Observable consequences of the hypothesis that the observed universe is a numerical simulation performed on a cubic space-time lattice or grid are explored. The simulation scenario is first motivated by extrapolating current trends in computational resource requirements for lattice QCD into the future. Using the historical development of lattice gauge theory technology as a guide, we assume that our universe is an early numerical simulation with unimproved Wilson fermion discretization and investigate potentially-observable consequences.この宇宙がシミュレートされたものであることをシミュレートする観測実験。立方時空格子における計算リソース要件とフェルミオン離散化
Among the observables that are considered are the muon g － 2 and the current differences between determinations of α, but the most stringent bound on the inverse lattice spacing of the universe, b－1>? 1011 GeV, is derived from the high-energy cut off of the cosmic ray spectrum. The numerical simulation scenario could reveal itself in the distributions of the highest energy cosmic rays exhibiting a degree of rotational symmetry breaking that reflects the structure of the underlying lattice.
The WholeCell model is based on data collected from 900 publications. Some 1,900 numerical values were extracted from these sources to become parameters of the model. This is an impressive compendium, which anchors the simulation in real data.全細胞シミュレーション
The network-extracted ontology (NeXO) contains 4,123 biological terms and 5,766 term-term relations, capturing 58% of known cellular components. We also explore robust NeXO terms and term relations that were initially not cataloged in GO, a number of which have now been added based on our analysis.
Using quantitative genetic interaction profiling and chemogenomics, we find further support for many of the uncharacterized terms identified by NeXO, including multisubunit structures related to protein trafficking or mitochondrial function. This work enables a shift from using ontologies to evaluate data to using data to construct and evaluate ontologies.
EMdeCODE densities improve significantly the prediction of enhancer loci and retroviral integration sites with respect to previous methods. Importantly, it can also be used to extract distinctive factors between two arbitrary conditions. Indeed EMdeCODE identifies unexpected epigenetic profiles specific for coding versus non-coding RNA, pointing towards a new role for H3R2me1 in coding regions.
This thesis explores the data analysis involved in genome-wide association stud- ies (GWAS) using Hadoop technologies and data mining techniques. GWAS is amongst the most popular study designs to identify potential genetic variants that are linked to the etiologies of diseases. In the future, GWAS will also play an important role in personalized medicine. The complex data analysis in GWAS calls for new technologies and techniques.
SemScape is developed as plugin for the latest version of Cytoscape, 3.0, which is released in beta at the time of this writing and presents a completely new architecture from previous versions. SemScape offers a range of functionalities, which are derived from what was implemented in RDFScape [2] and AGUIA [3]. However this system provides a newer, more eff cient and up to date implementation.
The Disease Ontology Annotation Framework (DOAF) to provide a comprehensive annotation of the human genome using the computable Disease Ontology (DO), the NCBO Annotator service and NCBI Gene Reference Into Function (GeneRIF). DOAF can keep the resulting knowledgebase current by periodically executing automatic pipeline to re-annotate the human genome using the latest DO and GeneRIF releases at any frequency such as daily or monthly.
DOAF provides a computable and programmable environment which enables large-scale and integrative analysis by working with external analytic software or online service platforms. A user-friendly web interface (doa.nubic.northwestern.edu) is implemented to allow users to efficiently query, download, and view disease annotations and the underlying evidences.
To improve accuracy, the team sequenced extremely deeply, ultimately generating some 5 billion reads on the SOLiD sequencing platform. “The data sets were incredibly massive,” Kundaje says. “Processing these data sets locally was quite a challenge.” The group turned to DNAnexus, uploading their sequence files to the cloud and preprocessing the data with the company’s probabilistic mapping tool. “DNAnexus made that process incredibly simple,"SOLiDで5億リードを生成、新手法で確率的マッピング
crAss, a novel more direct approach based on the same concept, i.e. using cross-assembly of reads from different metagenomes to assess the degree of similarity between the sampled communities. Thus, cross-metagenome assembly enables a sensitive comparison of entities that are shared between samples, including viruses with no homology to known sequences.未知の配列によるキメラ・シーケンスの影響を制限する非リファレンス依存のメタゲノム解析
approximately 73% of all protein-coding SNVs and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000?10,000?years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.人類の遺伝的変異は一万年で急速にポテンシャルを蓄積している
TrueSight, which for the first time combines RNA-seq read mapping quality and coding potential of genomic sequences into a unified model. The model is further utilized in a machine-learning approach to precisely identify SJs. Both simulations and real data evaluations showed that TrueSight achieved higher sensitivity and specificity than other methods. We applied TrueSight to new high coverage honey bee RNA-seq data to discover novel splice forms.
a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines.
