("Monarch of the Glen" by KENNETH BARKER)
□ José González and St. Vincent
♪ Step Out
2013年の締めくくりを飾るに相応しい新たな名曲。
本能を揺さぶるプリミティブなコーラス。
□ Nick Murray & Dominik Schwarzer / "Lift"
♪ I Can Feel You (ft. Tyler Gurwicz & Jenny Bae)
□ iPad Air やっと届きましたo(*゜▽゜*)o Wifi + Cellular 64GB Silver です。ニューヨーク出張に間に合って良かった。。！ふんわり軽い使用感！4Gでどこでも高速でつながる快適さ。
□ 研究開発において、『技術力で競争』というスローガン自体がもう通用しないのには半ば同意。エンジニアリングって雨後の筍だから、国際的な水平連携力だけがイニシアチブに直結する。こればっかりは政治がどうこう出来る次元じゃないよね。
□ バイオでもだけど、「装置」を用意出来ると利益が進展するという確証があって、如何に自明なことであっても、誰も責任を取りたくないと思ってる時点でリソースが足りてないんだよね。これは経済に乗ってこないという意味で、政治にキックスタートを期待するのは間違い。金の周りにしか体制は出来ない。
□ CrapBio's Quantum Atomic Capture Sequencer (QuACseq) with their SHTseq System: DNA Sequencing Takes a Quantum Leap:
>> http://thescienceweb.wordpress.com/2014/02/05/dna-sequencing-takes-a-quantum-leap/ …
Initially, QuACseq D-500 can only be purchased by governments in return for handing over all fiscal, legislative & military power to CrapBio
□ ArchiLD: Hierarchical Visualization of Linkage Disequilibrium in Human Populations
>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897757/ …
□ Illumina Launches Accelerator Program for Startups Working on NGS: $100,000 w/ customer networks, financial modeling
>>http://www.genomeweb.com/sequencing/illumina-launches-accelerator-program-startups-working-ngs …
□ Invitae:
Personal "Omics" Cloud and #GenomeManagement - #PMWC14 http://fb.me/2xRAiAJ7D
□ Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications
>> http://online.liebertpub.com/doi/pdf/10.1089/omi.2013.0149
By integrating DELSA researchers’ collective experiences with omics guidelines and publication requirements, one simplified, yet informative. NanoPubs and MicroPubs are two newer publication avenues that could serve to quickly and accurately share information.
□ "THE FIELD GUIDE to DATA SCIENCE" by Booz Allen Hamilton
>> http://www.boozallen.com/media/file/The-Field-Guide-to-Data-Science.pdf …
Excellent stuff!
If you only have knowledge of how items are connected to 1 another, start with Graph-based methods
□ pubchem:
PubChemRDF is released. It helps facilitate PubChem data integration and use with semantic web technologies. http://1.usa.gov/1db9Y4T
□ micheldumontier:
#FALDO paper on semantic sequence annotations now available on BioRxiv
http://www.biorxiv.org/content/early/2014/01/31/002121 … #bioinformatics #semanticweb
□ G-BLASTN: accelerating nucleotide alignment by graphics processors: http://m.bioinformatics.oxfordjournals.org/content/early/2014/01/24/bioinformatics.btu047.abstract …
□ A Universal Method for Species Identification of Mammals Utilizing NGS for the Analysis of DNA Mixtures:
>> http://www.plosone.org/article/info:doi/10.1371/journal.pone.0083761 …
メタ哺乳類ゲノミクス
#metamammagenomics
見たまんまゲノミクス
ゲノム読んで生態との関連を見出すよりも、異系統のゲノムが適応環境を探る動的なプロセスの方に興味がある。
□ Quantum Biosystems demonstrates First Reads using Quantum Single Molecule Sequencing: http://www.quantumbiosystems.com/we-did-a-presentation-pmwc-with-prototype-demo.html …
□ dgmacarthur:
Excellent 2014 predictions in the sequencing space by @OmicsOmicsBlog:
>> http://omicsomics.blogspot.com/2013/12/peering-through-flowcell-glass-darkly.html …
"All these changes in sequencing market, particularly for the companies built physical mapping platforms, OpGen, BioNano Genomics & Nabsys."
