□ figshare:
SmartRoot - a novel image analysis toolbox enabling quantitative analysis of root system architecture: http://shar.es/viv6L #botany
>> http://www.uclouvain.be/en-smartroot
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。
□ jeff_hayes:
Medical School and Classrooms of the Future http://goo.gl/P6NyF via @Docweighsin
(Constraint-based modeling of mammalian tissues.)
□ Network-Scale Engineering: Systems Approaches to Synthetic Biology
>> http://dash.harvard.edu/handle/1/9393259
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
>> http://t.co/RlLuTkTC
a new method for constructing and analyzing genetic circuits in eukaryotes which includes organisms from yeasts to humans.
□ A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions
>> http://www.cell.com/retrieve/pii/S0092867412007805
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
□ duportet:
PLoS ONE announces the launch of the Synthetic Biology Collection. http://bit.ly/Pi8Nc2
□ A mathematical model to guide antibiotic treatment strategies
>> http://www.biomedcentral.com/content/pdf/1741-7015-10-90.pdf
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.
□ Next-generation sequencing demands next-generation phenotyping: Medical Genetics Practice in a NGS-Driven Paradigm: http://onlinelibrary.wiley.com/doi/10.1002/humu.22048/full#sec1-2 …
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.
臨床医の為のゲノムサーバによる医療資源の節約。「変異に関連した表現型のナレッジベースの評価」とあるけど、NGSデータの定性と臨床診断プロセスのモードが重要。ギア的な役割
つまりBioinformaticsを運用するためのInformaticsが臨床では必要になる。それをデバイス依存にするアイデアもあるし、医師のための遺伝学カウンセラーを置くモデルも提唱されているけれど、これにNIH-NHGRIが2013年度予算に巨額を割いているわけ。
□ RNA Interference: A Futuristic Tool & its Therapeutic Applications
>> http://www.sciencedirect.com/science/article/pii/S1319562X12000629
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
>> #NGS12
>> http://www.healthtech.com/SequencingDataManagement
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
□ DNAnexus:
"Community-Inspired Collaborative & Scalable Data Technology Platform" >> http://www.healthtech.com/Conferences_Overview.aspx?id=114903&libID=114854
>> https://dnanexus.com/
DNAnexusの"Community-Inspired Collaborative & Scalable Data Technology Platform"はグーグルのあれ？ "Matrix Tool"のようなものだと予想してみる http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2812%2900060-1 …
#NGS12ではOxford Nanoporeはお預け（？）で、遅くともスポンサーになっている#BTG2012 (Beyound the Genome)で動きがあるということでおk？
□ BeyondtheGenome:
Announcing Oxford Nanopore as the poster prize sponsor for #BTG2012! @nanopore
□ MERmaid: A Parallel Genome Assembler for the Cloud:
>> http://www.cs.berkeley.edu/~kubitron/courses/cs252-S12/projects/reports/project1_report.pdf
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.
クラウド上のCommodityクラスタ全ゲノムアセンブラ。k-merカウントでAbyssに優位。
□ ctitusbrown:
Zam Iqbal expertly responds to my 'what does k control in assembly?' post: http://ivory.idyll.org/blog/the-k-parameter.html#comment-619101818 … and points to Cortex http://www.ncbi.nlm.nih.gov/pubmed/22231483
□ □ homolog_us:
Genome Assembly - MERmaid and Meraculous >> http://t.co/Z4NWXsDb
Velvet、AByss等アセンブラ(de-Brujin)はk-mers処理で差別化できる。ブルームフィルタによるk量体剪断。MERmaidは分散化・低メモリに。
□ TSUNAMI: New Method Introduced To Closely Model Diseases Caused By Splicing Defects: pathology w/ pre-mRNAs missplicing http://www.medicalnewstoday.com/releases/249017.php …
□ Massgenomics:
New appreciation for the detection challenges and key role of *de novo* mutations in human genetic disease: http://massgenomics.org/2012/08/de-novo-mutations-and-human-disease.html
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
□ RNA Folding Algorithms with G-Quadruplexes:
>> http://www.springerlink.com/content/yh0125361724m662/
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
□ genetics_blog:
Comparison of next-generation sequencing systems from BGI http://www.ncbi.nlm.nih.gov/pubmed/22829749
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.
