central role in models of perception for more than a century, but a look at probabilistic concepts in the literature raises many questions. Is being Bayesian the same as being optimal? Are recent Bayesian models fundamentally different from classic signal detection theory models? Do findings of near-optimal inference provide evidence that neurons compute with probability distributions? This review aims to disentangle these concepts and to classify empirical evidence accordingly.





Cenpk


□ A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

>> http://nar.oxfordjournals.org/content/early/2012/09/08/nar.gks804.full

Here, we asses the influence of genetic variation on the estimation of gene expression level using three different aligners for read-mapping (Gsnap, Stampy and TopHat) on S288c genome, the capabilities of five different statistical methods to detect differential gene expression (baySeq, Cuffdiff, DESeq, edgeR and NOISeq) and we explored the consistency between RNA-seq analysis using reference genome and de novo assembly approach. High reproducibility among biological replicates (correlation ?0.99) and high consistency between the two platforms for analysis of gene expression levels (correlation ?0.91) are reported.







c_z:
My latest upload : Systems Bioinformatics Workshop 2012 on @slideshare http://www.slideshare.net/keiono/systems-bioinformatics-workshop-2012




□ RNA-Seq analsys: FIMM - Institute for Molecular Medicine Finland (CSC - June, 2010) http://www.slideserve.com/oni/rna-seq-analysis




Reliancewf


□ ReLiance: a machine learning and literature-based prioritization of receptor?ligand pairings

>> http://homes.esat.k

bright summer lingers.

2012-09-09 21:25:32 | music12
Mirroredeye_2
(iPhone 4S; Camera; Instagram.)


あなたの瞳の色をした空に吸い込まれそうだった。
どんな景色を眺めていても、
隣にあなたの姿を映している。
雨上がりのような、澄んだ眼差しが好き。
おやすみ。



□ tunes of the day.

□ Patric O'Hearn / "Transitions"

♪ <script type="text/javascript" src="http://mediaplayer.yahoo.com/js"></script>Reaching Land


□ Suncatcher

Shoreline




Summercollide



□ Keith Kenniff / "Branches"

Branch







Article_Sep.1 / Aug.2-β

2012-09-01 09:02:17 | Science News
Rnaflux


□ RNA-seq Flux simulator: Modelling & Simulating generic RNA-Seq:

>> http://flux.sammeth.net/simulator.html
>> http://nar.oxfordjournals.org/content/early/2012/09/07/nar.gks666.full

Our models are implemented in a computer simulation pipeline called the Flux Simulator, and we show that read distributions generated by different combinations of these models reproduce well corresponding evidence obtained from the corresponding experimental setups. We further demonstrate that our in silico RNA-Seq provides insights about hidden precursors that determine the final configuration of reads along gene bodies

RNA加水分解の断片化予測分布パラメータによる解析モジュール。複数シーケンシング・プラットフォームに適用可能




Encode_screenshot



□ The ENCODE project: lessons for scientific publication

>> http://www.genomesunzipped.org/2012/09/the-encode-project-lessons-for-scientific-publication.php
>> http://www.nature.com/encode/#/threads/characterization-of-intergenic-regions-and-gene-definition

The ENCODE Project has this week released the results of its massive foray into exploring the function of the non-protein-coding regions of the human genome. This is a tremendous scientific achievement, and is receiving plenty of well-deserved press coverage; for particularly thorough summaries see Ed Yong’s excellent post at Discover and Brendan Maher at Nature.



Encodefeaturegraphic


□ What’s next for ENCODE?

>> http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312


□ Nature Encode (iPad app)

>> http://itun.es/i6DT65k

Nature EncodeのiPad app、帰宅して弄り倒してるけど面白い。記事の関連性や、研究の体系が直感的に連関した構成で読み応えある。でもinfographic系は苦手w





emblebi:
I liked a @YouTube video http://youtu.be/KiwXtHRfBC8?a ENCODE: Encyclopedia of DNA Elements

Ewan Birney of EMBL-EBI, Tim Hubbard of the Wellcome Trust Sanger Institute and Roderic Guigo of CRG talk about ENCODE, an international project which revealed that much of what has been called 'junk DNA' in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes.





