□ 構造物は時間発展的なcomponentの連なりであるが、実のところ、我々が認識する宇宙の中では、時間こそが局所スケールのLyapunov Timeによって定義される事象連続性の構造物に違いないのだ。
□ Mysterious Gamma Delphinid meteor shower expected to return
>> http://www.sciencerecorder.com/news/mysterious-gamma-delphinid-meteor-shower-expected-to-return/
いるか座γ（ガンマ）流星群って名前の圧倒的な流星感。
□ Controlling Self-Organizing Dynamics on Networks Using Models that Self-Organize: a self-organized critical system
>> http://prl.aps.org/abstract/PRL/v111/i7/e078701
"Controlling self-organizing systems is challenging because the system responds to the controller. Here, we develop a model that captures the essential self-organizing mechanisms of Bak-Tang-Wiesenfeld (BTW) sandpiles on networks, a self-organized critical (SOC) system. This model enables studying a simple control scheme that determines the frequency of cascades and that shapes systemic risk."
□ その生物学的意味とデータ利用価値まで知見として提供できるシステムやインフラの構築までがお仕事。解析サービスのみに将来性はない →"バイオインフォマティシャンの重要な役割は解析することではない（中略）生物学者に生物的意義を説明すること" http://kengg.blog75.fc2.com/blog-entry-263.html …
その辺りでの事業を考えて、市場調査なりをしてるのだけど、海外ではデータの解析・共有→仮説生成から自動化するインフラ構想も着々と進行していて、現場で技術者にしか出来ないことは減らす方向にある。Bioinformaticsの扱う専門領域が、研究と技術方面にどう分かれるのかも興味深い
ただ遺伝子データ関連のサービスプロバイダ事業を立ち上げる場合、現在の解析から踏み込んで施策・戦略アドバイザーまで提供すると、利益相反行為に触れるラインがありそうなので、そこをツールで自動化したいという試み
□ 4273π: New Raspberry Pi OS includes a 'Bioinformatics for Biologists' open access education on low cost ARM hardware http://www.biomedcentral.com/content/pdf/1471-2105-14-243.pdf …
□ QFAB_Bioinfo:
Can you run bioinformatics analysis on $35 hardware? See our blog about ARM processors. http://www.qfab.org/2013/08/22/bionformatics-future-hardware-from-arm/ …
□ Energy landscape analysis for regulatory RNA finding using scalable distributed cyberinfrastructure. http://www.zentralblatt-math.org/ioport/en/?id=27607&type=pdf …
□ Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for dominant genetic disorder http://m.nar.oxfordjournals.org/content/early/2013/08/19/nar.gkt725.short …
□ Stochastic algorithms for chemical kinetics: 化学反応速度論における離散確率的アルゴリズム: サブボリューム間の反応分子の転写と、URDMEを用いた核輸入シミュレーション http://jcp.aip.org/resource/1/jcpsa6/v138/i17/p170901_s1 …
□ A flexible count data model to fit the wide diversity of expression profiles arising extensively replicated RNA-seq: http://www.biomedcentral.com/1471-2105/14/254/abstract …
□ synobu:
□ General power and sample size calculations for high-dimensional genomic data: χ2 distributed test statistics: http://www.degruyter.com/view/j/sagmb.2013.12.issue-4/sagmb-2012-0046/sagmb-2012-0046.xml;jsessionid=FC90024156F84E21374F8643A4D1202F …
non-negative Conjugate Gradients algorithm (非負共役勾配アルゴリズム) の使いどころって、ある種の線形方程式の解法だけど、このベクトル処理の過程で逆問題を扱うみたい＞高次元ゲノムデータの冪とサンプルサイズ推定
□ GenomeBiology:
In BMC #Bioinformatics: RCircos enables simple, flexible generation of Circos 2D track plots http://bit.ly/1d73sRy pic.twitter.com/Q4ENEftuHi
□ DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments http://m.bioinformatics.oxfordjournals.org/content/early/2013/08/19/bioinformatics.btt422.short …
□ 自殺リスクを警告する血中マーカーが発見されたらしい 'Biological signal' of suicide risk found in blood http://www.medicalnewstoday.com/articles/265062.php …
□ Infernal: Computational identification of functional RNA homologs in metagenomic data based on “covariance models”
https://www.landesbioscience.com/journals/rnabiology/article/25038/ …
