□ Johann Johannsson [KCRW Live & Interview]
>> http://t.co/NTbnovIx
Icelandic pianist Jóhann Jóhannsson composes a range of elegant music from minimalist to baroque with cinematic overtones. We're excited to broadcast a live session in which he's joined by a string quartet on Morning Becomes Eclectic
Johann Johannssonのセッションがオンエア。『科学史三部作』の最終作はウィニペグ音楽祭の委嘱曲"A Prayer to the Dynamo"
□ Guy Laramee
□ OxfordJNLsJapan:
書籍の彫刻。書籍タイトルとアートのテーマがマッチしていて芸が細かいです。 ow.ly/8W5m1
>> http://japan.digitaldj-network.com/archives/51950751.html
□ Everything is a Remix Part 4: System Failure & Social Evolution
Our system of law doesn't acknowledge the derivative nature of creativity. Instead, ideas are regarded as property, as unique and original lots with distinct boundaries. But ideas aren't so tidy. They're layered, they’re interwoven, they're tangled. And when the system conflicts with the reality... the system starts to fail.
□ Wolfram Alpha Pro democratizes data analysis: could this shape the future of SaaS?
>> http://t.co/DwhvNlFe
Regular users may not have had much reason to dig into the service before now, but the ability to bring the entire brunt of Wolfram Alpha's computational engine on any arbitrary piece of data democratizes the idea of statistical analysis.
□ bioontology:
RT @nopiedra: Linking Earth & Climate Science #Semantic Search Supporting Investigation of #ClimateChange vsb.li/FgmhH2 #linkeddata
>> http://t.co/xIsgBv8s [PDF]
Linking Earth and Climate Science: Semantic Search Supporting Investigation of Climate Change
In this paper, we focus on the data in Earth and Climate Sciences and on the use of ontologies to facilitate search and integration of this data. Mercury, developed at Oak Ridge National Laboratory, is a tool for distributed metadata harvesting, search and retrieval. Mercury currently provides uniform access to more than 100,000 metadata records; 30,000 scientists use it each month.
We augmented search in Mercury with ontologies, such as the ontologies in the Semantic Web for Earth and Environmental Terminology (SWEET) collection. We use BioPortal, developed at Stanford University, as an infrastructure to store and access ontologies. We use BioPortal REST services to enable faceted search based on the structure of the ontologies, and to improve the accuracy of user queries.
気候変動調査のセマンティック検索『SWEET』。バイオポータルRESTを使用しクエリ精度を向上。NASAマーキュリーベースでバイオポータル呼び出し→オントロジー接続という離れ業。連邦規格を含め『ダーウィン・コア』など複数のMetadataをサポート。Webでの提供はW3C勧告非準拠
□ Obama's FY 2013: Fund for NIH remained flat at $31 billion
>> http://t.co/QPHUMKLD (Washington Watch)
Obama Budget: No Big Dollars for Health
Funding for the National Institutes of Health (NIH) remained flat at $31 billion. NIH director Francis Collins, MD, said the administration's decision not to cut NIH funding significantly reflects its "priority for biomedical research as an investment that promises to deliver better health and drive economic growth."
The budget request will enable NIH to support 9,415 new and competing research project grants, an 8% increase over the number of grants the agency is expected to award in fiscal 2012, Collins said in a statement.
オバマ政権2013年度予算教書。医療・保健関連予算に増加無し。NIHも横ばいで310億ドルを計上。方々に出資し競合している臨床ゲノミクス市場戦略を控えて心許ない気も…
□ DailyNewsGW:
DNAnexus Developing NGS Workflows with Geisinger, UCSF: bit.ly/A427aH
As part of the deals, laboratories at Geisinger and UCSF will leverage DNAnexus' cloud-based software platform to upload, store, and analyze sequencing data. Additionally, in conjunction with the Geisinger Clinical Program for Whole Genome Sequencing, Geisinger will be able to access DNAnexus' genomic data management capabilities, such as visualization, analysis, and storage.
DNAnexusとGeisingerが臨床ゲノミクス・ワークフロー開発で提携。契約金は非開示。当然DNAnexusにはGoogleと開発中の巨大DNAストレージも絡んでくるし、UCSF自体がゲノム・アプリ開発で先行。競合他社より頭一つ抜きん出そう
□ rnomics:
Life Technologies weighs in on Roche ? Illumina Deal: Last week an... bit.ly/AejuV0 #News #illumina #life_technologies #RNA-seq
Life Technologies社がロシュ社のイルミナ買収問題に対することで、顧客に懸念を表明するようなメールを送ってるらしい。
□ Illumina Array Customers 'Apprehensive' of Possible Roche Takeover, Fear Platform 'Stagnation'
>> http://t.co/hRt2fPdX
"Overall I think an acquisition of Illumina by Roche would be a very bad thing," said one such core lab director."They took over NimbleGen and ultimately hurt them ? our representation went from bad to worse," the director said of Roche."They took over 454 and have done nothing to push the platform along," the director said.