>> http://www.ncbi.nlm.nih.gov/pubmed/22827831
□ homolog_us:
Where are Innovative NGS Algorithms Coming from? (http://www.homolog.us/blogs/2012/08/16/where-are-innovative-ngs-algorithms-coming-from/ …)
最もイノベーティブなNGSアルゴリズムは何処から？：アセンブラ・SNP論文数。スケーリングと技術革新は相互排他的、物量投資と成果物を比高して緩慢化を招くかも。日本は…
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.
Homolog.usでも何度か取り上げられてるけど、JGIは「大規模なシーケンシングセンター」であり、少人数では経験しえない組織・運用的な問題に直面するという。その中で生まれるイノベーションもある一方で、逆に資金が潤沢であることが必ずしも他の組織について優位には働かない面もある。
□ 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.
インドのジェネリック医薬品への大手製薬会社ロビー活動が難航。協定運用を前提としても安価で救われる夥しい命の一方、粗悪品へのアクセス阻害を企業利益に先ずべき
□ Building an NGS Reference List (de novo assembly category):
>> http://www.homolog.us/blogs/2012/08/07/building-a-ngs-reference-list-please-add/ …
行間のせいなのか、私ちょっとこのページが見辛いです。。
□ Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds
>> http://www.biomedcentral.com/1471-2105/13/200/abstract
>> http://cloudgene.uibk.ac.at
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.
現在Cloud BioLinux, RStudioで、5つのバイオインフォプログラムを統合。それとも定義済システムは統合された2つのシステムとは別なのか
□ genetics_blog:
Hypothesis-Based Analysis of Gene-Gene Interactions and Risk of MI http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041730 … #Epistasis #Genetics
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
>> http://bit.ly/PzKCH9
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.
ゲノムデータ翻訳コンテスト。稀少疾患児のDNA配列をデコード。臨床ゲノミクスのモデル定義へ。
□ CRGenomica:
Computational biology: 'Whole-cell' computer model http://go.nature.com/xupyjP
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.
□ GenomicsIo:
http://bit.ly/OizAU7 Quantitative RNA-Seq analysis in non-model species #RSS #iftt #RNASeqBlog
>> http://www.biomedcentral.com/1471-2164/13/361/abstract
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
□ EurekAlertAAAS:
Iconic Darwin finch genome sequenced in Genome 10K international collaboration. http://eurekalert.org/e/4p6m
□ tarantulae:
Blogged about some Genetic Programming ideas and a LLVM JIT for Python ASTs http://pyevolve.sourceforge.net/wordpress/?p=2353 … #python #genetic-programming
□ SpringerSBM:
Reading: "A Push Grows Abroad for #OpenAccess to Publicly Financed #Research" http://ow.ly/cVmAc (TH) (via @JenHoward) #OA
□ edyong209:
The BMJ argues that pharma's innovation crisis is a fiction. Derek Lowe piledrives that argument into the mat http://t.co/lD71slO1
□ GSSHealth:
Strategies to Improve #Maternal and #Child #Health: The Investment Case Framework http://buff.ly/MDn98a @PLoSMedicine
□ Here's an Omical Tale: Scientists Discover Spreading Suffix [wsj]
>> http://t.co/VPsb2Emc
sociomics, physiomics, ecogenomics, metabolomics and pharmacogenomics, metagenomics and microbiomics at an annual conference called Copenhagenomics.
