(Cumulative rainfall anomalies and vegetation index anomalies for East Africa, Sudan and Southern Africa.)
□ GinnyBarbour:
#PLoS NTDs: Climate Teleconnections and Recent Patterns of Human and Animal Disease Outbreaks dx.plos.org/10.1371/journa…
東・南アフリカ及びスーダンの気候変動と疾病発生の時空間パターン相関。
Extremes in climate conditions forced by the El Niño/Southern Oscillation (ENSO) lead to severe droughts or floods, ideal ecological conditions for disease vectors to emerge, and may result in epizootics and epidemics of Rift Valley fever and chikungunya.
However, the immune status of livestock (Rift Valley fever) and human (chikungunya) populations is a factor that is largely unknown but very likely plays a role in the spatial-temporal patterns of these disease outbreaks. As the frequency and severity of extremes in climate increase, the potential for globalization of vectors and disease is likely to accelerate. Understanding the underlying patterns of global and regional climate variability and their impacts on ecological drivers of vector-borne diseases is critical in long-range planning of appropriate disease and disease-vector response, control, and mitigation strategies.
□ FX: an RNA-Seq analysis tool on the cloud. >> http://fx.gmi.ac.kr/
クラウド上で並列実行可能なRNA-Seqツール。ローカルHadoopクラスタ上でインストール可能
GMI-SNU FX: X is a user-Frendly RNA-Seq gene eXpression analysis tool, empowered by the concept of cloud-computing. With FX, you can simply upload your RNA-Seq raw FASTQ data on the cloud, and let the computing infra to do the heavy analysis.
□ BioWeatherMap
>> http://bioweathermap.org/
The BioWeatherMap initiative is a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life.
□ Improved prediction of RNA tertiary structure with insights into native state dynamics
>> http://t.co/OTwgbzyU [Bioinformatics]
RSIM ネイティブ状態ダイナミクスの知見からRNA立体構造予測を改良
We propose RSIM, an improved RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. This approach enhances the quality of predicted RNA tertiary structure, provides insights into the native state dynamics, and generates a powerful visualization of the RNA conformational space. RSIM is available for download from http://www.github.com/jpbida/rsim.
RSIMによるRNA立体配座空間予測。基本的にフラグメント・アセンブリによるモンテカルロ法の改良プロセス。MC自体がリファイン実装可能なのだが、ループ構造の選択に独自手法を適用、FARNAやRNA2D3Dを凌ぐベンチマークを示すらしい。
□ 直接シミュレーション・モンテカルロ法に分子間ポテンシャルを実装するという提案。あらゆる球面体モデルに適用可能。 Direct simulation Monte Carlo method for an arbitrary intermolecular potential http://ow.ly/8FQ4p
□ A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi
>> http://t.co/mdA5NXUG
The SPSE uses biomedical ontologies as the core knowledge resource and data model along with related Semantic Web technologies. Early in this project we realized the importance of provenance to scientists' data analysis needs. Hence, domain-specific (i.e., semantic) provenance [13] has been tightly integrated within the SPSE. The SPSE provides an environment for researchers to query the data as well as the associated provenance information, all stored in a RDF triples, with or without external databases, using a visual query tool.
SPSE: セマンティクス環境による生物学問題解決プラットフォーム。視覚的クエリツールCuebeeを使用し、複雑な構文を不要で研究者の呼び出しに対応。外部データベースの有無に関わり無く、照会情報のRDFトリプルを提供する。
□ Bio_Network:
SoMART, a web server for plant miRNA, tasiRNA and target gene analysis dlvr.it/171gM8
>> http://somart.ist.berkeley.edu/
miRNA/tasiRNA解析の為のサーバとリソース、sRNA Mapper
The server includes four sets of tools: 'Slicer detector' for detecting sRNAs targeting input genes, 'dRNA mapper' for detecting degradome (d)RNA products derived from input genes, 'preMIR detector' for identifying miRNA precursor (MIR) or tasiRNA precursor (TAS) of input sRNAs, and 'sRNA mapper' for mapping sRNAs onto input genes.
□ SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
>> http://t.co/Uj3b6vnA
SOAP3 is the first short read alignment tool that leverages the multi-processors in a graphic processing unit (GPU) to achieve a drastic improvement in speed. We adapted the compressed full-text index (BWT) used by SOAP2 in view of the advantages and disadvantages of GPU.
□ emblebies:
Web Services (via REST/SOAP) for several EMBOSS sequence translation tools are now available at the EBI: bit.ly/coZ99k
□ sebhtml:
I finished porting the Ray genome assembler to the plugin architecture of RayPlatform. github.com/sebhtml/ray/tr… #Ray #RayPlatform #illumina
□ Understanding Big Data: Analytics for Enterprise Class Hadoop and Streaming Data
>> http://t.co/IM0MNixu
IOD2011で公開されていたらしいFlashbookの書籍版。
FedX - Optimization Techniques for Federated Query Processing on Linked Data
View more presentations from aschwarte
□ BrainCatalog:
Linked data in a federation: FedX bit.ly/wUqdO1
FedX is a practical framework for transparent access to Linked Data sources through a federation. It incorporates new sophisticated optimization techniques combined with effective variants of existing techniques and is thus a highly scalable solution for practical federated query processing.
