その中にあってDead Can Danceが蘇生させたかったものとは何なのか。ニューエイジ音楽家たちが夢見た『異界幻想』。自らの原始的なルーツへの憧憬。それらはもしかしたら存在しなかったのかもしれない。彼らの多くは「フェイク・エスノ」とも言うべき、土着音楽らしい要素という要素を散りばめて、己の内面世界を表現してきた。
Director: Ridley Scott
Writers: Jon Spaihts, Damon Lindelof
Stars: Noomi Rapace, Logan Marshall-Green and Michael Fassbender
Music: Marc Streitenfeld
Additional Music: Harry Gregson-Williams
SmartRoot is a semi-automated image analysis software which streamlines the quantification of root growth and architecture for complex root systems.
The software combines a vectorial representation of root objects with a powerful tracing algorithm which accommodates to a wide range of image source and quality.
The software supports a sampling-based analysis of root system images, in which detailed information is collected on a limited number of roots selected by the user according to specific research requirements.
SmartRoot is an operating system independent freeware based on ImageJ and uses cross-platform standards (XML, SQL, Java) for communication with data analysis softwares.
□ eurogene:
Relevant for the genomics and other omics data deluge: The Fourth Paradigm: Data-Intensive Scientific Discovery http://bit.ly/OAqfnG
3年前の文献だけど読み応えがある。データ爆発が環境科学・医療・生物学・コミュニティをどう変えるか。
The field of Systems Biology seeks to measure and model the properties of biological phenomena at the network scale. We present the application of systems biology approaches to synthetic biology, with particular emphasis on understanding and remodeling metabolic networks.
Chapter 2 demonstrates the use of a Flux Balance Analysis model of the Saccharomyces cerevisiae metabolic network to identify and construct strains of S. cerevisiae that produced increased amounts of formic acid. Chapter 3 describes the development of synthetic metabolic pathways in Escherichia coli for the production of hydrogen, and a directed evolution strategy for hydrogenase enzyme improvement. Chapter 4 introduces the use of metabolomic profiling to investigate the role of circadian regulation in the metabolic network of the photoautotrophic cyanobacterium Synechococcus elongatus PCC 7942
□ phylogenomics:
Interesting story on aphids using energy of sunlight but w/o carbon fixation this is NOT photosynthesis http://shar.es/70FKk
□ druvus:
Researchers Cram 700 Terabytes of Data Into One Gram of DNA http://zite.to/QddT5d #synbio #metagenomics
□ New Technique In Synthetic Biology Uses Materials Within The Cell
We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions.
<fontsize=1>We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks.
元の論文。Zinc fingerによる真核生物の転写機能プログラミング設計
□ KurzweilAINews:
Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves: Nathan Myhrvold, Founder and CEO, Intellect... http://bit.ly/Q6hmT6
Mathematical models are one approach to understand how antibiotic usage patterns may be optimized. However, the classical approach to modeling the emergence of MDR relies on the simplifying assumption that resistance is acquired at a constant rate. In their model, Obolski and Hadany introduce the notion of horizontal gene transfer and stress-induced mutation, with antibiotics constituting an environmental stressor of particular relevance. Finally, from this complex mathematical model, the authors propose predictions for minimizing MDR in bacteria depending on strategies of antibiotic treatment.
NGS and informatics will provide a handful of possibilities and allow clinicians to perform focused and efficient further assessments of the patient. So, clinical skills and acumen of medical geneticists will remain essential and only will shift from a pretest differential diagnosis generation mode to a post-test diagnostic assessment mode. Medical geneticists will use their skills, deployed in a new way, to make more, more accurate and faster diagnoses at lower cost.
Clinical trials with RNAi have now begin, but major obstacles, such as off-target effects, toxicity and unsafe delivery methods, have to be overcome before RNAi can be considered as a conventional drug.