□ research_uk:
Via BBSRC: Bioscience to battle global hunger: http://bit.ly/PhppSp
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
□ Algorithmic Composition: Computational Thinking in Music: 11世紀から体系づけられる西欧音楽史において、コンピュータによる「自動化された」アルゴリズム作曲とは何か。音楽と意識の関係 http://cacm.acm.org/magazines/2011/7/109891-algorithmic-composition/fulltext …
□ PaulAtInsight:
Managers, repent and sin no more....... @HarvardBiz The Seven Deadly Sins of Management http://s.hbr.org/OzFovd
マネージメントにおける七つの大罪: 私にはこの記事自体が皮肉に映るし、それが狙いなのだろうけれど、世の成功例は一つ一つ大罪を犯しているように見える。犯しつつ修正せよ。
□ 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
□ Triple V pavilion: この写真が好き。空間に斬り込むような建築物に惹かれる: Wallpaper* Case Studies iPad: http://www.wallpaper.com/gallery/architecture/-/17052192/58806 …
□ RichardDevine:
Fauna by XOXOS - Waveguide Model Plugin flexible platform for synthesis of abstract and animal voices: http://youtu.be/bAmZhaMiywE
□ infoecho:
ipython 0.13 notebook for visualizing De Bruijn Graph, maybe useful for understanding some short read assemblers. https://github.com/cschin/ipython_d3_mashup/blob/master/ipython_13_vis_example/De_Bruijn_VIS.ipynb
□ SethSHorowitz:
Exceptionally well preserved 2500 year old human brain -
>> http://www.academia.dk/BiologiskAntropologi/Tafonomi/PDF/Brains/Britains_Oldest_Brain.pdf
□ Slate:
Google Earth may have just discovered some previously hidden ancient pyramids: http://slate.me/Qvc9Vq
□ DEMETER298:
Plant Genome DataBase Japan（かずさ）完成途上の公開。利用者側からのご意見募集中。 http://pgdbj.jp/
ページの上部には系統群で「オルソログクラスタ」の組成に関する情報も表示しています。MOMP:multiple-organism multiple-protein clustersとは、複数の生物種が所属している「オルソログクラスタ」を指しています。SOMP:single-organism multiple-protein clustersとSOSP:single-organism single-protein clustersは、単独の生物種のみが所属している「オルソログクラスタ」です。後者は、単独のアミノ酸配列のみが含まれた「オルソログクラスタ」です。
□ c_z:
GSoCの結果をリリースし始める時期になりましたが、とりあえず一つ。セマンティックウェブ関連のプラグインです： vsdlc3 Visualizing Semantic Data Landscapes with Cytoscape 3.0 http://vsdlc3.blogspot.com/
□ tri_iro:
サマースクールでSimpsonの定理について話してくれというリクエストがあったので証明を読んでいたけど、ある種の力学系のハウスドルフ次元や位相エントロピーといった大域的な量が、空間のたった一点の情報だけから得られるって不思議な定理だよなあ、と改めて思う。
□ 理研、今年度限りで「基幹研究所」廃止へ－組織の変更も
>> http://t.co/KBfBdB29
: 再編に伴う名称変更も「廃止」と表現することはあるけれど、『環境や医療技術の進展など社会的なニーズに応えるよう求めた』の文言には危うさを感じる。基幹よりニーズを追う研究はリソース先細り
□ hinaichigo:
さっきから日刊工業新聞発の理研基幹研究所廃止へ、のニュース流れているけど改組とかでなくて廃止とかにわかに信じがたい ゲノム科学総合研究センター(先代のGSC)を発展解消させてシステム計算生物学は基幹研究所もってったらしいのに、廃止するの？
□ gaou_ak:
Semantic Webの最も良い（SWらしさ、という意味でも、成功事例としても）例は、UniProtの内部である。ただ、UniProtとの連携を考える時には、SWは必ずしも最適解ではない。この二つの避けられない事実を未だにみんな良く理解できていないと思う。
□ rubbish talk.
音楽の消費・供給スタイルの変容が、歌詞の希薄化・粗製濫造につながっているという言説は、裏をかえせば「自分で歌わない歌の歌詞を生産」するというフォーマットに問題があるのだと言い換えることも出来そうだけど、私はそれが「音楽の低品質化」を招いているとは全く思わない。
楽曲であろうと歌詞であろうと、「プロダクト」に付加する為の価値は、どれもがいずれも「自己表現」であるべきだ。職業音楽家だろうと、シンガーソングライターだろうと、世の労働価値やモチベーションは平等に生産者の評価基準と切り離せない。作曲家・作詞家なりとも矜恃を持って仕事をすべきなのだ
実際に音楽が希薄になっていると訴える人たちは、プロダクトのターゲット層の分布の粗密化、あるいは偏向を、市場規模で均して捉える徒労を冒しているのかもしれない。
安直な歌詞が増えたかと言えば、それは確かにそうかもしれない。たとえば「メールが来ただの来ないだの」と「天城越え」に涙する感性や複雑性の程度は異なるだろう。だけど、私は前者により深く共感できるし、世相や風俗を深く切り込むという時代の傾向そのものを無批判に肯定し、あるいは感情の深度を表面的な尺度で揶揄する姿勢こそ、メタだけど、聴衆側における「意見の均一化」の賜物ではないか。受け入れられてるものをこうあるべきでないと批判する前に「なぜ受け入れられているのか」の力学を注視する。
言っても私は、「歌い手が作詞・作曲した歌」が好きだし、自ずとそういうアーティストばかり追って来たけどね。