□ Sustainability of Bioinformatics Databases: バイオインフォマティクス関連データベースの運用状況。リソースのコストで淘汰傾向。EUはELIXIRに統合を計画 / NAR DB Collecition http://nar.oxfordjournals.org/content/40/D1/D1.full
These recent developments show that the importance of the public database resources, which is obvious to any biologist, needs to be constantly highlighted to the national and international financing bodies.
In Europe, coordination of the bioinformatics infrastructure is planned through the EU-sponsored ELIXIR (European Life Sciences Infrastructure for Biological Information, http://www.elixir-europe.org) project, which aims at guaranteeing seamless access to biological information by integrating data generators and data centers throughout Europe.
□ Sagebio:
Developing predictive molecular maps of human disease through community-based modeling bit.ly/whMR8T #openscience #bigdata
Sage Bionetworks Commons project, including the efforts made to date in building a computational platform and a data and model repository that includes the associated analysis tools, as well as the development of data sharing rules and policies. We explain how this environment will drive us toward the generation of better maps of disease and become a forum for reproducible and reusable data and analyses.
Community involvement will be necessary to address the many concerns that such a complex endeavor will encounter, including ways to incentivize data sharing, to promote the appropriate attribution for the data generators and map builders and to address policy issues associated with the protection of human data. Engagement of stakeholders across different constituencies to drive the development of the policies and resources necessary for the project is crucial
SageBioコモンズ: ヒト疾患予測分子マップ開発をコミュニティベースでモデリング: クラウドソース・データ共有の最適なコミュニティ帰属。
□ Chris_Evelo:
Nature Genetics publishes our commentary "Towards interoperable bioscience data": bit.ly/xMIw7p
Toward interoperable bioscience data
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.
バイオサイエンス・データの相互運用・報酬メカニズムを検討する。ISA commonsはコミュニティ帰属の国際的生態系リソースとしてメソッドを呈示している。
>> http://isacommons.org/
The ISA Commons is a growing community that uses the ISA metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of datasets in an increasingly diverse set of life science domains.
□ Embattled RNAi Technology Tries New Tack
>> http://t.co/hs0iKFnq
RNAi技術の晒されている深刻な状況と、見通されている可用性。ハイコンテンツ・スクリーニング。ランダム・フォレスト法による分類モデル選択フレームワーク等。
High-content screening for RNAi can provide a rich source of high-dimensional phenotypic data to explore the effects of knockdown in a variety of ways that move beyond simple threshold-based selection methods.
“We developed a series of tiered models in order to refine groups into finer populations, allowing us to apply gene ontology (GO) enrichment analysis methods to provide functional annotations and hence prioritize genes for follow-up analysis.”
□ SAGRudd:
Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing = #awesome j.mp/y5WE1P
We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes… The results underscore the potential and challenges of deploying NGS in clinical settings.
□ BrainCatalog:
National Center for Biomedial Ontology is having a Hackathon: j.mp/ziL2uE
□ CSHLnews:
CSHL's @mike_schatz explains some aspects of next-gen #sequencing's "storage saga" in this @GenomeWeb story bit.ly/slFRp4 #genomics
□ genomeresearch:
MT @attilacsordas: CRAM format mentioned in Storage Saga by @GenomeWeb bit.ly/wA799a paper at tinyurl.com/6p2ofpj
Storage Saga
>> http://www.genomeweb.com/informatics/storage-saga
sequencing technology is evolving at a much faster pace. At present, the per-base cost of sequencing is dropping by about half every five months, and this trend shows no sign of slowing down. Also, by some estimates, there are 1,700 high-throughput sequencers in operation across the globe, sequencing more than a million human genomes ? upwards of 13 petabases ? per year. Factor in all of these variables, and the logarithmic graphs start looking like signs of a data-management doomsday.
□ Roche_com:
More details regarding the @Illumina offer can be found on this dedicated website: transactioninfo.com/roche #ngs
□ LifeSciWorld:
Seattle Genetics and Millennium Report Data from Phase I Trial of ADCETRIS(TM ... - MarketWatch (press release) bit.ly/y2ALGt
□ Analyzing US Government Contract Awards in R
>> http://t.co/idizcXRv
Rで米国政府の契約受注状況を分析する。連邦政府の予算配分・入札競争を可視化。
As I was exploring open data sources, I came across USA spending. This site contains information on US government contract awards and other disbursements, such as grants and loans.
First, we note that 15.7 billion dollars in federal contracts were obligated to vendors in the state of Maryland in the fiscal year 2011. Next, we note that about 11.5% of the total federal money allocated in contracts went to Lockheed Martin! In fact, the top 10 companies in terms of dollar value of contracts received were given 41% of all the contracted dollars, which amounts to about 6.5 billion dollars. The top 100 contractors received 72% of all contracted dollars.