□ Genome in a Bottle Consortium 2013: standards for validating high-throughput variant detection: Platinum Genome, GRCh38 http://smallchangebio.wordpress.com/2013/08/16/genome-in-a-bottle-consortium-2013-standards-for-validating-high-throughput-variant-detection/…
□ Biology must never develop its own big-data systems:
>> http://www.eaglegenomics.com/2013/08/biology-must-never-develop-its-own-big-data-systems/ …
□ A sort of H-index for quantifying the coverage/diversity of bioactivity databases: http://chembl.blogspot.co.uk/2013/08/a-sort-of-h-index-for-coverage-of.html?m=1 …
□ Predicting the behavior of a chaotic pendulum with a variable interaction potential: カオス振り子の挙動予測。モデル化されたシステムのバイアス源の特定 http://m.chaos.aip.org/resource/1/chaoeh/v23/i3/p033103_s1 …
□ maskot1977:
Conquering computational challenges of omics data and post-ENCODE paradigms
http://genomebiology.com/2013/14/8/310
□ Genohub: The Next-Generation Sequencing Market: specialized NGS matching engine to link NGS providers to customers https://genohub.com/
□ Accuracy versus F score: Machine Learning for the RNA Polymerases: http://tata-box-blog.blogspot.jp/2013/08/accuracy-versus-f-score-machine.html
□ CyTargetLinker: a generic Cytoscape app to build regulatory networks http://projects.bigcat.unimaas.nl/cytargetlinker/
□ BioStorage Technologies launches INTEGRITY study: preparation methods on DNA / RNA samples, storage times are applied http://www.medicaldevices-business-review.com/news/biostorage-technologies-launches-integrity-study-150813 …
□ Software for Computing and Annotating Genomic Ranges: Software Based Infrastructure: 80 other Bioconductor packages
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118
□ Phylogenomic Distance Method for Analyzing Transcriptome Evolution based on RNA-seq Data: http://m.gbe.oxfordjournals.org/content/early/2013/08/11/gbe.evt121.full.pdf#page=1 …
□ Adam and Eve DID live in Africa at the same time - but they probably didn't know each other
>> http://www.dailymail.co.uk/sciencetech/article-2382653/Adam-Eve-DID-live-Africa-time--probably-didnt-know-other.html
'Y-chromosomal Adam’ is thought to have walked the Earth between 120,000 and 156,000 years ago
This places him nearer to Eve who was around 99,000 to 148,000 years ago
Researchers say it is ‘extremely unlikely’ they were exact contemporaries
□ davecl42:
Pandoraviruses: giant viruses that share only 7% of their genome with other forms of life. Hint at 4th domain of life http://www.nature.com/news/giant-viruses-open-pandora-s-box-1.13410 …
□ The Deepest Uncertainty: Set theory: When a hypothesis is neither true nor false: CH and Large Cardinal Axioms
>> http://nautil.us/issue/2/uncertainty/the-deepest-uncertainty …
□ Can Quantum Bayesianism Fix the Paradoxes of Quantum Mechanics?
>> http://www.scientificamerican.com/article.cfm?id=can-quantum-beyesnism-fix-paradoxes-quantum-mechanics
□ Waters Acquires Omics Informatics Firm Nonlinear Dynamics: SYNAPT G2-SとTransOmicsの共同開発から買収へ。イオンモビリティベースで非データ依存性オミクス構築 http://www.genomeweb.com/informatics/waters-acquires-omics-informatics-firm-nonlinear-dynamics …
□ CasesDatabase:
We've just indexed our 28,000th case report! Explore http://www.casesdatabase.com/ today - because every new diagnosis starts with a single case!