We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties, and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large (n=1340) microarray and Illumina GAII RNA-seq transcriptomics datasets.
ISCB: computational tools for NGS, cancer informatics, and cloud and work flows for reproducible biology. ISCB is known for hosting a variety of international meetings including ISMB, while BGI of Shenzhen is one of the world's largest sequencing centers.
SCCG: The local and international scientific community is highly encouraged to participate in this extraordinary event that is bringing together some of the world’s thought leaders in the fields of computational biology, biomedical informatics, and genomics, as well as providing a forum for the presentation of the excellent research being d
In probability theory and information theory, the ‘relative entropy’ or the ‘Kullback?Leibler divergence’ is an accepted measure of the difference between two probability distributions.野生型および変異型RNA構造アンサンブルの相対的エントロピー計算のための動的プログラミング・アルゴリズム
We designed a novel efficient dynamic programming algorithm remuRNA to compute the relative entropy between the wild-type and mutant ensembles. We present the mathematical relationships on which our dynamic program is built in the following subsection.
Clarity LIMS, Intuitive Lab Management Software for Regulated and Research Labs. from GenoLogics on Vimeo.
Clarity LIMS is built for NGS laboratories that are CLIA certified or aiming to become certified. Clarity LIMS increases user adoption through exceptional usability and will assist clinical lab directors to ensure adherence to their lab’s SOPs through workflow enforcement.
ブートストラップ、ジャックナイフでのモンテカルロ法、パーミューテーションテスト（並べ替え検定）、マルコフ連鎖モンテカルロ（MCMC）法などの高度な統計手法を用いた解析についてきちんと解説し、その使用法を示したもの。解析についてはR により、統計学的コンピューティングの事例によるアプローチで計算統計の古典的な主要問題を解説した。全事例にR のコードを付け、R 言語のプログラミングの概念の説明を補足するようにした。
Bioclipse, a graphical workbench for the life sciences, provides functionality for managing and visualizing life science data. We introduce Bioclipse-R, which integrates Bioclipse and the statistical programming language R. The synergy between Bioclipse and R is demonstrated by the construction of a decision support system for anticancer drug screening and mutagenicity prediction, which shows how Bioclipse-R can be used to perform complex tasks from within a single software system.
Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3' UTR. We present a perspective on current work and new single-molecule sequencing methods for detecting RNA base modifications.
Transthyretin-mediated amyloidosis has become the single-most important factor for the 3-5 year valuation of certainly Alnylam, and possibly ISIS Pharmaceuticals as well. After TTR, Z-alpha-1-antitrypsin (Z-AAT) is gearing up as the next Alnylam(RNAi)-ISIS(antisense) battleground. Expect to hear competitive language from the two camps why their approach will prove superior over the other. It is, however, worth keeping in mind that having two candidates race towards approval can also have significant pie-enlarging benefits.Alnylam社とISIS医薬品による、トランスサイレチン(TTR)アミロイドーシス治療を主戦場とした競争。最初に商業的成功を収めるのは、RNAi TherapeuticsかRNaseH antisenseか
Modifications can be incorporated into synthetic oligonucleotides in a variety of ways. Standard DNA bases are synthetically coupled via phosphoroamidite chemistry. The reaction proceeds in the 3’ to 5’ direction where the 5’ hydroxyl group of each base attaches to the 3’ phosphate group of the next base. Many modifications, such as 6-FAM, standard biotin, and internal Cy3, can be attached via phosphoroamidite chemistry directly on the synthesis column
MetaVelvetとかSparseAssemblerとかGlimmer-MG入れてるとか良いカスタマイズね。
Cases Database, a continuously-updated, freely-accessible database of over 10 000 medical case reports from multiple publishers, including Springer, BMJ and PubMed Central.