□ boolean3 (beta) an R package for modeling causal complexity
>> leftcensored.skepsi.net/2012/01/24/an…
Additional theoretical content can be found at the Boolean Statistics homepage. Braumoeller and Carson have a 2011 paper titled “Political Irrelevance, Democracy, and the Limits of Militarized Conflict” in the Journal of Conflict Resolution that provides a useful example of the approach.
□ ribozyme:
GNS BioModel platform to perform Bayesian inference networks #PMWC
□ QIAGEN to Provide siRNA Libraries in Labcyte Acoustically Compatible Microplates
>> http://t.co/QW0OgSws
Labcyte Inc., the developer of acoustic liquid handling, and QIAGEN, the leading global provider of sample and assay technologies, announced today that QIAGEN FlexiPlate siRNA reagent libraries are now available in Labcyte Echo® qualified microplates. These microplates enable researchers to use the Echo® liquid handler to miniaturize the transfer of small interfering RNA reagents.
□ plantbiology:
Current Biology 'Rapid Establishment of Genetic Incompatibility through Natural Epigenetic Variation' ow.ly/8Idhn
□ SciSolutions:
#genetics RNA therapeutics: beyond RNA interference and antisense oligonucleotides bit.ly/zgtXVs
□ kaythaney:
RT @NatureNews: Most popular on our site now: Going paperless: The digital lab ow.ly/8GXk9
□ hadleybeeman:
Data Catalog Vocabulary (DCAT): RDF vocab for gov data catalogs. W3C Editor's draft, 2012 bit.ly/w7CpEv #W3C #eGov #GLD #linkeddata
□ Socrates_Logos:
German Hackers Building DIY Satellites For New Uncensored Internet bit.ly/zJH8Jd
The Hackerspace Global Grid was borne out of a call to action at the Chaos Communication Congress in Berlin, where hackers of all stripes gather to mull the issues of the day as they relate to their craft. Hacker activist Nick Farr?motivated by legislation like the Stop Online Piracy Act (SOPA) in the U.S.?called on the community to contribute to a project that would remove the power of censorship from governments and corporations by creating an uncensored Internet in the free frontier of space.
□ AIP_Publishing:
Researchers hide 3D object with "plasmonic cloak" ow.ly/8IsCZ #AIP_PT
□ NatureJapan:
「1着になれる」ウマの遺伝子 （Nature Communications）: NPG Nature Asia-Pacific nature.asia/yb8mCX
競走馬の走速度を高める遺伝子の起源が明らかになった。（中略）Tアレルが祖先型であることがわかったが、Cアレルについては、英国原産の雌馬に由来するサラブレッド種の基礎段階でCアレルが一度導入されていたことが判明した。18世紀と19世紀の著名な競走馬において、Cアレルがまれにしか見られなかったが、最近の有力な種馬を介して、現存種において拡散したことを指摘している。 サラブレッド種の運動能力が、有利な環境だけでなく、運動能力に有意な影響を与える座位におけるDNA多型の最適な組み合わせを受け継ぐことにも依存している
□ tri_iro:
強零集合モドキみたいな概念を考えると、コルモゴロフ複雑性の増大度が非常に遅いけれどK-トリビアルでない0-1列を大量に作れることが分かったので、予想通り、強零集合モドキで、そういう自然数列の並びのランダム性に切り込めそうという感想。
□ yucca_watanabe:
未知small RNAのマッピングをしたいのですが（イントロン領域にあたる可能性も考慮して），精度重視でTopHatとNovoalignとどちらが良いとか，もっと良いものがあるとか，ご存知の方いらっしゃいますか．#ngsfield
□ yuifu:
カーゴカルトプログラミングを真似て、「カーゴカルト統計（学）」という言葉を思いついたけど、英語圏で既出だった。日本でも広めたい。 // Computational Intelligence: Cargo Cult Statistics …mputational-intelligence.blogspot.com/2011/11/cargo-…
One of the nice things about working in a world-class ecology group is the statistical rigor with which ecologists analyse their results. Unfortunately, this rigor is often missing in computational intelligence…
□ Bioinformatics week in Odaiba 2011（BiWO2011）
>> http://www.cbrc.jp/biwo2011/
□ CBRC_info:
明日2012年1月24日より4日間、CBRC公開ワークショップを中心に、バイオインフォマティクス関連の学術集会をBiWO2011(Bioinformatics Week in Odaiba)cbrc.jp/biwo2011/index…と題して集中開催致します。奮ってご参加ください。
□ CBRC/Biwo2011: お台場で開催中のバイオインフォマティクス関連学術集会。今日は『次世代シークエンサ研究の現在』関連ツイートが少なくて残念。Ust配信もないのは、暗黙にクローズド・コミュニティなりの効果を期待してるのかな。
□ シーケンスアプリケーション： ゲノム解析／エクソーム濃縮
>> http://t.co/nWL0QWsj
DHCなノリw
【エクソーム応援キャンペーン】7,350円でヒト全エクソン＆UTRの濃縮が可能に!急速な勢いで進むエクソーム解析研究をさらに加速させるために、イルミナはご好評頂いているTruSeqエクソーム濃縮キットの応援キャンペーンを実施いたします。