□ Eureka Genomics to offer Next-Generation Sequencing & Bioinformatics Services for the Ion Torrent Proton™ System http://www.pharmiweb.com/pressreleases/pressrel.asp?ROW_ID=77801 …
□ TRON_MZ:
TRON technologists have developed LIMS for a NGS laboratory within the existing Galaxy platform (http://bit.ly/1422pK3 )!
□ Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003172
computational design of RNA logic gates
□ davidgifford:
#lod2013 http://citydata.jp/ ranks Japan's citizen data (3rd LOD Challenge Day Ideathon / Datathon @ Mixi) #lod #linkeddata #opendata
□ YusukeKomiyama:
□ Robustness and Compensation of Information Transmission of Signaling Pathways:
"阻害された経路の情報量の損失を他の経路が補償して情報量を堅牢に保って伝達"
>> http://www.sciencemag.org/content/341/6145/558 …
Information transmission to the biological output of neurite extension appeared robust. Cells may use information entropy as information so that messages can be robustly transmitted despite variation in molecular activities among individual cells.
>> http://www.s.u-tokyo.ac.jp/ja/press/2013/35.html
□ A multidimensional platform for the purification of non-coding RNA species
>> http://m.nar.oxfordjournals.org/content/early/2013/08/01/nar.gkt668.full
a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species.
□ A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
>> http://www.biomedcentral.com/content/pdf/1471-2164-14-530.pdf
□ Leaf: Bioinformatic pipelines in Python: plan-driven / change-driven develop environment: LGL形式言語でパイプライン定義を保持し単ノードを分離
>> http://www.biomedcentral.com/content/pdf/1471-2105-14-201.pdf
□ LAMP: limitless arity multiple-testing procedure （無限次数多重検定法）: Statistical significance of combinatorial regulations: http://m.pnas.org/content/early/2013/07/22/1302233110 …
□ rapodaca:
Recoding Pharma's cultural DNA http://bit.ly/17vengt
□ NIH mulls rules for validating key results
US biomedical agency could enlist independent labs for verification.
>> http://www.nature.com/news/nih-mulls-rules-for-validating-key-results-1.13469
□ Mysterious Gamma Delphinid meteor shower expected to return
>> http://www.sciencerecorder.com/news/mysterious-gamma-delphinid-meteor-shower-expected-to-return/
いるか座γ（ガンマ）流星群って名前の圧倒的な流星感。
□ Controlling Self-Organizing Dynamics on Networks Using Models that Self-Organize: a self-organized critical system
>> http://prl.aps.org/abstract/PRL/v111/i7/e078701
"Controlling self-organizing systems is challenging because the system responds to the controller. Here, we develop a model that captures the essential self-organizing mechanisms of Bak-Tang-Wiesenfeld (BTW) sandpiles on networks, a self-organized critical (SOC) system. This model enables studying a simple control scheme that determines the frequency of cascades and that shapes systemic risk."
