□ nutsci:
Ioannidis and colleagues apply GWAS-like analysis on NHANES data for 188 enviro factors on lipids (they call EWAS) http://bit.ly/GNAVke #OA
Systematic evaluation of environmental factors:
persistent pollutants and nutrients correlated with serum lipid levels.
EWAS: NHANESデータのGWAS的解析。環境化学因子と血清脂質濃度の相関をスクリーニング。188要因のピアソン相関を示すヒートマップも
□ International Human Microbiome Congress, organized by MetaHIT
19-21 March, 2012 - Palais Brongniart, Paris #IHMC2012
>> http://www.metahit.eu/index.php?id=paris-2012
□ MaliciaRogue:
Une petite mise en bouche : "Exclusif : Bioinfo-fr au Congrès sur le microbiome humain #IHMC2012" http://t.co/8ar6EPzb #IHMC2012 #francais
ヒトmicrobiomeの国際コンソーシアム。
ヒト単位でのメタゲノム解析と大規模データセットに特化したアプローチを開発。
□ MaliciaRogue:
Other differences in datasets: sequencing type & depth, analysis pipelines, impact of unknown metadata, statistical assumptions,.. #IHMC2012
Use of indiv residue variation: uncharted territory but promising, Hypervariable loci in the human gut virome http://www.ncbi.nlm.nih.gov/pubmed/22355105 #IHMC2012
Data generation -> Tech transfer -> external validation -> clinical validat° => 4 years, 20M euros #IHMC21012
□ tjsharpton:
#IHMC2012 Jacques Ravel (University of Maryland, USA) Transcriptional dynamics of the vaginal microbiome http://ff.im/Tj8yq
□ The future of human microbiome research funding is uncertain but promising
>> http://bit.ly/GGOajk
International Human Microbe Program Looks Ahead
Lita Proctor, coordinator of the NIH-funded Human Micrometer Project (HMP) adds that the field is now mature enough to start having debates about the data, including whether the controversial claim that humans can be classified into three different "enterotypes" depending on their microbial profiles is valid. "At first we were just focused on methodology," Proctor told ScienceInsider, "but now we are having debates about different ideas and perspectives."
ヒトmicrobiome研究の資金拡充と企業誘致に期待感。国際コンソーシアムなどを受けて。NIH、EC、Enterome。生物多様性に、ヒトと微生物の相関を組込む。
NIHの"Human Micrometer Project"による、Microbiome研究への次年度投資継続については激しい議論が交されている模様。人間のMicrobiome解析には、大規模ハイスループットと、その処理の為の計算インフラを要する。ECは資金提供に前向き。
IHMC2012では、パテントのオファーが余りにも多くて辟易した。というツイートもあったけど、記事のEnteromeのCEOは、Microbiomeの発展には商業的可能性を達成する為の特許学術研究が重要と強調。オープン性を保てるかどうかは、機関やコミュニティの投資と後押し次第かな
□ NatRevGastroHep:
Couldn't make it to Paris for #IHMC2012? MT @nutrigenomics Excellent google+ coverage by @emergentnexus http://bit.ly/GCF5I4
□ DailyNewsGW:
Enterome Raises $6.6M in Series A Round: http://bit.ly/GWgmjw
□ PLoSCompBiol:
Physicists may have discovered how the brain encodes memory - http://sciencefreaks.co.uk/?p=931 (about a PLoSCB paper http://dx.plos.org/10.1371/journal.pcbi.1002421)
Using molecular mechanics modeling and electrostatic profiling, we find that spatial dimensions and geometry of the extended CaMKII kinase domains precisely match those of MT hexagonal lattices. This suggests sets of six CaMKII kinase domains phosphorylate hexagonal MT lattice neighborhoods collectively, e.g. conveying synaptic information as ordered arrays of six “bits”, and thus “bytes”, with 64 to 5,281 possible bit states per CaMKII-MT byte.
Signaling and encoding in MTs and other cytoskeletal structures offer rapid, robust solid-state information processing which may reflect a general code for MT-based memory and information processing within neurons and other eukaryotic cells.
(Overview of SHAPE-Seq. (A) Experimental pipeline. A DNA bar code is added to the 3′ end of template molecules, enabling SHAPE chemistry and sequencing library generation to be done on a mixture of bar-coded RNAs. (B) Bioinformatics and analysis pipeline. The automated pipeline separates reads by handle pools and bar code and maps the reads onto RNA sequences. )
□ iGenomics:
SHAPE-seq, a tech can measure quantitative, single nucleotide-resolution 2nd and 3D structural info for 100s of RNAs http://is.gd/KfHwER
SHAPE-Seq thus repre- sents a powerful step toward making the study of RNA secondary and tertiary structures high throughput and accessible to a wide array of scientific pursuits, from fundamental biological investiga- tions to engineering RNA for synthetic biological systems.
