□ rubbish_talk.
生命情報が莫大なデータを占有するのは、マクロな事象とミクロな原理との境界面で、データを意味のある主体として電子信号に記銘する知性という秩序行動の、それを内包する生命システムへの自己繰り込みから生成されるランダム構造の顕現の一面を投影しているのかもしれない。
□ What, exactly, is a paradox?: パラドックスとは実際にはどういう事なのか？
http://oxford.ly/rxS7Sb #philosophy
(Figure 1. Evolution of plant and inflorescence architecture during maize domestication.)
□ Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize
：トウモロコシの雄蕊と雌蕊の花序の差異を決定する遺伝子構造
>> http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002383
(Figure 3. Relationship between QTL frequencies and effects.)
Effects from joint linkage (top) and GWAS (bottom) analyses are grouped by trait categories and scaled as in Figure 2.
花序を特徴づけるQTL及びSNP頻度(Joint LinkageとGWASのKolmogorov-Smirnov検定による)
□ BlasBenito:
Scientific Software Development Is Not an Oxymoron (PLOS Computational Biology) j.mp/vH2hBn
計算生物学における研究プロジェクトとソフトウェア開発の課題：分業化と品質管理という視点に立ち再現性のあるガイドラインを確立するべき。
□ STUDIES ON THE MESSENGER RNA IN RAT LIVER: ΧΑΤΖΗΒΑΣΙΛΕΙΟΥ, ΑΝΤΩΝΙΟΣ (1966, Ιδρύματα Εξωτερικού): http://thesis.ekt.gr/thesisBookReader/id/4205#page/1/mode/1up
(Εθνικό Αρχείο Διδακτορικών Διατριβών)
□ Solving Uganda’s budget puzzle: OpenSpending & Publish What You Fund’s Uganda Visualisations Featured in the Guardian. shar.es/oY3Dc (Open Knowledge Foundation)
ウガンダだけでなく、アフリカ全域で進められているOpen Access事業とか、開発国で実験段階にあるインフラソリューションを、途上国のガバナンスの整理や予算の透明化、福祉サービスに臨床的に応用していくという試みは、旧態然としたシステムに閉塞する先進国との明暗を分ける可能性もある
□ YusukeKomiyama:
Ag2O3 clathrate is a novel and effective antimicrobial agent [PDF] http://www.springerlink.com/content/831q480317723456/fulltext.pdf 宮城の高校生による新抗菌物質精製の国際ジャーナル掲載の快挙。しかも偶然じゃなくて、高校生自身の研鑽の成果
□ BioMedCentral:
Semantic Web Life Sciences #Hackathon: the movie ow.ly/7OD6S @petermurrayrust #openaccess #opendata
□ □ dritoshi:
切実。日本のゲノムシーケンス市場って対競争的商業基盤に乏しく、理研等に代表される著名機関・企業への受託解析が主要シーン。Complete GenomicsやBGIの安価で良質なマスプロに対しアドバンテージがあるとは言い難い。ハード部分で追いつけないなら、人材と連携にベットするしか
□ Linked Data: A Way out of the Information Chaos and toward the Semantic Web http://net.educause.edu/ir/library/pdf/ERM1145.pdf
□ Linked Open Data Challenge 2011.
>> http://lod.sfc.keio.ac.jp/challenge2011/index.html
□ LodJapan: LodJapan
[エントリ情報]アイデア部門i004 作品名称:ヒストリンク：ジオコードを持つ歴史等の情報をLinked Data化し、地図等から利用する。 #lod2011
□ [エントリ情報]i003: Linked Smart City:産業別, 分野別のエコ地域LODを作成し, 環境オントロジーとデータリソースを作成することで, 社会の最適化をはかる. 地域の事例を元に日本全国にLODの枠を広げ, 最終的にはグローバルに利用されるデータセットの提供をはかる。
□ koujikozaki
BioLOD.org ７００クラス，１０億トリプル…がダウンロード可能． #lod2011O
The Download Hub of Biological Linked Open Databases for Phenomes.