□ NCBI:
Now available: a new NCBI News! 1000 Genomes Browser, new PubMed tools, BLAST updates, Rhesus in HomoloGene, & more... http://1.usa.gov/On64PD
□ NGx: Next-Generation Sequencing Data Analysis conference
Sequencing a genome is only the beginning. Several layers of analysis are necessary to convert raw sequence data into understanding of functional biology. First, error sources in the original raw data from multiple platforms and diverse applications must be accounted for. Then, as computational methods for assembly, alignment, and variation detection continue to advance, a broad range of genetic analysis applications including comparative genomics, high-throughput polymorphism detection, analysis of coding and non-coding RNAs, and identifying mutant genes in disease pathways can be addressed. CHI’s Next-Generation Sequencing Data Analysis conference combines unique perspectives from a variety of researchers, engineers, biostatisticians, and software developers involved in NGS data analysis
MER- maid is open-source and was designed to be run on com- modity clusters rather than supercomputers. It has been tested and is verified to run on Amazon Elastic Compute Cloud (EC2)2, which everyone has access to. In the future, an Amazon Machine Image (AMI)3 containing MERmaid will be released,
k-mer A substring of a read of size k. We describe the importance of dividing reads into k-mers.
1. On average, humans acquire ~74 de novo single nucleotide variants (SNVs) per genome per generation.
2. The rate of de novo mutations seems higher in individuals with genetic diseases, particularly sporadic disorders such as intellectual disability and autism.
3. Perhaps surprisingly, the de novo mutational load seems correlated with paternal (as opposed to maternal) age.
4. Mutations linked to sporadic disease are usually highly disruptive to gene function, often affecting important domains of developmental genes.
"Because true de novo mutations occur randomly (and newly) in individuals, there's no database like dbSNP to guide discovery."
家族ベースのexomeシーケンシングの統計：人間は世代当たり74の一塩基変異体(SNVs)を取得するが、社会変容に伴い子を持つ年齢が上昇し、de novo変異に伴う疾患が増加する傾向にあるとする指摘。遺伝変異の自然選択と適応効果が気になる
G-quadruplexes are abundant locally stable structural elements in nucleic acids. The combinatorial theory of RNA structures and the dynamic programming algorithms for RNA secondary structure prediction are extended here to incorporate G-quadruplexes using a simple but plausible energy model. With preliminary energy parameters we find that the overwhelming majority of putative quadruplex-forming sequences in the human genome are likely to fold into canonical secondary structures instead.
□ myoshioka:
Agilent Series, Part 1: Anticipate System Level Design Challenges: Bridging Design Domain Gaps: http://lnkd.in/SHa_Rh
NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis.
NGSシステム比較は食傷でも、BGIが言うならそうなんだろうなw
□ A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers.
the real problem faced by NGS. It is scaling . Big universities usually solve scaling problems by buying large computers or moving to supercomputers. The scaling issue is so severe for genome centers that they could not keep throwing money at it. They had to innovate their way out of it. So, all labs listed in 1-5 were closely associated with genome centers, or genome centers themselves.
Why is JGI not in the top list? Once again, it is very likely that money is their real problem.
□ iplab:
Big Pharma lobbies hard to curb generics ? Times of India: TrademarkBig Pharma lobbies hard to curb genericsTime... http://bit.ly/Sp0cC9
MUMBAI: India's tag of 'pharmacy of the developing world' is at a serious threat. Not only has the US devised new treaties to challenge generic drugs being shipped from India, the EU has also upped the ante. Worse, Big Pharma is increasingly adopting tactics to protect its intellectual property, challenging domestic industry in courts, all of which may adversely impact access to legitimate generic medicines in developing countries.
At stake is a huge portion of the $10-billion drugs exported from the country to save lives of millions, particularly in developing countries.