□ ENCODE計画: ヒトゲノムのガイドブック: ENCODE計画の成果を印刷版とオンラインで紹介

>> http://www.natureasia.com/ja-jp/nature/highlights/38750

ENCODE(Encyclopedia of DNA Elements;DNAエレメントの百科事典)計画は、ヒトゲノム中にコードされているすべての機能エレメントについて記述することを目的とするものである。ENCODEが開始されてから9年が経ち、その主な成果は今回30本の共同研究論文として発表されて、計画は完結した。





appistry:
ENCODE project global collaboration that wrangled more than 15 TB of genetic data from 32 labs globally http://goo.gl/frKcx #bigdata

Big data and DNA: What business can learn from junk genes



□ GENCODE: The reference human genome annotation for The ENCODE Project http://genome.cshlp.org/content/22/9/1760.full


genomeresearch:
ENCODE data integration on a massive scale requires new methods and guidelines http://genome.org


http://itunes.apple.com/app/id553487333 RT @elisadonnard: Downloaded the ENCODE App! :)


mark_g_vero:
http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312 … ENCODE phase has come to a close, signalled by publication of 30 papers, in Nature, Genome Research...




simplystats:
The discussions generated by #ENCODE motivated this: Top down versus bottom up science: data analysis edition http://tmblr.co/ZFlMwwSxoN3i




Modencode


genomeresearch:
ChIP-seq #ENCODE style http://tinyurl.com/d9duuwq

Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals.




dnanexus:
Full ENCODE article on @genomeresearch: Revealing remarkable chromatin diversity @ regulatory elements. http://genome.cshlp.org/content/22/9/1735.full

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements




cshperspectives:
Should we re-define the gene? http://bit.ly/OXMxTs http://bit.ly/Q0HovP #ENCODE




ewanbirney:
Good Economist write up on #ENCODE. http://www.economist.com/node/21562186

A long-term effort to catalogue all the bits of the human genome that do something has released its results




WSJJapan:
「ヒトゲノムのほぼ80%の領域に生化学的機能があるとの発見」――。複雑な連関もあるようで、遺伝子研究がワンステップ上がった印象です。(YS)→遺伝子の砂漠、活動に満ちていた-プロジェクトで判明 http://on.wsj.com/ORyxKI





dgmacarthur:
Fantastic post by Sean Eddy on what ENCODE's results actually mean: http://selab.janelia.org/people/eddys/blog/?p=683




□ Spark for ENCODE data: A navigational paradigm for genomic data exploration:

>> http://genome.cshlp.org/content/early/2012/09/07/gr.140665.112.abstract




□ De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells : http://m.pnas.org/content/early/2012/08/31/1203831109.full.pdf




Systemflowanalyze



□ RNA-seq Coverage Effects on Biological Pathways and GO Tag Clouds

>> http://www.aporc.org/ISB/2012/Proceedings/Papers/ISB2012F41.pdf

Two functional annotation methods for clustered gene groups including biological pathways and GO terms were employed in this study. A biological pathway is one of the most meaningful clustering representations for biological function analysis.

Another functional annotation method often applied to describe gene products is Gene Ontology (GO). The GO is a set of structured vocabularies defined by Gene Ontology Consortium [10], which is aimed to provide a universal standard of functional annotation for gene products.

複数データセットでの差動発現解析の為の生物学的経路と遺伝子オントロジー・アノテーションの統合ワークフロー。

生物学的経路(KEGG)と遺伝子オントロジー(GO)を含むクラスタ化された2つの機能アノテーション・メソッド。RNA-seqのカバレッジ情報を統合し、シーケンシング時点のDEG発現及び変異株のダイナミック・ステータスを明示。従来は見落とされていた分析リソースにもアプローチする

そういえばMEDALSにもKaPPA-View4という代謝経路データベースがあり(略


バイオインフォマティクスにおいても、オミクスデータ由来の自動化された"hypothesis bulider"みたいなコミュニティベースの共有型プラットフォームを実現する場合、複数データセットのカバレッジ・アノテーションの統合・評価メソッドはもっと重要になっていくのだろうな。




neilfws:
Prokaryotes do it too: CRISPR, an RNA-based adaptive immune system in UniProt release 2012_08 http://bit.ly/NdkUaw

The new Genomics Laboratory is a central hub for global molecular DNA work for all Hendrix Genetics divisions, and is already producing new innovations in breeding.

Blood and tissue samples are taken from the pig, poultry and aquaculture divisions, and also from customers' stocks. Samples are then transported to the laboratory, where DNA is extracted and stored in a BioBank.

After in-house analysis and genotyping, geneticists use these to develop breeding programmes.





□ CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis: AJAX-based web browser http://bioinformatics.oxfordjournals.org/content/28/18/2382.short?rss=1




Genomicswatch:
Hendrix launches new genomics centre - FarmersWeekly http://bit.ly/Qth4tJ




pathogenomenick:
Assemblage: tools for working with 2nd-gen assemblies, fasta, etc. https://github.com/sujaikumar/assemblage




□ Fluctuation tolerant read scheme for ultrafast DNA sequencing with nanopore device: ナノポアデバイスの回路スキーマ。従来のDNAシーケンサより6桁速い。 http://ieeexplore.ieee.org/xpl/articleDetails.jsp?reload=true&arnumber=6271754




□ BIoHAckathon 2012.

□ HyQue Architecture:

>> http://semanticscience.org/projects/hyque/index.html

evaluating scientific hypotheses about molecular event in the context of the galactose gene network



dbcls:
Michel Dumontier Knowledge Discovery using an Integrated Semantic Web ( #BH12 live at http://ustre.am/C6Wz )

dbcls:
The BioHackathon2012 symposium will start at 9:30 JST ( #BH12 live at http://ustre.am/C6Wz )



□ EnvO:

>> http://environmentontology.org/

A community Ontology tool for semantically controlled environmental description. annotation of any organism or biological samles...




□ BioInterchange: automatically creates RDF from TSV, XML etc…: Ruby code for generating RDF, potentially from GTF/GFF http://www.biointerchange.org






jervenbolleman:
#BH12 my slides of real complex #SPARQL queries in #bio using multiple datasources using SERVICE keyword @slideshare http://www.slideshare.net/jervenbolleman/uni-protsparqlcloud




fstrozzi:
#BH12 G-project speech recognition + AI engine.Talk to your computer to query biological semweb databases.Outstanding! https://github.com/dbcls/bh12/wiki/G-language-project




mbeisen:
outstanding clinical dissection of ENCODE claims by @TRyanGregory http://www.genomicron.evolverzone.com/2012/09/encode-2012-vs-comings-1972/ ”ENCODE (2012) vs. Comings (1972)."




Forestry_2


TheICF:
Free review article from Forestry: Boreal forest soil carbon: distribution, function and modelling http://forestry.oxfordjournals.org/content/85/2/161.full?sid=5a9df926-f6d7-4f97-9779-ffb8980e0be6 … @OxfordJournals

In this review, we address these issues through a discussion of the size and character of boreal forest soil C pool, its role in ecosystem function, the potential impacts of climate change on soil C, efforts to model these processes and the role of soil C in boreal resilience to the impacts of climate change. Soil C is fundamental to ecosystem function in terms of improving soil physical properties, increasing soil biotic activity and enhancing insulation all of which improve site productivity.





Gasic


□ GASiC: Genome Abundance Similarity Correction:

>> http://sourceforge.net/projects/gasic/
>> http://nar.oxfordjournals.org/content/early/2012/08/30/nar.gks803.full

Genome Abundance Similarity Correction (GASiC), a method to estimate true genome abundances via read alignment by considering reference genome similarities in a non-negative LASSO approach. We demonstrate GASiC’s superior performance over existing methods on simulated benchmark data as well as on real data. In addition, we present applications to datasets of both bacterial DNA and viral RNA source. We further discuss our approach as an alternative to PCR-based DNA quantification.

メタゲノム資源量推定と生物種レベル診断テスト、非負値Lassoアプローチによる参照ゲノム配列の類似性を考慮したアラインメントから存在量を推定




□ An automated framework for hypotheses generation using literature:

>> http://www.biodatamining.org/content/pdf/1756-0381-5-13.pdf

The proposed HGF shares similar end goals like the SWAN but are more holistic in nature and was designed and implemented using scalable and efficient computational models of disease-disease interaction. The integration of mapping ontologies with latent semantic analysis is critical in capturing domain specific direct and indirect “crisp” associations, and making assertions about entities (such as disease X is associated with a set of factors Z).

文献ベース仮説生成自動化フレームワーク。潜在意味解析とマッピングオントロジー統合。疾患相互作用の計算設計




Ssrnai


□ Isis Pharm. Demonstrates The Potential Of Single-Stranded RNA-Like Antisense Technology To Activate The RNAi Pathway:

>> http://ir.isispharm.com/phoenix.zhtml?c=222170&p=irol-newsArticle&ID=1730310
>> http://www.sciencedirect.com/science/article/pii/S0092867412010094

Isis Pharmaceuticals, Inc. (NASDAQ: ISIS) announced today the publication of two papers in the journal Cell demonstrating that single-stranded short interfering RNA (ss-siRNA) molecules distributed broadly, activated the RNA interference (RNAi) pathway and reduced