□ その生物学的意味とデータ利用価値まで知見として提供できるシステムやインフラの構築までがお仕事。解析サービスのみに将来性はない →"バイオインフォマティシャンの重要な役割は解析することではない（中略）生物学者に生物的意義を説明すること" http://kengg.blog75.fc2.com/blog-entry-263.html …
その辺りでの事業を考えて、市場調査なりをしてるのだけど、海外ではデータの解析・共有→仮説生成から自動化するインフラ構想も着々と進行していて、現場で技術者にしか出来ないことは減らす方向にある。Bioinformaticsの扱う専門領域が、研究と技術方面にどう分かれるのかも興味深い
ただ遺伝子データ関連のサービスプロバイダ事業を立ち上げる場合、現在の解析から踏み込んで施策・戦略アドバイザーまで提供すると、利益相反行為に触れるラインがありそうなので、そこをツールで自動化したいという試み
□ 4273π: New Raspberry Pi OS includes a 'Bioinformatics for Biologists' open access education on low cost ARM hardware http://www.biomedcentral.com/content/pdf/1471-2105-14-243.pdf …
□ QFAB_Bioinfo:
Can you run bioinformatics analysis on $35 hardware? See our blog about ARM processors. http://www.qfab.org/2013/08/22/bionformatics-future-hardware-from-arm/ …
□ Energy landscape analysis for regulatory RNA finding using scalable distributed cyberinfrastructure. http://www.zentralblatt-math.org/ioport/en/?id=27607&type=pdf …
□ Rational design of antisense oligonucleotides targeting single nucleotide polymorphisms for dominant genetic disorder http://m.nar.oxfordjournals.org/content/early/2013/08/19/nar.gkt725.short …
□ Stochastic algorithms for chemical kinetics: 化学反応速度論における離散確率的アルゴリズム: サブボリューム間の反応分子の転写と、URDMEを用いた核輸入シミュレーション http://jcp.aip.org/resource/1/jcpsa6/v138/i17/p170901_s1 …
□ A flexible count data model to fit the wide diversity of expression profiles arising extensively replicated RNA-seq: http://www.biomedcentral.com/1471-2105/14/254/abstract …
□ synobu:
明日からDBCLSにてライフサイエンス分野のデータRDF化、トリプルストア運用、オントロジー開発、SPARQLクエリのノウハウを共有する開発会議 SPARQLthon11 を開催します。興味のある方は気軽にご参加ください！http://wiki.lifesciencedb.jp/mw/index.php/BH12.12/SPARQLthon11#.E5.8F.82.E5.8A.A0.E8.80.85 …
課題出し2。ゲノム統計情報スタンザ, ゲノムブラウザ（JBrowse/SAPRQL EP）スタンザ化, DAS/SPARQL, INSDCオントロジー, RefSeq/RDFのUBSID対応検討, 文献アノテーションNanoPub対応 #SPARQLthon
□ General power and sample size calculations for high-dimensional genomic data: χ2 distributed test statistics: http://www.degruyter.com/view/j/sagmb.2013.12.issue-4/sagmb-2012-0046/sagmb-2012-0046.xml;jsessionid=FC90024156F84E21374F8643A4D1202F …
a pilot-data based method for power and sample size analysis which can handle more general experimental designs and uses pilot-data to obtain estimates of the effect sizes. The method can also handle χ2 distributed test statistics which enables power and sample size calculations for a much wider class of models, including high-dimensional generalized linear models which are used, e.g., for RNA-seq data analysis.
non-negative Conjugate Gradients algorithm (非負共役勾配アルゴリズム) の使いどころって、ある種の線形方程式の解法だけど、このベクトル処理の過程で逆問題を扱うみたい＞高次元ゲノムデータの冪とサンプルサイズ推定
□ GenomeBiology:
In BMC #Bioinformatics: RCircos enables simple, flexible generation of Circos 2D track plots http://bit.ly/1d73sRy pic.twitter.com/Q4ENEftuHi
□ DRAW+SneakPeek: Analysis workflow and quality metric management for DNA-seq experiments http://m.bioinformatics.oxfordjournals.org/content/early/2013/08/19/bioinformatics.btt422.short …
□ 自殺リスクを警告する血中マーカーが発見されたらしい 'Biological signal' of suicide risk found in blood http://www.medicalnewstoday.com/articles/265062.php …
□ Infernal: Computational identification of functional RNA homologs in metagenomic data based on “covariance models”
https://www.landesbioscience.com/journals/rnabiology/article/25038/ …
□ Genome in a Bottle Consortium 2013: standards for validating high-throughput variant detection: Platinum Genome, GRCh38 http://smallchangebio.wordpress.com/2013/08/16/genome-in-a-bottle-consortium-2013-standards-for-validating-high-throughput-variant-detection/…
□ Biology must never develop its own big-data systems:
>> http://www.eaglegenomics.com/2013/08/biology-must-never-develop-its-own-big-data-systems/ …
The terminologies/ontologies chosen to annotate data may be biological in nature, but at the technical level the aggregation and integration of disparate data sources from multiple repostories by means of querying and integrating at the metadata level through common or inter-mapped annotation standards is absolutely generic in nature and applies to all data management problems, not just biology. For biology as a whole to try and build its own specialist tools to manage this is just as bad as the situation today where individual labs are building their own in-house versions.