http://biolod.org/ BioLOD.org
□ 32nm:
g-language bookmarklet g-language.org/wiki/bookmarkl… #lod2011t
□ sa2hi:
□ ogishima:
□ bluenove: ゲームでオープンイノベーション・マネージメントを学ぶ
L'affiche du Serious Game InnovNation prête pour #LeWeb11 ! bit.ly/vxJFtj #OpenInnovation @InnovNation
<object width="350" height="291"><param name="movie" value="http://www.scivee.tv/flash/embedCast.swf"/><param name="allowfullscreen" value="true" /><param name="allowscriptaccess" value="always" /><param name="flashvars" value="id=26568&type=3"/><embed src="http://www.scivee.tv/flash/embedCast.swf" allowfullscreen="true" allowscriptaccess="always" width="350" height="291" flashvars="id=26568&type=3"></embed></object>
□ ayrrisbio: ayrrisBIO - Appistry
Twitter in Bioinformatics by @OpenHelix bit.ly/uUTxVb
(September 28, 2011. Next-Gen 101: Video Tutorial on Conducting Whole-Exome Sequencing Research)
□ MishaAngrist:
Ethics and IRB Issues Related to Whole-Exome Sequencing (video of Sara Hull from NHGRI)
http://www.genome.gov/27545880
□ ibm-cbc-genomic-tools GenomicTools: a computational platform for developing high-throughput analytics in genomics. code.google.com/p/ibm-cbc-geno…
□ selective 2′-hydroxyl acylation analyzed by primer extension(SHAPE): XMRVの高感度形状解析でRNA折畳みの一般的な規制構造同定。異種間で規制領域のアーキテクチャが類似 http://pubs.acs.org/doi/abs/10.1021/ja2070945
Femtomole SHAPE Reveals Regulatory Structures in the Authentic XMRV RNA Genome
□ Differential expression in RNA-seq: A matter of depth
>> http://genome.cshlp.org/content/21/12/2213.full?rss=1
NOISeq: 示差的発現をもたらす遺伝子カウントデータ識別の為のノンパラメトリックな差動式メソッド。正規化手順とベンチマーク。
NOIseqにおけるシーケシングの深さと、MAQCデータセットに対する真陽性と偽陽性の発現数。RPKMのような長さ補正の正規化において、SDバイアスのパターンでは偽陽性を検出し、NOIseqでは低レベルの真陽性を維持した。
□ emblebi: EMBL-EBI
EBI's metagenomics site is launched! Your feedback on the new beta site is welcomed. Take a look: bit.ly/scm0pa
□ GigaScience:
Here are Alexandra's slides for her talk at #InCoB today on "A Journal’s Perspective on Data Standards and Biocuration" slidesha.re/ucjEdy
□ SAGRudd:
#InCoB BGI has completed 540 reference plant and animal genomes! Parrot to oyster. They seem to eat everything in BGI canteen!
□ BlastR 2.1 - Searching and Clustering RNA: a new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. http://t.co/qOgA8heQ
□ DailyNewsGW: NHLBIがGO ESP計画に年間150万ドルまでのグラントを提供
NHLBI to Fund Studies to Enhance Exome Sequencing Data: read more bit.ly/rC1mPQ
□ eurogene:
NHS data mining will lead 2 plenty of these scare stories - NHS details with private sector 'rings alarm bells' tgr.ph/tBwLJA
□ DailyNewsGW:
Rosetta Pays Prometheus $650K; Not in Compliance With Nasdaq Requirement: read more bit.ly/ukg4Y5
□ n0rr:
A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNAseq bit.ly/vC5GFI
生命情報が莫大なデータを占有するのは、マクロな事象とミクロな原理との境界面で、データを意味のある主体として電子信号に記銘する知性という秩序行動の、それを内包する生命システムへの自己繰り込みから生成されるランダム構造の顕現の一面を投影しているのかもしれない。
□ What, exactly, is a paradox?: パラドックスとは実際にはどういう事なのか？
http://oxford.ly/rxS7Sb #philosophy
Quine (1966) offered his classic characterization of the notion of paradox, a taxonomy for paradoxical arguments and some vocabulary for discussing them. In this article, I shall generalize Quine’s taxonomy and defend a simpler characterization. The simpler characterization will have the virtue or the flaw (as might be) of making paradox a matter of degree.
