Creating Civilizations.

□ MrPrudence:
Creating Civilizations - Robert Strati http://creatingcivilizations.tumblr.com/ Architectural/mathematical/notational schematic fictions via @socks_studio






(Genomic HyperBrowser server: Schematic overview: HBサーバの統計分析・生体仮説検定までの概略図。モンテカルロ法によるP値評価が適切か、漸近計算を用いるかをシステムが決定し、最適化する )


□ The Genomic HyperBrowser: analysis web server for genome-scale data:
ゲノムスケールのデータ分析の為のオープンエンドWebサーバ。統計分析と仮説検定をシステムに包括

>> http://m.nar.oxfordjournals.org/content/early/2013/04/29/nar.gkt342.full …

The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

□ RT @ScienceNOW: Breathtaking image of a hurricane swirling around Saturn's north pole pic.twitter.com/kDePPEIidW

土星の北極の嵐を捉えた衛星写真が凄すぎる。神威を感じる。

OBLIVION GFX Montage from GMUNK on Vimeo.

□ OBLIVION GFX Montage: (Bradley G Munkowitz/GMUNK) 今や国際的に引っ張りだこのグラフィック・デザイナー集団、GMUNKによる映画『オブリビオン』の為のモニターデザイン。ライトテーブル綺麗




□ Race, Poverty and Deprivation in South Africa: 南アフリカにおける人種、貧困、物的困窮:

>> http://jae.oxfordjournals.org/content/22/2/187.full.html

If a factor were likely to be the main contributor to the higher income and material deprivation of Africans, it would be education.

この所得分布や物質的剥奪濃度曲線を導いている“反実仮想分析”は、ベイズを用いた統計的因果推論の一つ。






□ ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria

>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063083

ExtremeDB is a freely available web based relational database which integrates general characteristics, genome-proteome information, industrial applications and recent scientific investigations of the seven major groups of 865 extremophillic microorganisms. The search options are user friendly and analyses tools such as Compare and Extreme BLAST have been incorporated for comparative analysis of two or more extremophiles and determining the sequence similarity of a given protein/nucleotide in relation to other extremophiles respectively. The effort put forth herein in the form of database, would open up new avenues on the potential utility of extremophiles in applied research.

極限性古細菌・微生物の統一レポジトリ。非情報系研究者に高度なUIを提供する流れの成果




□ ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats

>> http://bioinformatics.oxfordjournals.org/content/early/2013/05/15/bioinformatics.btt277.short

遺伝子座タンデムリピートを推定し配列のエラーを修正するプログラム




□ ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores

>> http://bioinformatics.oxfordjournals.org/content/early/2013/05/16/bioinformatics.btt268.short




□ Fighting against uncertainty: An essential issue in bioinformatics

>> http://arxiv.org/abs/1305.3655v1

estimation problems on high-dimensional discrete spaces in which the number of possible discrete solutions is immense. In the analysis of biological data or the development of prediction algorithms, this uncertainty should be handled carefully and appropriately.

In this review, I will explain several methods to combat this uncertainty, presenting a number of examples in bioinformatics. The methods include (i) avoiding point estimation, (ii) maximum expected accuracy (MEA) estimations, and (iii) several strategies to design a pipeline involving several prediction methods.

□ m_hama:

Briefings in Bioinformatic に、バイオインフォマティクスの推定問題における解の不確実性に関するレビュー論文がアクセプトされました。プレプリント版はarXivから入手可能です

Bioinformaticsの推定問題については、つい先週NIHから、P-valueやAUC推定の不安定さを指摘する論文が出てましたね The limits of p-values for biological data mining http://www.biodatamining.org/content/pdf/1756-0381-6-10.pdf




□ Global Bioinformatics Market Expected to Hit USD 7.5 Billion by 2017

>> http://www.biotechdaily.com/business_news/articles/294746327/global_bioinformatics_market_expected_to_hit_usd_75_billion_by_2017.html

バイオインフォマティクス市場は五年後に75億ドル規模に。収益は解析ソフトウェアと分析サービス。無数のツール、ペタバイト級商用プラットフォーム(GenoMiner等)、ストレージギャップに言及。でも統一規格が現れたら、ある程度収斂しそう




□ Elsevier Launches Genomics Data App in Collaborate with Illumina in BaseSpace: エルゼビアとイルミナが大規模ゲノムデータ共有アプリを立ち上げ。レビュー容易に http://www.prnewswire.com/news-releases/elsevier-launches-genomics-data-app-in-collaboration-with-illumina-208421961.html …