□ NanoString tops Omics stocks http://www.genomeweb.com/nanostring-pacbio-fluidigm-lead-december-charge-omics-tools-mdx-stocks …
stock market: Among the top performers in the omics tools space were PacBio, which closed the year up 208%, and Affymetrix, up 170%
Among the other top gainers for the year were Accelerate Diagnostics (+203 %), Fluidigm (+168 %), and Illumina (+99 %).
□ PLINK 1.90 alpha: 100-1000x faster identity-by-state matrix computation, distance-based clustering, LD-based pruning
>> https://www.cog-genomics.org/plink2/
□ Climate change the state of the science (data visualization)
□ RichardDevine:
"Gibber": creative coding environment for audiovisual performance and composition:… http://instagram.com/p/h_jM5ADQkX/
(Clockwise from top right, the genomes of a human, a chimpanzee, a mouse and a zebrafish are arranged in a circle, with each color square corresponding to a pair of chromosomes. Lines connect similar DNA sequences, visually emphasizing just how much DNA we share with other species. Image: Martin Krzywinski/EMBO)
□ Martin Krzywinski: Bioinformatics Scientist/Biological Data Designer:
>> http://mkweb.bcgsc.ca
CircosやHive Plotsなど、近年の生物学的データ視覚化のトレンドを築いたデザイナー
>> Circle of Life: The Beautiful New Way to Visualize Biological Data
>> http://www.wired.com/wiredscience/2013/11/wired-data-life-martin-krzywinski/#slideid-324601
Circos, an open source visualization tool that arranges tabular data in circular form. It was a simple idea, but transformative: It’s since been used for thousands of visualizations, and its distinctive aesthetic is synonymous with the informational richness of our moment.
□ Bioconductor:
http://bioconductor.org/packages/2.14/bioc/html/AtlasRDF.html … AtlasRDF Gene Expression Atlas query and gene set enrichment package.
□ The Multiscale Backbone of the Human Phenotype Network based on Biological Pathways
>> http://www.biodatamining.org/content/pdf/1756-0381-7-1.pdf …
PHPN can discover genetic connections b/w PTs, characterizing the shared mechanisms in the former identifying unifying traits in the latter. Recognizing the connections b/w different traits/phenotypes is an integral first step in understanding the dynamic of most complex disease.
□ The New York Genome Center Purchases Illumina HiSeq X Ten Sequencing System:
>> http://www.nygenome.org/news/the-new-york-genome-center-purchases-illumina-hiseq-x-ten-sequencing-system/ …
□ Illumina TruSeq synthetic long-reads empower de novo assembly/resolve complex highly repetitive transposable elements http://biorxiv.org/content/early/2014/01/19/001834 …
□ llumina Launches Two New Platforms at JP Morgan Conference; Claims $1,000 Genome
>> http://bit.ly/L0TWDQ
□ Tech Specs of HiSeq X and NextSeq 500: http://res.illumina.com/documents/products/datasheets/datasheet-hiseq-x-ten.pdf … & http://nextgenseek.com/2014/01/illumina-hiseq-x-ten-and-nextseq-500-a-first-look/ …
"Illumina’s NextSeq 500 will have sequencing throughput of 150Gb with 400 Million 2x 150bp reads."
□ Graph-based computational analysis reveals a correlation of exon-skipping events w/ splicing/transcription/epigenetic
>> http://nar.oxfordjournals.org/content/early/2013/12/24/nar.gkt1338.long …
exon-skipping regions are then identified by iteratively navigating the sub-graph patterns to reveal those corresponding to a skipping event.
□ GECellBiology:
The 2013 Cell Image Competition; view the beautiful cell images & vote for your favourite http://goo.gl/yCHYJL pic.twitter.com/0JBhY6SjRX
□ Comparison of Metatranscriptomic Samples Based on Alignment-free k-Tuple Frequencies for pyrosequencing 454, Illumina
>> http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084348 …
three d2-type dissimilarity measures, one dissimilarity measure in CVTree, one relative entropy based measure & classical lp-norm distances.