匿名コメント読む限り、ロシュのNimbleGen引継ぎはアレだったのか。
"Right now the Illumina management seems to have a good strategy," the director continued."They've made their share of decisions that have messed us up ? they are constantly discontinuing array products ? but overall Illumina seems to have good direction," the director said.
コアラボ・ディレクターの市場観を代弁する一言 "Illumina became the leaders in this space without Roche and would like to see them remain on their own."
□ dnatimes:
Life Programming Software - need for a virtual world for testing? My vote.... ... anyone that relies on someone else… plus.google.com/10684110936075…
□ ayrrisbio:
Interesting study from Singapore investigates the epigenome using Next-generation sequencing 1.usa.gov/yad1o4 /via @NEBioLabs
The recent developments of third generation sequencing technologies have shown promising results of directly sequencing methylated nucleotides and having the ability to differentiate between 5-methylcytosine and 5-hydroxymethylcytosine.
第3世代シーケンシングの鍵はメチル化ヌクレオチドの直接解析と、5-メチルシトシン及び5-ヒドロキシメチルシトシンの判別能力？
□ ART: a next-generation sequencing read simulator
>> http://www.niehs.nih.gov/research/resources/software/art/
>> http://t.co/HzXtGDtD
ART is a set of simulation tools that generate synthetic next-generation sequencing reads. ART generates simulated sequencing reads by emulating the sequencing process with built-in, technology-specific read error models and base quality value profiles parameterized empirically in large sequencing datasets. We currently support all three major commercial next-generation sequencing platforms: Roche's 454, Illumina's Solexa and Applied Biosystems' SOLiD. ART also allows the flexibility to use customized read error model parameters and quality profiles.
□ NONCODE v3.0: integrative annotation of long noncoding RNAs
>> http://www.noncode.org/NONCODERv3/
we have updated the NONCODE database (http://www.noncode.org) to version 3.0 to include the first integrated collection of expression and functional lncRNA data obtained from re-annotated microarray studies in a single database. NONCODE has a user-friendly interface with a variety of search or browse options, a local Genome Browser for visualization and a BLAST server for sequence-alignment search. In addition, NONCODE provides a platform for the ongoing collation of ncRNAs reported in the literature. All data in NONCODE are open to users, and can be downloaded through the website or obtained through the SOAP API and DAS services.
□ BiologIT:
Mytoe: Automatic analysis of mitochondrial dynamics.: Publication Date: 2012 Feb 9 PMID: 22321700Authors: Lihava..
>> http://www.ncbi.nlm.nih.gov/pubmed/22321700?dopt=Abstract
We present Mytoe, a tool for analyzing mitochondrial morphology and dynamics from fluorescence microscope images. The tool provides automated quantitative analysis of mitochondrial motion by optical flow estimation and of morphology by segmentation of individual branches of the network-like structure of the organelles. Mytoe quantifies several features of individual branches, such as length, tortuosity, and speed, and of the macroscopic structure, such as mitochondrial area and degree of clustering.
□ egonwillighagen:
Fwd: BridgeDB and Semantic Web for the Life Sciences bit.ly/zcGpyX
>> http://www.bridgedb.org/
BridgeDB was recently published (doi:10.1186/1471-2105-11-5) and is a combination of Open Source, a web services, and Creative Commons-licensed mapping data, that links many bio- and cheminformatics related databases.
□ Trends_Ecol_Evo:
Unobserved phenotypes: low fitness or developmental constraint? Lovely article on this (even if I do say so myself! Ed) bit.ly/yFvykd
From an adaptation perspective, unoccupied patches of morphological space are inferred to be empty because they are of low fitness and selected against. These inferences hinge on venturesome assumptions, because emptiness is explained by low fitness and low fitness is inferred from emptiness. Moreover, non-adaptive factors, such as developmental constraint, could also plausibly account for empty morphospace.
Train online
View more PowerPoint from EMBL-EBI
□ emblebi:
Our slides from the Database Workshop at #PAGXX, the Plant and Animal Genome conference, are now available.