□ A sort of H-index for quantifying the coverage/diversity of bioactivity databases: http://chembl.blogspot.co.uk/2013/08/a-sort-of-h-index-for-coverage-of.html?m=1 …
□ Predicting the behavior of a chaotic pendulum with a variable interaction potential: カオス振り子の挙動予測。モデル化されたシステムのバイアス源の特定 http://m.chaos.aip.org/resource/1/chaoeh/v23/i3/p033103_s1 …
□ maskot1977:
Conquering computational challenges of omics data and post-ENCODE paradigms
http://genomebiology.com/2013/14/8/310
□ Genohub: The Next-Generation Sequencing Market: specialized NGS matching engine to link NGS providers to customers https://genohub.com/
□ Accuracy versus F score: Machine Learning for the RNA Polymerases: http://tata-box-blog.blogspot.jp/2013/08/accuracy-versus-f-score-machine.html
□ CyTargetLinker: a generic Cytoscape app to build regulatory networks http://projects.bigcat.unimaas.nl/cytargetlinker/
□ BioStorage Technologies launches INTEGRITY study: preparation methods on DNA / RNA samples, storage times are applied http://www.medicaldevices-business-review.com/news/biostorage-technologies-launches-integrity-study-150813 …
□ Software for Computing and Annotating Genomic Ranges: Software Based Infrastructure: 80 other Bioconductor packages
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118
Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures.
These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.
□ Phylogenomic Distance Method for Analyzing Transcriptome Evolution based on RNA-seq Data: http://m.gbe.oxfordjournals.org/content/early/2013/08/11/gbe.evt121.full.pdf#page=1 …
□ Adam and Eve DID live in Africa at the same time - but they probably didn't know each other
>> http://www.dailymail.co.uk/sciencetech/article-2382653/Adam-Eve-DID-live-Africa-time--probably-didnt-know-other.html
'Y-chromosomal Adam’ is thought to have walked the Earth between 120,000 and 156,000 years ago
This places him nearer to Eve who was around 99,000 to 148,000 years ago
Researchers say it is ‘extremely unlikely’ they were exact contemporaries
□ davecl42:
Pandoraviruses: giant viruses that share only 7% of their genome with other forms of life. Hint at 4th domain of life http://www.nature.com/news/giant-viruses-open-pandora-s-box-1.13410 …
□ The Deepest Uncertainty: Set theory: When a hypothesis is neither true nor false: CH and Large Cardinal Axioms
>> http://nautil.us/issue/2/uncertainty/the-deepest-uncertainty …
□ Can Quantum Bayesianism Fix the Paradoxes of Quantum Mechanics?
>> http://www.scientificamerican.com/article.cfm?id=can-quantum-beyesnism-fix-paradoxes-quantum-mechanics
QBism, which combines quantum theory with probability theory, maintains that the wave function has no objective reality. Instead QBism portrays the wave function as a user's manual, a mathematical tool that an observer uses to make wiser decisions about the surrounding world?the quantum world.
□ Waters Acquires Omics Informatics Firm Nonlinear Dynamics: SYNAPT G2-SとTransOmicsの共同開発から買収へ。イオンモビリティベースで非データ依存性オミクス構築 http://www.genomeweb.com/informatics/waters-acquires-omics-informatics-firm-nonlinear-dynamics …
□ CasesDatabase:
We've just indexed our 28,000th case report! Explore http://www.casesdatabase.com/ today - because every new diagnosis starts with a single case!