□ Microbial Annotation in the Cloud: CloVR and Ion Torrent on EC2
>> http://www.edgebio.com/microbial-annotation-cloud-clovr-and-ion-torrent
With Ion Torrent sequencing the focus is on providing these results quickly and efficiently to our customers. While there are many tools and options for microbial annotation, one particularly useful and interesting option is CloVR. Our experience using the CloVR-Microbe pipeline for annotation of Ion Torrent data.
About E Coli DH10B dataset, CloVR predicted a total of 4,883 genes in this dataset. Of the 4,883 predicted genes, 4,644 unique predictions were found and 2,644 predictions had an actual gene ID. The 2,000 other genes were predicted hypothetical proteins and did not have an actual gene ID to cross-reference in reference genbank files.
CloVRパッケージ、昨年も紹介したけど使用感あまり聞かない。
CloVR: >> http://clovr.org/
Cloud virtual resource automated pipeline for sequence analysis from the desktop
CloVRを用いたResearch publicationsが、2011年時点で4本。主にバクテリア(Microbe)関連。でもこれからは、ion torrentとEC2、CloVR-Metagenomicsでメタゲノムって流れもアリのような気がする。
って書いたら、すかさず @LifeTechSupportさんからリプライが飛んできたw
□ SAGRudd:
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer http://bit.ly/GNV2Kt
Mapsembler is the first software that enables de novo discovery around a region of interest of repeats, SNPs, exon skipping, gene fusion, as well as other structural events, directly from raw sequencing reads. As indexing is localized, the memory footprint of Mapsembler is negligible. Mapsembler is released under the CeCILL license and can be freely downloaded from http://alcovna.genouest.org/mapsembler/.
□ ongenetics:
I am crowdsourcing graduate education in genetics. I am calling on you to recommend Literature on Genetics http://ongen.us/LitOnGen
□ First Open Government Day in Macedonia:
>> http://t.co/F4chEzLH
The first Open Government Day in Macedonia will be organized on March 21, 2012 (Hotel Holiday Inn, Millennium II Conference Room) by MISA, World Bank and UNDP. The organizers invite you to participate in the Open Government Day and actively contribute to the Open Government Initiative of the Republic of Macedonia within the framework of the global Open Government Partnership.
マケドニアもOpenGovへ。
Opportunities and Challenges for Opening up Government Data in Macedonia
View more PowerPoint from Metamorphosis
(Open Data vs Linked Data)
□ Macedonia:
Open Government Partnership Draft Action Plan Presented
>> http://t.co/7HwmbyqG
Some of the main points included that open government and open data are not just IT issues, but related to institution management and legal framework; implementation of Freedom of Information (FOI) Law ? The Law on Free Access to Information of Public Character is crucial for the whole process and for the overall advancement of active citizen participation. Important factors include education of the population (related to bridging the digital divides) and the development of trust between all stakeholders.
□ razvigor:
Ppl on site of #OpenGov #OpenData #openDTA conference in #Macedonia choose the #OpenGovMk hashtag as "official" (shorthand). Pls RT
□ fmeta:
#OpenGovMk - хаштаг за денешниот Ден за отворена власт/отворени податоци. Агенда: http://www.metamorphosis.org.mk/mk/vesti/makedonija/2131-prv-den-za-otvorena-vlada-vo-makedonija
□ OpenLink:
Virtuoso Open Source Edition development archive now available on GitHub: http://github.com/openlink/virtuoso-opensource #semanticweb #linkeddata #lod
Virtuoso is a scalable cross-platform server that combines Relational, Graph, and Document Data Management with Web Application Server and Web Services Platform functionality.
□ AIP_Publishing:
Physical aspects of biological activity and cancer http://ow.ly/9PS6j #AIP_ADV #PhysofCancer
Physical processes in cancer cell are disturbed due to suppression of oxidative metabolism in mitochodria (Warburg effect). Water ordering level in the cell is decreased, excitation of microtubule electric polar oscilations diminished, damping increased, and non-linear energy transformation shifted towards the linear region. Power and coherence of the generated electrodynamic field are reduced. Electromagnetic activity of healthy and cancer cells may display essential differences.