>> www.ebi.ac.uk/training/online/
Train online (www.ebi.ac.uk/training/online/) is a free, web-based learning resource for life scientists. Train online helps you make the most of the huge amount of biological data that EMBL-EBI makes publicly available for the research community. Using a combination of tutorials, guided examples, exercises and quizzes, Train online guides you towards becoming a confident user of open-access data resources. This training portal is there for you to learn in your own time and at your own pace, anywhere in the world. You do not need previous experience in bioinformatics to benefit from our courses.
□ CompleteGenomic:
This translational research agreement is with @MayoClinic‘s Ctr. for Individualized Medicine. Info about the Ctr: bit.ly/yStyJK
□ DailyNewsGW:
Complete Genomics' Shares Soar on Mayo Clinic Sequencing Contract: bit.ly/xTxx2J
□ appliedgenomics:
Pardon the press release, but this interesting - Mayo Clinic to outsource whole genome sequencing to Complete Genomics: bit.ly/wvi9N9
As a result of the deal, researchers at Mayo will now be able to use Complete Genomics' sequencing service for some large-scale whole genome sequencing projects. Mayo's center operates a comprehensive sequencing laboratory in its own Medical Genome Facility, but decided that Complete Genomics could supplement its offerings, the Mountain View, Calif.-based company said.
□ pfanderson:
Getting started in text mining ploscompbiol.org/article/info:d…
At the other end of the spectrum, a rule-based system might use sophisticated linguistic and semantic analyses to recognize a wide range of possible ways of making assertions about those classes of things. It is worth noting that useful systems have been built using technologies at both ends of the spectrum, and at many points in between. In contrast, statistical or machine-learning?based systems operate by building classifiers that may operate on any level, from labelling part of speech to choosing syntactic parse trees to classifying full sentences or documents.
For evaluation of suitability for internal use, the best paradigm might not be the publishing-oriented corpus-based one, but rather a test suite built on the principles of software engineering and structured software testing.
生物医学・計算生物学のテキスト・マイニング。機械学習システム等のルールベースと統計ベースのユーセージ。出版指向のコーパスベースは最善ではない
□ scbsc:
Call For Abstracts | 8th ISCB Student Council Symposium 2012 fb.me/1BmnQYsTN
□ portablegenomic:
Pacific upgrades PacBio RS DNA sequencing system chemistry and software - Pharmaceutical Business Review bit.ly/yI83hU
□ Paradoxical Evidence Integration in Rapid Decision Processes
>> http://bit.ly/wysT7o
Here, we show that one-stage models cannot explain psychophysical experiments on feature fusion, where two visual stimuli are presented in rapid succession. Paradoxically, the second stimulus biases decisions more strongly than the first one, contrary to predictions of one-stage models and intuition. We present a two-stage model where sensory information is integrated and buffered before it is fed into a drift diffusion process. The model is tested in a series of psychophysical experiments and explains both accuracy and reaction time distributions.
意思決定プロセスの第二刺激バイアス一段モデルの逆説的統合によるラピッド化。
□ Leveraging in Statistical Analysis of RNA-Seq
>> http://bit.ly/x4KIbd
In this talk, I will present some statistical analysis for bias correction in RNA-Seq short-read counts. Since the sample size is over tens of millions, routine statistical computing is infeasible. Our statistical computing is conducted using a subsampling method called leveraging. I will present some statistical properties of the leveraging algorithm. Real RNA-Seq examples will also be presented to demonstrate the empirical performance of our method.
□ Rcomputing:
Classifying Breast Cancer as Benign or Malignant Using RTextTools rtexttools.com/1/post/2012/02…
□ Rcomputing:
Book of the Day: Engineering Long-Lasting Software: An Agile Approach Using SaaS and Cloud Computing, Alpha Edition... amzn.to/xq5WLX
□ LSEImpactBlog:
Do more tweets mean higher citations? bit.ly/z5uqRj
□ 2012 AGBT Meeting.
>> http://agbt.org/
Now in its 13th year, the Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 15-18, 2012. This annual gathering is now fully entrenched within the genomics research community, representing the most complete scientific forum for acquiring information about the latest advances in DNA sequencing technologies and their myriad applications.
>> https://twitter.com/#!/search?q=%23AGBT #AGBT
□ omespeak: Analysis of Oxford Nanopore
Speculations on the science behind Oxford Nanopore's sequencing technology to be announced at #AGBT : bit.ly/AjfKfi
On Oxford Nanopore’s ‘disruptive’technology
Given the promise of nanopore sequencing,and the relatively teasing nature of ONT’s press release,there has been much speculation on the interwebs about the nature of their device,its costs,performance parameters etc. The most comprehensive discussion on this topic is at Dr. Keith Robison’s blog (highly recommended read). While I agree with much of his conjectures,his post is looking at the device mainly from the point of view of genomics applications. Over here,I would like to cover some of the more basic science,and methodology aspects,outlining the challenges of nanopore sequencing and how ONT might be tackling them.