In addition to MapReduce programs, Cloudgene can also be used to launch predefined systems (e.g. Cloud BioLinux, RStudio) in public clouds. Currently, five different bioinformatic programs using MapReduce and two systems are integrated and have been successfully deployed.
a biological hypothesis, under which MI risk is modulated by interactions between variants that are known to be relevant for its risk factors; and a statistical hypothesis, under which interacting variants individually show weak marginal association with MI. In a discovery sample of 2,967 cases of early-onset myocardial infarction (MI) and 3,075 controls from the MIGen study, we performed pair-wise SNP interaction testing using a logistic regression framework.
□ Contest Underway to Clarify Best Practices for Genomic Data Interpretation
In all, 30 contestants, ranging from small biotech startups to the National Institutes of Health, are part of the CLARITY Challenge (Children's Leadership Award for the Reliable Interpretation and Transmission of Your genomic information), which aims to address technical and bioinformatics questions in the analysis of DNA sequences, standardize the analysis of genetic variants, and generate a "comprehensive, actionable report" to guide clinicians, genetic counselors, and patients.
By producing a mathematical model of an entire human bacterial pathogen, researchers have made predictions about its cellular behaviour. The model accounts for the functions of the bacterium's known genes and the interactions between its constituent molecules.
Quantitative RNA-Seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species
□ appistry:
Researchers encoded an entire book into DNA, and then accurately read back the text with next-generation sequencing http://goo.gl/QkkA4
A high-level Global Nutrition Event marked the closing of the Olympics and called on the world to improve malnutrition in the world's poorest countries. BBSRC's Chief Executive, Professor Douglas Kell, joined representatives from international governments, charities and businesses at 10 Downing Street to strengthen commitments and challenge the world to find new ways of working to tackle malnutrition.
□ eurogene:
changing landscape of genetic testing and its impact on clinical and laboratory services and research in Europe http://bit.ly/P0fv3F
□ TrendsCognSci:
TiCS FREE Sci & Soc: @tomstafford & @vaughanbell discuss how social media have transformed scientific communication http://bit.ly/NpYGDf
□ wyattsgirl:
EHR system poses barriers to biobank consent process - FierceHealthIT
□ InsideScience: http://bit.ly/RnKf4r - Higgs Boson Could Help Explain Existence - Newly found particle could supply missing piece of cosmic puzzle #ISTV
□ StreamComputing:
Call for Proposals for allocations on the Blue Waters High Performance Computing System: http://bit.ly/RZiHBy #HPC #GPGPU #OpenCL
Music Video終盤で登場するシンセサイザーは、"Nord lead 2x"。 プリセットとして"Delerium Pad"なる音源がバンクされている。1995年に発表され、一世を風靡したアナログ・モデリング・シンセサイザー。"Nord lead 2"は、実際Front Line Assembly (=Delerium)やMike Oldfieldも使用している。というか、90年代を経過したあの辺のアーティストで使ってない人を見つける方が難しいのかも。
プリセットとして"Delerium Pad"なる音源がバンクされている。
□ Delerium / "Music Box Opera" album tracklisting.
01. Consciousness Of Love
02. Monarch
03. Days Turn Into Nights
04. Chrysalis Heart
05. Light Your Light
06. Rain Down
07. The Sky
08. Hammer
09. Awakening
10. Frostbite
11. Keyless Door
12. Music Box Opera
"Music Box Opera" hat mehr von einem elektronischen Album denn von World Music. Es ist ätherisch mit einem Schuss Pop. Wir haben versucht, diese beiden Welten miteinander zu verflechten und zu verschmelzen. Während das letzte Werk dunkler und ?weltlicher’ war, mit Gitarren und echten Drums, sind wir diesmal elektronischer und passend zur Stimmung der Songs vorgegangen.“
Release Date; 20/07/2012
Director: Christopher Nolan
Writers: Jonathan Nolan (screenplay), Christopher Nolan (screenplay)
Cast: Christian Bale, Tom Hardy and Anne Hathaway
Music: Hans Zimmer
Produced by Delerium.
Written by Bill Leeb, Rhys Fulber and Nadina Zarifeh.
Lyrics and vocal Performance by Nadina Zarifeh.
Album art by Carylann Loeppky