(Figure 1. Evolution of plant and inflorescence architecture during maize domestication.)
□ Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize
：トウモロコシの雄蕊と雌蕊の花序の差異を決定する遺伝子構造
>> http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002383
We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population.
(Figure 3. Relationship between QTL frequencies and effects.)
Effects from joint linkage (top) and GWAS (bottom) analyses are grouped by trait categories and scaled as in Figure 2.
花序を特徴づけるQTL及びSNP頻度(Joint LinkageとGWASのKolmogorov-Smirnov検定による)
Inflorescence traits have larger effects than flowering or leaf traits across a range of QTL and SNP frequencies (Figure 3; Kolmogorov-Smirnov test p<10－16 for joint linkage and GWAS), and ear traits have larger effects than tassel effects (Kolmogorov-Smirnov test p = 0.004 for joint linkage and p<10－15 for GWAS). </font>
□ BlasBenito:
Scientific Software Development Is Not an Oxymoron (PLOS Computational Biology) j.mp/vH2hBn
We are starting with the premise that scientific software development brings together different cultures. A “certified technology stack” might mean a robust n-tiered architecture to some and an expensive waste of resources to others. We want to avoid fanning controversy over interdisciplinary science [4,5] and misunderstandings inherent at the interface between engineering and science.
計算生物学における研究プロジェクトとソフトウェア開発の課題：分業化と品質管理という視点に立ち再現性のあるガイドラインを確立するべき。
□ STUDIES ON THE MESSENGER RNA IN RAT LIVER: ΧΑΤΖΗΒΑΣΙΛΕΙΟΥ, ΑΝΤΩΝΙΟΣ (1966, Ιδρύματα Εξωτερικού): http://thesis.ekt.gr/thesisBookReader/id/4205#page/1/mode/1up
(Εθνικό Αρχείο Διδακτορικών Διατριβών)
□ Solving Uganda’s budget puzzle: OpenSpending & Publish What You Fund’s Uganda Visualisations Featured in the Guardian. shar.es/oY3Dc (Open Knowledge Foundation)
Even in countries where national budgets are relatively easy to access and analyse, aid spends are all too often the crucial, missing pieces of the puzzle, creating huge headaches for governments and civil society groups eager to make sure precious resources are wisely spent.
Part of the challenge is that developing countries, on average, receive aid from an increasing number of donors. While in the past a country might receive aid from two or three, now it more likely has to deal with dozens, each with different sets of priorities and different ways of allocating and reporting aid.
ウガンダだけでなく、アフリカ全域で進められているOpen Access事業とか、開発国で実験段階にあるインフラソリューションを、途上国のガバナンスの整理や予算の透明化、福祉サービスに臨床的に応用していくという試みは、旧態然としたシステムに閉塞する先進国との明暗を分ける可能性もある
□ YusukeKomiyama:
効果10倍の抗菌物質（過酸化銀）、仙台の高校生が新製法 ：日本経済新聞 s.nikkei.com/vL8LNO; "Ag2O3 clathrate is a novel and effective antimicrobial agent" springerlink.com/content/831q48…
Ag2O3 clathrate is a novel and effective antimicrobial agent [PDF] http://www.springerlink.com/content/831q480317723456/fulltext.pdf 宮城の高校生による新抗菌物質精製の国際ジャーナル掲載の快挙。しかも偶然じゃなくて、高校生自身の研鑽の成果
□ BioMedCentral:
Semantic Web Life Sciences #Hackathon: the movie ow.ly/7OD6S @petermurrayrust #openaccess #opendata
□ □ dritoshi:
具体的に書くと、エビジェネティックな状態やDNA変異を自在に扱えて、in vitro でアッセイできる系を作らなければならない。3/4/Hi-C や MBD, mRNA, Histon modification などのデータを統合して、試験管で再現できる実験技術を作ってほしい。