□ Eureka Genomics to offer Next-Generation Sequencing & Bioinformatics Services for the Ion Torrent Proton™ System http://www.pharmiweb.com/pressreleases/pressrel.asp?ROW_ID=77801 …
□ TRON_MZ:
TRON technologists have developed LIMS for a NGS laboratory within the existing Galaxy platform (http://bit.ly/1422pK3 )!
□ Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003172
computational design of RNA logic gates
We designed several YES, NOT, AND, and OR logic gates, including the design of combinatorial riboregulators. In sum, our de novo approach provides a new paradigm in synthetic biology to design molecular interaction mechanisms facilitating future high-throughput functional sRNA design.
□ davidgifford:
#lod2013 http://citydata.jp/ ranks Japan's citizen data (3rd LOD Challenge Day Ideathon / Datathon @ Mixi) #lod #linkeddata #opendata
□ YusukeKomiyama:
政府統計API関係のまとめ（復習用）： ・統計におけるオープンデータの高度化 http://www.soumu.go.jp/main_content/000230116.pdf … ・次世代統計利用システム http://www.soumu.go.jp/main_content/000230118.pdf …
#lod2013
□ Robustness and Compensation of Information Transmission of Signaling Pathways:
"阻害された経路の情報量の損失を他の経路が補償して情報量を堅牢に保って伝達"
>> http://www.sciencemag.org/content/341/6145/558 …
Information transmission to the biological output of neurite extension appeared robust. Cells may use information entropy as information so that messages can be robustly transmitted despite variation in molecular activities among individual cells.
細胞は信号のばらつきを自律的に補償して情報を堅牢（ロバスト）に伝達する
>> http://www.s.u-tokyo.ac.jp/ja/press/2013/35.html
細胞の情報伝達をシャノンの情報理論を用いて解析したところ、信号がばらついても情報が堅牢に伝えられることを見出しました。その仕組みの一つに、補償性がありました。今後堅牢性を生み出すしくみを解明して、薬剤の作用を効率的にコントロールしたり、生命のもつしなやかな通信システムの原理を人工通信システムへ応用します。
□ A multidimensional platform for the purification of non-coding RNA species
>> http://m.nar.oxfordjournals.org/content/early/2013/08/01/nar.gkt668.full
a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species.
□ A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets
>> http://www.biomedcentral.com/content/pdf/1471-2164-14-530.pdf
a reliable pipeline that can process Illumina-RNA-seq metatranscriptome data by linking the sequence reads to reference gene databases, their assigned functions, and predicted phylogenetic origin. The information retrieved from the processed data can be employed to obtain comprehensive biological insights in the ecosystem’s activity patterns. We employed this pipeline for the primary interpretation of the activity patterns of the human small intestine microbiome using effluent samples obtained from individuals with an ileostoma.
□ Leaf: Bioinformatic pipelines in Python: plan-driven / change-driven develop environment: LGL形式言語でパイプライン定義を保持し単ノードを分離
>> http://www.biomedcentral.com/content/pdf/1471-2105-14-201.pdf
□ LAMP: limitless arity multiple-testing procedure （無限次数多重検定法）: Statistical significance of combinatorial regulations: http://m.pnas.org/content/early/2013/07/22/1302233110 …
□ rapodaca:
Recoding Pharma's cultural DNA http://bit.ly/17vengt
□ NIH mulls rules for validating key results
US biomedical agency could enlist independent labs for verification.
>> http://www.nature.com/news/nih-mulls-rules-for-validating-key-results-1.13469
in 2012, scientists at Amgen, a drug company based in Thousand Oaks, California, reported their failure to replicate 89% of the findings from 53 landmark cancer papers.
ENCODE tested more than 200 antibodies targeting modifications to proteins called histones and found that more than 25% fail