□ DailyNewsGW:
ICR, Wellcome Trust, Illumina Launch Clinical Genetic Testing Effort http://bit.ly/13BV8Qq




□ GigaScience:
"squishome" in @biomemagazine Paving the way to large-scale biodiversity research: Xin Zhou on PCR-free metabarcoding http://www.biomedcentral.com/biome/paving-the-way-to-large-scale-biodiversity-research-xin-zhou-discusses-pcr-free-metabarcoding/ …




□ physorg_com:
#RNA capable of catalyzing electron transfer on early earth with #iron's help, study says http://phy.so/288172502 @georgiatech




□ ProMED_mail:
PRO/AH/EDR> MERS-CoV - Eastern Mediterranean (05): Tunisia ex Saudi Arabia/Qatar, fatal, RFI http://bit.ly/115pDlC






□ Life Before Earth

>> http://arxiv.org/pdf/1304.3381v1.pdf …

at biosemiotics perspective: Linear regression of genetic complexity, origin of life = 9 bn yrs ago

Linear regression of genetic complexity (on a log scale) extrapolated back to just one base pair suggests the time of the origin of life = 9.7 ± 2.5 billion years ago. Adjustments for potential hyperexponential effects would push the projected origin of life even further back in time, close to the origin of our galaxy and the universe itself, 13.75 billion years ago.

Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet. As a result the doubling time of human functional complexity has reached ca. 20 years. Finally, we discuss the issue of the predicted "technological singularity" and give a biosemiotics perspective on the increase of life’s complexity.

ゲノム長と片対数グラフから、生命の起源は90億年前（地球形成よりも前）とする説。さりげにENCODEプロジェクトにも言及w 生物活性をメモリ、自己触媒をコーディング要素として哲学ぽい


□ physorg_com:
Researchers use Moore's Law to calculate that #life began before #Earth existed http://phy.so/285498237




□ Evolvability Is Inevitable:: Increasing Evolvability without the Pressure to Adapt:

>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0062186 …

種の進化に選択圧や生存競争は無関係？遺伝子型空間を介在した進化モデルを数理シミュレート。表現型発散と分布の受動ドリフトモデル 。

Why evolvability appears to have increased over evolutionary time is an important unresolved biological question. Unlike most candidate explanations, this paper proposes that increasing evolvability can result without any pressure to adapt.

The insight is that if evolvability is heritable, then an unbiased drifting process across genotypes can still create a distribution of phenotypes biased towards evolvability, because evolvable organisms diffuse more quickly through the space of possible phenotypes.

Furthermore, because phenotypic divergence often correlates with founding niches, niche founders may on average be more evolvable, which through population growth provides a genotypic bias towards evolvability. Interestingly, the combination of these two mechanisms can lead to increasing evolvability without any pressure to out-compete other organisms, as demonstrated through experiments with a series of simulated models.

Thus rather than from pressure to adapt, evolvability may inevitably result from any drift through genotypic space combined with evolution's passive tendency to accumulate niches.

私は幼い頃から直観で信じていたのだけど、それぞれの生命種が「何かをする為に、何かを進化させることはない」ということ。なぜなら、それはシステマとモチベーションが前後交錯した詐術に近いのだから。ただ意志というものが感じられるなら、それは予め決定論的にビルドインされた機能の影なのだと。

数千年先の未来、何世代も崖に住み続けたペンギンの中に、飛べるようになるものが現れるかもしれない。その偶然は恰も、ペンギンが飛ぶことを願って適応したという意志が感じられるのかもしれない。


□ EurekAlertAAAS:
Computer scientists suggest new spin on origins of evolvability : http://ow.ly/ksFKU




□ Kolmogorov Complexity of Categories: programming language for describe categories, functors & natural transformations http://link.springer.com/chapter/10.1007%2F978-3-642-38164-5_25 …




□ Open Questions: A logic (or lack thereof) of genome organization:

>> http://www.biomedcentral.com/content/pdf/1741-7007-11-58.pdf

ゲノム組成における論理の欠乏。統計的アプローチでは相互作用に関する推定に不利。機械論的仮説ではどうか

Many approaches to the question have looked for statistical signatures of sequence under selective constraint. However, selection could, for example, be on the process of transcription not the product of transcription. A stronger, or perhaps complementary, approach is to start with a mechanistic hypothesis.