PCoA is to find X1,X2,…,Xn,where
Xi is a vector in an N-dimensional Euclid space, N＜n, to optimize the
function min Σ(||Xi-Xj|| - dij)^2
□ moorejh:
Body Atlas Reveals Where We Feel #Happiness and Shame - summary of PNAS paper
>> http://blogs.discovermagazine.com/d-brief/2013/12/30/body-atlas-reveals-where-we-feel-happiness-and-shame/#.UsHWGPRDvmc … #physiology pic.twitter.com/4Bx2mkfT2u
□ ntegrative analysis of histone ChIP-seq & transcription data using Bayesian mixture models: naive separate analysis
>> http://bioinformatics.oxfordjournals.org/content/early/2014/01/07/bioinformatics.btu003.short …
□ PaleoDB Navigator Alpha 1.0: new app explore the Paleobiology Database maps extinct species in space, time & taxonomy
>> http://paleobiodb.org/navigator/
□ WaferGen Bio-systems Acquires a Leading NGS Library Preparation Business, Announces Changes to its Board of Directors
>> http://www.wafergen.com/wafergen-bio-systems-acquires-a-leading-next-generation-sequencing-ngs-library-preparation-business-and-announces-changes-to-its-board-of-directors/ …
The fully automated Apollo 324 library prep with innovative new applications and integrated products that include the SmartChip TE platform.
the acquired business was composed of an up-front cash payment of $2.0 million, a $1.25 million secured promissory note due on Jan. 6, 2017
□ Google invests into DNAnexus: aging-driven big data bioinformatics without the Hadoop Ecosystem?
>> http://pimm.wordpress.com/2014/01/03/google-invests-into-dnanexus-aging-driven-big-data-bioinformatics-without-mapreduce-hadoop/ …
□ DNAnexus builds online hub for scientists to store and share genetic data:
>> http://venturebeat.com/2014/01/03/dnanexus-builds-online-hub-for-scientists-to-store-and-share-genetic-data/ …
□ NCBI:
Introducing the New Human Genome Assembly: GRCh38
>> http://wp.me/p2Tuqy-6x
□ A Taxonomy of Innovation: based on the people designing for and the complexity of the systems in which you operate.
>> http://hbr.org/2014/01/a-taxonomy-of-innovation/ar/1 …
□ 日本政府 各府省の保有データのオープンデータ化 試行版
>> http://data.go.jp
□ What We’ve Learned about Evolution from the LTEE: 長期進化実験から得られたもの。リターンエピスタシスと動的モデルを組み込んだ、LTEE集団50,000世代の適応度の予測軌道 http://telliamedrevisited.wordpress.com/2013/12/08/what-weve-learned-about-evolution-from-the-ltee-number-2/ …
□ EXCAVATOR: detecting copy number variants from whole-exome sequencing data
>> http://genomebiology.com/content/pdf/gb-2013-14-10-r120.pdf
EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outper- forms the other methods and is therefore a valuable tool for the investigation of CNVs in large- scale projects, as well as in clinical research and diagnostics.
a novel heterogeneous HMM-based algorithm (HSLM) that, by exploiting the sparseness of coding regions throughout the genome, allows for the detection of both small isolated events and large alterations. Testing HSLM on synthetic data showed that it was able to detect, with a comparable accuracy, large genomic regions covered by many exons as well as small genomic regions covered by few exons. Moreover, synthetic simulations were also exploited to compare the performance of HSLM to the CBS algorithm.
□ Variation Ontology for annotation of variation effects and mechanisms in any organism and genetic / nongenetic origin
>> http://genome.cshlp.org/content/early/2014/01/02/gr.157495.113.full.pdf …
□ IRB develops ChroGPS, a new generation visual browser of the epigenome
>> http://www.eurekalert.org/pub_releases/2013-12/ifri-idc122013.php
This is a software application that provides easily interpretable maps from which to analyse and understand the immense volume of epigenetic and genetic data available
□ Flow Cytometry Bioinformatics:
>>