機械学習な人は、オミックス比較・統合の部分、特に、因果推定から物理モデルに持っていく間を埋めるところに活躍が期待される。物理・数学は物理モデルのところ。生物・化学クラスタはゲノムコンテキストへの摂動の技術開発へ。
IT業界では、優秀な研究・技術者がネットや勉強会などでプレゼンスを示していて、それが企業の技術レベルの高さの評判になっている事実がある。バイオもそうなるべき。営業さんの顔しか見えず、優秀な技術者の顔がみえない企業は、低価格なうえ技術開発も持っているBGIなどに淘汰されているだろう
切実。日本のゲノムシーケンス市場って対競争的商業基盤に乏しく、理研等に代表される著名機関・企業への受託解析が主要シーン。Complete GenomicsやBGIの安価で良質なマスプロに対しアドバンテージがあるとは言い難い。ハード部分で追いつけないなら、人材と連携にベットするしか
□ Linked Data: A Way out of the Information Chaos and toward the Semantic Web http://net.educause.edu/ir/library/pdf/ERM1145.pdf
□ Linked Open Data Challenge 2011.
>> http://lod.sfc.keio.ac.jp/challenge2011/index.html
□ LodJapan: LodJapan
[エントリ情報]アイデア部門i004 作品名称:ヒストリンク：ジオコードを持つ歴史等の情報をLinked Data化し、地図等から利用する。 #lod2011
□ [エントリ情報]i003: Linked Smart City:産業別, 分野別のエコ地域LODを作成し, 環境オントロジーとデータリソースを作成することで, 社会の最適化をはかる. 地域の事例を元に日本全国にLODの枠を広げ, 最終的にはグローバルに利用されるデータセットの提供をはかる。
□ koujikozaki
BioLOD.org ７００クラス，１０億トリプル…がダウンロード可能． #lod2011O
The Download Hub of Biological Linked Open Databases for Phenomes.
BioLOD.org (Biological Linked Open Data) databases provide biological open data, according to the W3C LOD standard format of the World Wide Web Consortium Linking Open Data project, not only similar to the DBpedia and Bio2RDF projects, but also including ontology capabilities such as with Web Ontology Language (OWL) and Open Biomedical Ontology (OBO).
BioLOD.org databases integrate 756 tables and 8.24 million rows of biological data as of November 2011. These data are identified by URI references in the form of:
http://biolod.org/(Original ID)/(GUID)
http://biolod.org/ BioLOD.org
□ 32nm:
g-language bookmarklet g-language.org/wiki/bookmarkl… #lod2011t
□ sa2hi:
萩野先生： オープンガバメントにも使われるLOD、米国政府の38万種のRawデータが活用されようとしている #lod2011 #lod2011O
□ ogishima:
ライフサイエンス分野のLODは非常に複雑なネットワークになるが、遺伝子を中心としたネットワークに整理する #lod2011 #lod2011T
Le Serious Game Innov'Nation from bluenove on Vimeo.
□ bluenove: ゲームでオープンイノベーション・マネージメントを学ぶ
L'affiche du Serious Game InnovNation prête pour #LeWeb11 ! bit.ly/vxJFtj #OpenInnovation @InnovNation
Innov’Nation est un Serious Game de formation à distance, qui permet de former l’ensemble des collaborateurs à la gestion de projets innovants, que ce soit dans leurs interactions internes (Innovation collaborative) ou avec l’écosystème de partenaires de l’entreprise (Innovation ouverte).
□ ayrrisbio: ayrrisBIO - Appistry
Twitter in Bioinformatics by @OpenHelix bit.ly/uUTxVb
(September 28, 2011. Next-Gen 101: Video Tutorial on Conducting Whole-Exome Sequencing Research)
□ MishaAngrist:
Ethics and IRB Issues Related to Whole-Exome Sequencing (video of Sara Hull from NHGRI)
http://www.genome.gov/27545880
□ ibm-cbc-genomic-tools GenomicTools: a computational platform for developing high-throughput analytics in genomics. code.google.com/p/ibm-cbc-geno…
GenomicTools is a flexible computational platform for the analysis and manipulation of high-throughput sequencing data such as RNA-seq and ChIP-seq. GenomicTools implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address a wide spectrum of tasks from preprocessing and quality control to meta-analyses.