Comparing two enormous sequences is very difficult too. Say you want to see the patterns or differences that exist between the human and chimpanzee genomes. Some of the world’s most powerful supercomputers are required in order to meaningfully align such long strings of DNA bases, letter by letter, piece by piece.
a powerful method for graphical representation and analysis of DNA. It creates a scatter plot derived from a DNA sequence. Each of the points on the plot corresponds to one base of the sequence, A, C, T, or G. The first nucleotide of the sequence is plotted halfway between the center of the unit square and the corresponding corner of the nucleotide. The next point is plotted halfway between the next corresponding corner and the previous point. This cycle continues until all nucleotides of the sequence have been read, and the sequence has been plotted.ゲノム配列の相違をフラクタル・パターンで可視化・比較する"CGR"
Albeit relatively new, cloud computing promises to address big data storage and analysis issues in the bioinformatics field. Here we review extant cloud-based services in bioinformatics, classify them into Data as a Service (DaaS), Software as a Service (SaaS), Platform as a Service (PaaS), and Infrastructure as a Service (IaaS), and present our perspectives on the adoption of cloud computing in bioinformatics.
SRA contains >10^15 bases (a PetaBase!) of data w/ 390TB of open-access data & 610TB of controlled-access clinical data.http://1.usa.gov/RztMKU
DIANA-LncBase hosts transcriptome-wide experimentally verified and computationally predicted miRNA recognition elements (MREs) on human and mouse lncRNAs. The analysis performed includes an integration of most of the available lncRNA resources, relevant high-throughput HITS-CLIP and PAR-CLIP experimental data as well as state-of-the-art in silico target predictions.
The experimentally supported entries available in DIANA-LncBase correspond to >5000 interactions, while the computationally predicted interactions exceed 10 million. DIANA-LncBase hosts detailed information for each miRNA?lncRNA pair, such as external links, graphic plots of transcripts’ genomic location, representation of the binding sites, lncRNA tissue expression as well as MREs conservation and prediction scores.
@leonidkruglyak @SamWangPhD What I wonder is, what advances in genomics & AI are newsworthy? Promethean revolutions or modest increments?
3W2III-7 12月13日 17:43 第2会場 データベースと機械学習を利用した新しい 1細胞RNA-seq 法とそのデータ解析の開発 http://goo.gl/KNE4n #mbsj2012 よろしくです。
Vanderbilt-Ingramがんセンター、次世代シーケンサーで難治乳がんの分子標的を洗い出し: 米国Vanderbilt-Ingram Cancer Centerのresearch faculty、Justin M.... http://nkbp.jp/VHJ1CR
間もなく開始16時~。午前中は質問も沢山いただきましたRT @elsevierjp: 図書館員の皆様向）世界の著者識別子ORCIDとScopusの連携ツール※ このツールはScopusのご契約がない機関の方でも利用可能です。http://ow.ly/1PSk5T