生物活性と癌細胞の物理的側面: ミトコンドリアのエネルギー媒介における陽子輸送と静的電界変化の非線形特性。癌細胞では顕著な振動減衰。
□ ABSalBiotec:
Entrevista a Ramón Serrano, catedrático de Bioquímica y Biología molecular en la UPV http://t.co/VABQYZld
□ isatools:
Google Summer of Code Project with Nescent and ISA-tools http://wp.me/pXDzM-5v
□ MaliciaRogue:
#Database of Middle Age #Arabic documents http://ow.ly/9RAF2
□ Hypios:
Hypios files European patent for its core semantic technology. http://hyp.in/GKIpAs
□ CERC_Columbia:
DNA sequencing techniques in plant genome analysis: - http://ow.ly/9jvb8
□ [NCBI] Aspera Connect client:
to download large data, 5 gigabit per second to transfer. http://1.usa.gov/GHYSqq
download: http://1.usa.gov/GBQ0Va
□ JSMC: Jena School for Microbial Communication http://www.jsmc.uni-jena.de/
□ gigaom:
Why big data needs real-time intelligent systems http://dlvr.it/1LlQqZ
□ togo_annotation:
TogoAnnotation was released as a production environment. http://togo.annotation.jp/
□ nakachiy:
Testosterone-mediated sex differences in the face shape during adolescence | Horm Behav http://bit.ly/GBUEES 面白い！計測してPCAして性差だけでなくホル濃度や遺伝型まで！
(HadCRUT4/HadCRUT3 Temperature anomaly)
□ [Real Climate] Updating the CRU and HadCRUT temperature data
>> http://t.co/QZYvybzk
the new CRUTEM4 product is in press at JGR (Jones et al, 2012), and makes a number of important observations. First, on the evolution of the CRU temperature data set, from CRUTEM1 back in the mid 1980s, which used a limited selection of station data and ‘in-house’ homogenization, to CRUTEM2 around 2003, CRUTEM3 in 2006, and now CRUTEM4 which has a wider data sources and relies much more on homogenization efforts from the National Met Services themselves.
□ FQXi:
Albert Einstein's complete archives to be posted online http://gu.com/p/36aa8/tw via @guardian
>> http://alberteinstein.info/
アインシュタインの完全なアーカイヴがオンライン公開へ。始めにヘブライ大学が、未公開書簡や研究ノートを含む2,000ドキュメントをリリース。E-MC^2の手書きの解説や、恋人への私信も
Parametropophonics from Topophonie Group on Vimeo.
□ matthieusavary:
Parametropophonics: generated, parametric, audiographic shapes http://vimeo.com/37967817 #Cinder #CCGL #CataRT (w/ Diemo Schwarz, IMTR, @iIRCAM)
that find their roots in sound grains' descriptions: pitch, volume, spectral centroid… as well as standard 3D models (.OBJ files).
□ 陪審員の規模を数学的に計量する:
>> http://bit.ly/GX3iun
The Mathematics of Jury Size -
Statistical model shows several interesting properties of jury sizes
□ NatureJapan:
曲がり角の向こう側に隠された物体の姿をとらえる （Nature Communications）: NPG Nature Asia-Pacific http://nature.asia/GF2B6W
□ as_expected:
情報がいかに高次の生命現象を生み出しているか。逆に。高次の生命現象がいかに情報を生み出しているか。なるほど。相当冗長で過度に複雑なシステムをどう見るか。細胞周期のポール・ナース。 http://www.nature.com/nature/journal/v454/n7203/full/454424a.html
□ yuifu:
Hausslerのグループによる「論文をテキストマイニングしていいか」という問い合わせに対する、医学生物学系ジャーナルからの回答まとめ http://text.soe.ucsc.edu/progress.html
UCSC Genocoding: Text Mining allowed without permission? publisher's response: Current coverage of Pubmed 30% 2.7M articles
□ n0rr:
シーケンス長以上の本数のmRNAが転写されている遺伝子についてはPCR duplicate を除くことができない
培養された細胞のmRNA発現がdysregulated されたようにisolated brain の情報伝達もまたdysregulated されるんじゃないかと思ってるの
□ Rubbish_Talk:
□ Sex Metagenome
もうしばらく前から、ヒトの性交時における体液交換で往来する微生物群のトラフィックやコ・ハビタンスに興味があるのだけど、男女の交配をそういう視線でばかり見てしまう。セックス・メタゲノムをコホート調査してみたい。
IHMC2012では、妊婦から胎児へのMicrobe分析が紹介されていましたね。
□ Sex Microbe Analsys
実際、どうやって性交時のメタゲノム解析を行うかというと、技術的課題と倫理的問題が山積。しかもその後の他人同士のトラフィックを追跡するとなると、ほぼ不可能性。中にヒトが入るだけで、共生微生物群を体内からスキャンして分類する未来の装置が必要。
□ 「ハイコンテクスト文化」というのが良く分からないのだけども、そういう共通認識前提のコミュニケーションというのは古今東西、指向するコンテンツがどのようなものであれ、その認知度と寿命に依存して有効な期間が発生する。映画を観終わった後のセリフの応酬などがそれだ。
「ハイコンテクスト文化」というのは、そういう共通認識が断片的な情報の交換を持って有効になる濃度の高さ、及び範囲の本来的な局在性が、ネットによって遍在的な時空間分布を帯び始めていることを指す言葉なのかもしれない。文化の特質表現ではなく、コンテンツトラフィックの変容そのものを示す。