□ TechnionLive:
DNA and other biomolecules combine to create computing power, capable of solving equations and ? someday ?... http://fb.me/2EkGbm0j2




□ Discovering how we evolved: Evolving genes lead to more evolving genes:ヒト進化を促すFOXP2調節遺伝子。GC含量、再結合速度の比較にバイオインフォマティクス応用 http://sangerinstitute.wordpress.com/2013/05/21/discovering-how-we-evolved-evolving-genes-lead-to-more-evolving-genes/ …

FOXP2 in Europeans, but not in Asians/Africans. Does this mean that Europeans have enrichment conferring a different advantage?

The selected genes have multiple roles in cellular development, signalling, reproduction and immunity. Selection of these genes in Europeans is more likely to reflect local population adaptations to the climate, diet or pathogens that they encountered as their ancestors spread across Europe after splitting from the ancestors of Asian populations.

□ sangerinstitute:
Surprising discoveries about human development revealed by Qasim’s technique to find selection signatures. bit.ly/10LZjHs #evolution

ゲノミクスやジェネティクスやBioinformaticsで「○○が出来るようになる」ネタは面白いけど、統計をとったくらいで「ある遺伝子の進化への作用が分かる」というのは、詐術に近い部分が大きいのではないかと思う。作用系の数理的体系の確立がないから、統計的手法に縋るのであって




□ Algebraic classifiers: a generic approach to fast cross-validation, online training, and parallel training http://jmlr.org/proceedings/papers/v28/izbicki13.pdf …




□ n0rr:
Implications of fidelity difference between the leading and the lagging strand of DNA for the acceleration of evol. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472163/ …




□ RNA-seq Workflows & Tools: various workflows for analyzing differential gene/exon/isoform expression w/ RNA-seq data http://figshare.com/articles/RNA_seq_Workflows_and_Tools/662782 …




□ NIH is losing $1.7 billion from sequestration and other cuts, lowering its budget to $29.15 bn: グラントがNIH依存なのも考えものかな http://news.sciencemag.org/scienceinsider/2013/05/sequesters-5-cut-rolls-through-b.html …




□ ins20:
政府　「日本版ＮＩＨ」構想で臨床試験・治験のＤＢ構築へ: 　菅義偉官房長官は22日の産業競争力会議で、6月中旬にまとめる「健康・医療戦略」の骨子を提示した。 http://bit.ly/16PQa9Y




□ tjvision:
Too clever by half. Software for Bayesian analysis of biogeography from UC Berkeley named... BayArea. https://www.datadryad.org/resource/doi:10.5061/dryad.8346r …




□ Vertebrate Taxonomy Ontology: extinct/extant comprehensive hierarchy. Based on the NCBI, PaleoDB, TTO & AmphibiaWeb http://bioportal.bioontology.org/ontologies/50317/ …




□ http://re3data.org launched: registry of research data repositories: funding organizations, libralies, publishers http://www.re3data.org/




□ Ubiquitous clinical sequencing: finding rare disease mutations: The data are much easier to share, process and query http://www.biomedcentral.com/biome/ubiquitous-clinical-sequencing-matthew-bainbridge-talks-about-finding-rare-disease-mutations/ …




□ DFID_Research:
Integrating Global and National Knowledge to Select Medicines for Children: The Ghana National Drugs Programme http://ow.ly/lhf0J




□ The Ultimate Biotech Diversification Strategy: The $80bn behemoth has increased by intriguing compounds into pipeline http://www.fool.com/investing/general/2013/05/26/the-ultimate-biotech-diversification-strategy.aspx …




□ Krionarheim:
Will gov. make progress? Building a More Equitable Global R&D System http://blogs.plos.org/speakingofmedicine/2013/05/24/demonstrating-progress-building-a-more-equitable-global-rd-system/ … @SuerieMoon @jarottingen @PLOSMedicine #WHA66




□ First GWAS hits for cognitive ability: SNPbased heritability estimates significant fraction of total genetic variance http://infoproc.blogspot.jp/2013/05/first-gwas-hits-for-cognitive-ability.html




□ isatools:
ORCID codefest 2013 http://wp.me/pXDzM-8p




□ cytoscape:
cytoscape.js 2.0 released! JavaScript library for network visualization. https://groups.google.com/forum/?hl=en&fromgroups#!topic/cytoscape-discuss/GV2vr4d4EQI …




□ bioclinica:
Data importing/exporting and integration considerations. http://ow.ly/lnJa2




□ Bioinformatics Law examines legal issues associated w/ tools, procurement& licensing, in-house&contracted development http://apps.americanbar.org/abastore/index.cfm?pid=5450067&s