□ nabsys:
Nabsys to present first single-molecule, solid-state re-sequencing data @ #AGBT & EMBL Omics & Personalized Health Conf prn.to/xW3fx6
In contrast to other approaches referred to as "nanopore sequencing," positional sequencing does not attempt to discriminate individual nucleotide bases passing through an electrical detector. Instead, the Nabsys approach involves hybridization of short oligonucleotide probes to very long DNA templates, passage of probe-bound templates through solid-state nanodetectors, and electronic detection of the locations of hybridized probes.
#AGBT の一つの注目点は、次世代シーケンサーの酵素利用技術の欠点を克服するプラットフォーム、"Nanopore Seq" vs. "Solid-State Seq"の双璧。Oxford nanoporeにはIlluminaのサポート。NabsysはNHGRIから"$1000ゲノム"賞をで受賞した最初の会社。
□ GridION & MinION: Electronic, scalable platform for real time nanopore analyses
>> http://www.nanoporetech.com/
Miniaturising the GridION system: - The MinION
Nanopore technology and the GridION system are well suited to miniaturisation of the sensing device. The MinION is a small., portable, single-molecule analysis device that is compatible with Oxford Nanopore's DNA sequencing and protein analysis techniques.
USBでGridION！Oxford Nanopore はじまりすぎワロタw
Oxford nanoporeのminION、USBポートと電源があれば、フィールドワークでサンプルをシーケンス出来るから、世界各地のバイオレポジトリ構築に革命的な動きがありそう。アフリカでのバイオレポジトリは欧州に集約される方針だけど、将来的には僻地医療で現地シーケンスとか胸熱。
先陣はOxford Nanoporeだったけど、NABsysのSolid-State(6塩基単位の配列プログラム）とNoblegenのOptipore SequencingにminION並みの隠し球があるかというと容易じゃないと思う。GridIONのアドバンテージは大きかった。
Illumina株も一時的に下落してるけど、Oxford nanoporeの戦略提携企業でナノポア事業の利益共有社だからね。NABsys社が何をコメントしたのか気になる。EMBLはNABsysのSolid-State推しだった気がする
そういえばNASAが昨年、Vomit Cometで無重力下のPCR駆動テストやってたが、minIONは仕様上、宇宙旅行中の過酷な環境に耐えうるんだろうか。
会議中AGBT監視してて、Oxford Nanopore minION始まり過ぎワロタって発言したら、お偉いさんから「取り敢えず何処の株を買えばいいんだ」って聞かれてワロタw 「PacBio(暴落中）を買い叩いときましょうかw」 (半分嫌がらせ)
□ dud3k:
errr correction, on yesterday's close. RT @dudek Wow, them markets don't snooze. $ILMN $LIFE $PACB all down 5-6% in last hour. #agbt
□ GenomeWeb:
Impact of @nanopore's #minIon announcement on rest of sequencing market is pretty telling: bit.ly/zMJzYe #AGBT
□ nakedideas:
We just launched the new @nanopore website in a #Apple Keynote style whirlwind for #AGBT So exciting! Congrats to them! nanoporetech.com
□ gaou_ak:
しっかし、順調に大本命がIon ProtonとMinIon/GridIonに変わったなぁ。次々とでてくる新型シーケンサーがあっさり旧型に取って代わるあたりが戦国時代だ。まぁMinIon/GridIonに関してはデータ見てみるまでなんともだけれど。
例えば、今結構安めのところで、グライナーのシーケンシングサービスが、36runで６万円。http://bit.ly/xUaiv7 MinIonは今のドル円レートだと、$900=約7万2千円で、1kbpが100runできる計算になる。しかもそれぞれx512。エラーとかありえない。
□ BiologicalB:
TRADE NEWS Agilent Technologies Extends TargetEnrichment Platform to Desktop Sequencers: AGBTAgilent Technologie... bit.ly/wDa2DU
(AGBT)--Agilent Technologies Inc. (NYSE:A) today expanded its SureSelect target-enrichment system with the HaloPlex target enrichment system for desktop sequencers.
“The combined application of HaloPlex enrichment technology with Ion Torrent semiconductor sequencing provides a versatile and rapid setup for high-throughput, small-footprint target gene resequencing.”
□ illumina:
Keane @sangerinstitute : #NGS storage challenges, expect 2K Tb sequence in 2012. New file formats needed - CRAM. #AGBT
□ Symbionticism:
#AGBT Matt Blow from jgi shows that pacbio + Illumina improves assemblies vs just illumina, but did not show pacbio data alone as control.