そういえば、今日のBiosupercomputing Symposiumのプログラム内容。スライドとかあるので、バイオシミュレーションについて興味が有る方は。【PDF】 / “4th-BSCS-proceedings.pdf” http://htn.to/zUNRfY
スーパーコンピュータ「京」をターゲットとして、ライフサイエンス分野のグランドチャレンジングな一貫ソフトとして、分子・細胞・臓器・全身・脳に亘るシミュレーションソフトと、データ・解析融合手法 及び 生命体基盤ソフトウエアを2006年10月から５年あまり６グループ百数十名(?)で開発してきた成果が発表されます。（今年が最終年度）合わせて、海外からこの分野の先端研究グループの指導的研究者9名の講演があります。
Xeon Phi、おそらく来年と再来年のISMBまわりで徐々にBioinformaticsでのアプリケーションが見えてくるんだろうし、MICアーキテクチャ自体には結構期待しているが、バイオインフォマティクスにおける深刻なノイマンボトルネックはMICではより深刻なはず。
プログラムなんて先に送っておけばいいので気にしないんですが、Xeon Phi のリングバスはたいていのバイオインフォのアプリでボトルネックになるでしょうね。メモリ帯域使うアプリ多いし。
ロブスターアルゴリズムって結構いけてるね。エントロピー使ってリードの中にSTR含むものを選択して、繰り返し領域はあえてマップせず、その両脇の配列を特定して、その距離から繰り返し数を特定してるのか。ただSTRより長い繰り返しがあるとき、エントロピーがどうなるのか気になった。
マーケットプレイスで高騰してる... / 「Rによる医療統計学」はRの使い方と統計解析の基礎が学べる良書（ただし入手困難） - Wolfeyes Bioinformatics beta http://yagays.github.com/blog/2012/11/29/review-introductory-statistics-with-r/ …
RT @myuuko 嫌悪の原因となるものが、知り合いと関連しているときより、知らない人と関連しているときに、嫌悪の感情は強く（実験1）、心拍は低下し（実験2）、回避行動が素早くなる（実験3）。感染症回避の観点から考察。 http://ow.ly/1PSlvY
胎児の細胞が脳血液関門を越えて母親の脳に入って増殖するマイクロキメラ現象はマウスの研究でわかっていた。ヒトでも男性しかない遺伝子が成人女性の脳にあったとのこと。 母親は生物学的に子供との（少しではあるが）キメラになっているということか。 http://news.sciencemag.org/sciencenow/2012/09/bearing-sons-can-alter-your-mind.html#.ULp9Z2nbYPQ.twitter …
BLASTとは生命科学において多くの研究者から信仰を集めている神の名前である。研究者が供物として自身の研究データを差し出すと「奇跡」よって論文に記載すべき謎の文字列を与える。なお、奇跡と呼ばれるだけあって何をしているのか分からないので、信者は何も考えずただデータを差し出せばよい。
結局みずもと先生は、カントールの対角線論法の議論を「救う」ため、トップオラクルを持つ二階算術は対角線論法が適用できないウィトゲンシュタイン的理論のモデルとなっていると主張したいのだろうか。構成主義者の「計算可能実数は可算個しかない」と言う主張を退けておいて、大して変わらない主張。
で、ウィトゲンシュタイン的な数学の哲学の有益さに関する個人的の疑問は、それが静的で浅い相対主義で「いくつもの異なるアプローチがあり得る」とただ言うだけのように見えてしまうことです。だからなんだ。異なるアプローチが並列する現状、そしてそれら間の複雑なインタラクションを捉えていない。
(5) 水本さんのトップオラクルモデルじゃ上手く行ってなくね？ ちょっと色々調べてみよう。 ⇒ (6) おお、無限時間チューリング計算可能なものだけからなるトポスを考えると、実数から自然数への単射がある！！すげーー！！ ⇒ (7) 完。
なるほど、15台クラスタ構成で1億レコードではimpalaはhiveの8倍くらいの性能だったけど、10億レコードではスワップ多発で2倍程度になったとのこと。これでImpalaの現状の性能はだいぶわかった感がある http://www.atmarkit.co.jp/ait/articles/1212/07/news011.html …
@syuichiao @DrMagicianEARL 「星座」といえばISIS-2試験。Lancetはサブグループ解析を要求。解析に懐疑的な筆者は、双子座と天秤座の患者さんにアスピリンの二次予防効果が認められなかったことを公表して反撃。http://www.ncbi.nlm.nih.gov/pubmed/2899772
あなた具体的に虚偽を指摘されたら指摘してきた相手をブロックしてますよね @mariscontact 反原発連合のこの方、よく私にいちゃもんつけてくるよ。具体性もなく、虚偽と言い →野間易通@kdxn エートスについて竹野内真理が流している情報のほとんどは虚偽。
@oldmoon_1 反原発論者で悪目立ちしてる人たちに関しては、「自分たちに同調しないものはみんな敵だ」という排他的な印象が確かに強いですね。「今は無理でも最終的には脱原発を」っていう人たちとの間にも明確な溝がありますし（この溝こそが彼らの最大の問題と個人的には思っています）。
自民党の憲法改正草案http://bit.ly/SODuHJ 第百二条「全て国民は、この憲法を尊重しなければならない」自民党内に「医師法が医師に対する規定であるように、憲法は国家に対する規定であって、国民に対するものではないですよ」と義務教育レベルの指摘をする人はいなかったのか…
普通選挙とは、統計学の成果を全否定しランダムサンプリングに納得できない人が納得するために全数検査を行い莫大なコストを支払う儀式である。 ってのが100年後くらいの教科書に載っていそう。 #人類が皆統計学を理解する日は来ない
ランダムサンプリングによる有権者調査で議席数が分かるなら、選挙権って要らないんじゃないかなぁ。 選挙速報にしても、開票率0%で当選確実が出るような世界だし。 政治家が統計を使わないことを馬鹿だというのであれば、統計の力によって議員を選出しないのもまた馬鹿なんじゃないのかなぁ。