□ selective 2′-hydroxyl acylation analyzed by primer extension(SHAPE): XMRVの高感度形状解析でRNA折畳みの一般的な規制構造同定。異種間で規制領域のアーキテクチャが類似 http://pubs.acs.org/doi/abs/10.1021/ja2070945
Femtomole SHAPE Reveals Regulatory Structures in the Authentic XMRV RNA Genome
□ Differential expression in RNA-seq: A matter of depth
>> http://genome.cshlp.org/content/21/12/2213.full?rss=1
NOISeq: 示差的発現をもたらす遺伝子カウントデータ識別の為のノンパラメトリックな差動式メソッド。正規化手順とベンチマーク。
a novel approach?NOISeq?that differs from existing methods in that it is data-adaptive and nonparametric. Our results reveal that most existing methodologies suffer from a strong dependency on sequencing depth for their differential expression calls and that this results in a considerable number of false positives that increases as the number of reads grows.
NOIseqにおけるシーケシングの深さと、MAQCデータセットに対する真陽性と偽陽性の発現数。RPKMのような長さ補正の正規化において、SDバイアスのパターンでは偽陽性を検出し、NOIseqでは低レベルの真陽性を維持した。
□ emblebi: EMBL-EBI
EBI's metagenomics site is launched! Your feedback on the new beta site is welcomed. Take a look: bit.ly/scm0pa
Metagenomics is the study of all genomes present in any given environment without the need for prior individual identification or amplification. For example, in its simplest form, a metagenomic study might be the direct sequence results of DNA extracted from a bucket of sea water.
The EBI Metagenomics service is an automated pipeline for the analysis and archiving of metagenomic data that aims to provide insights into the functional and metabolic potential of a sample. You can freely browse all the public data in the repository.
Alexandra Basford, InCoB 2011: A Journal’s Perspective on Data Standards and Biocuration
View more presentations from GigaScience, BGI Shenzhen
□ GigaScience:
Here are Alexandra's slides for her talk at #InCoB today on "A Journal’s Perspective on Data Standards and Biocuration" slidesha.re/ucjEdy
□ SAGRudd:
#InCoB BGI has completed 540 reference plant and animal genomes! Parrot to oyster. They seem to eat everything in BGI canteen!
□ BlastR 2.1 - Searching and Clustering RNA: a new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. http://t.co/qOgA8heQ
□ DailyNewsGW: NHLBIがGO ESP計画に年間150万ドルまでのグラントを提供
NHLBI to Fund Studies to Enhance Exome Sequencing Data: read more bit.ly/rC1mPQ
Through a new grant funding opportunity, NHLBI will provide up to $1.5 million per year for researchers who sift through the data generated by the Grand Opportunities Exome Sequencing Project (GO ESP).
The GO ESP effort sequenced 7,500 samples from well-phenotyped populations to discover all the variations in exons and to provide the largest exome dataset for studying heart, lung, and blood diseases. Genotype data and detailed sequencing and phenotype data from the project also is being made available, and NHBLI plans to fund genomic investigators, statisticians, and biologists who will identify rare or lower frequency variants from these sets that may be related to diseases.
□ eurogene:
NHS data mining will lead 2 plenty of these scare stories - NHS details with private sector 'rings alarm bells' tgr.ph/tBwLJA
□ DailyNewsGW:
Rosetta Pays Prometheus $650K; Not in Compliance With Nasdaq Requirement: read more bit.ly/ukg4Y5
□ n0rr:
A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNAseq bit.ly/vC5GFI
The advent of ultra-high-throughput sequencing (UHTS) technology has invoked a paradigm shift in the field of genomics and transcriptomics. It is now possible to obtai