□ assemblathon:
RT @illumina: HiSeq 2500 "Genome in a Day" data viewable in BaseSpace: ow.ly/964yF #AGBT
From the beginning, we designed BaseSpace to be a place where things moved quickly. We did this largely so that our customers and partners could easily deploy their own apps on the platform (more to come on that in a later post), but we also did it out of necessity to keep pace with the breakneck innovation from our sequencing systems.
**************************************************************
□ rOpenSci:
BibSoup API, fun: require(RJSONIO) fromJSON("http://bibsoup.net/query?q=ecology")
□ 『情報ダイナミクスの定量生物学』
>> http://symposium.crmind.net/infodynamics2012/Home.html
JSBi 第5回応用システムバイオロジー研究会
『遺伝情報は生命システムを規定する情報の全てではありません』『情報理論の枠組みは定量的なデータから生命システムの定性的な特性を抜き出してくる数理的基礎として…』
生命システム全体を遺伝情報という枠組みで代替出来ないのは、それは『遺伝（転写）』するための情報の側面しか捉えていないから。しかし尚、生命現象の振る舞い自体は、情報という電子の影に転写可能だと思う。生命が情報というのは可塑的な表現で、情報こそが生命の信号交換行為（翻訳）の代替表現
□ hinaichigo:
鶴岡の温泉からメタゲで世界最小微生物の発見ての面白そうよね http://t.co/PWbuKoLV
□ _masaka:
Ontology for Media Resources 1.0 bit.ly/A3RJ6o ウェブ上で流通する画像、動画、音声などのメタデータ記述語彙をRDF/OWLで定義し、DC、ExifからYouTubeに至る既存語彙とのマッピング表も用意。W3C勧告に
□ suketake:
iBooks authorを使ってマルチタッチテキストブック「AlgalSex ー藻類の有性生殖ー」を作成しました。生物系iBooksとしては日本語初なんじゃないでしょうかw。iBooksストアで配信できないのでßをつけています。bit.ly/AkYMgg
□ rubbish_talk.
Twitterを仮想空間上にプロットして、その連続性を追体験する、というアイデアは様々なパターンが試行出来そうだけれど、将来的にテキスト間の断続性を機械的に埋めて、Tweetから自己や他者の体験そのものをショーウィンドウ的に再現するとか。可搬性という点でツイッター組込の必然もある。
□ Hornet_B:
『ＯＥＣＤ加盟30カ国のうち「返済の必要のない給付制奨学金制度」があるのは28カ国で、大学の授業料無償化は15カ国で実施』だって。貧しい層が高等教育を受けるチャンス、日本人だと相当に狭いじゃない！
□ n0rr:
返済免除というものがあってだな
私は奨学金返済に苦労したタチなので、あまり楽観視出来ない。とは言っても、もともと奨学の成果として返す見込みで契約を結んだ奨学金が返済できない、負荷が著しいというのは、制度上の欠陥という他ない。
地味に怖いのが低金利という謳い文句で目立たない『延滞金』という取り決め。何らかの理由で返済が滞った場合、これと利息のWで年13%ずつ元金から増えていくことになる。今の時代、国立で200万借りて就職したとして、直後に生活に逼迫したりすることも珍しくない。また保証人や家庭の状況で再猶予が認められるとは限らず「銀行ローンや消費者金融より良心的」と世間から褒め称される制度の陰で奨学金という性格から元本が巨額なことを無視され社会的弱者に転落する図式。
「借りたものは返す」は当然なこと。日本学生支援機構の案内にも『当然返還すべき金額に加えて延滞金を支払っていただくことになります。』（原文ママ）とある。そういう契約を交わした以上、そうなるということ。支援機構の掲げる大義名分とは全く無関係に。
どちらにせよ滞納者が20万人超いて、民間の取り立て業者に債権譲渡せざるえなくなったという時点で制度の破綻を認めるべきなんだろうけどね。今奨学金返済で悩んでる人、経済事情は「個別のトランザクション」だから、「私は○○だけど△△して払ったぞ」という全く無価値な議論は取り合う必要ない。それと日本は一度、大学と奨学金制度の関係の中の搾取構造は洗うべき。奨学金の恩恵を得る人が大勢いて、当然の如く借りたら良いという圧の存在。
誰でも大学に進学出来る「豊かさ」。当然のように大卒資格を要求する社会。当然のように金を貸し付ける奨学金機構。豊かさを担保されたかのように借り受ける若者。数十万人が滞納者。それが日本の豊かさの実像。