□ 生命機構とエネルギー効率の問題について
「生命システム」という定義に係る問題だけれど、そもそも生命は、システムを指向せずしてシステムに「ならざるを得ない」。アルゴリズムは即ちダイナミクスである。遺伝子創出プロセスはエネルギーの過渡状態で、そのトポロジカルともフラクタルともいえるエネルギー準位や形状の決定が可干渉かどうか
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gaou_ak:
（承前）3. バランス的に、多くの機構は単純でエネルギー効率が良く処理されていて、ロングテールとして複雑な機構が他数ある。エネルギー使用や効率がスケールフリー分布か対数正規分布に乗るなら（僕は乗りそうな直感がある）、３である可能性が結構あって、まさにこれが僕の今の不安に直結する。
結局ね、そういう『複雑』な細胞内制御の新機構を報告する論文って、それがあたかもセントラルドグマを覆す重大な作用機構で、普遍的かつ網羅的に効いている、という論調のものが多いんだけど、それが気にくわないんだと思う。それはハブなのか、ロングテールなのか。
生命システムには、要素（広義の遺伝子）、要素間相互作用、要素のパラメータがあり、選択圧はそれぞれにかかるが、生物にとっての変化コストは要素＞相互作用＞パラメータだが、おそらく変化によって系に与えうる影響もこの逆なので、どこまでがパラメータやリワイヤリングで対応しうるのか、が課題。
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n0rr:
@gaou_ak また、微生物やカビなどの単細胞生物でも普遍的に複雑な機構を持っていることは、１個体あたり利用可能なエネルギー量を考えますと持ち過ぎであり、これが機構の希少さを示すのではないかと思います。
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dritoshi:
微生物はわりとシステムのパラメータと仕組みの両方が準安定っぽいかも。多細胞生物が持つ高次機能 (組織や器官など)は、ad hoc なシステムもたくさんありそう。
生命科学が解いている問題には「歴史の理解」と「原理の理解」の2つがまざっているのを意識するだけでだいぶクリアになる。
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tonets:
生命ってその場凌ぎ的な局所最適にしかできてないんだろうなぁ．Levinthalのparadoxみたいな話．
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DailyNewsGW:
NHGRI to Fund New Africa Genomics Grants, Biorepositories: read more
bit.ly/sZxZRX
The National Human Genome Research Institute has just issued two new funding opportunities for research institutions in Africa seeking to conduct genomics projects focused on diseases, building genomics infrastructure, and launching biorepositories around the continent for supporting research projects.
These biorepositories will be tasked with supporting the entire H3Africa Consortium, and will be required to deal with as many as 100,000 samples per year including blood and DNA in liquid, frozen, and dry forms. They also must be able to ramp up their abilities to receive and store these samples and distribute them throughout the consortium.
米NHGRIが、アフリカにおけるゲノムプロジェクト、ゲノムインフラの構築に向けて資金調達。H3Africa ConsortiumをハブにしたDNAサンプリングの為のバイオレポジトリの開発など。
□
InsideScience:
bbc.in/vvn8D0 - BBC says LHC reports first new particle--Chi_b (3P)--excited state made of beauty quark and beauty anti-quark!
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□
MSF_access:
Read MSF’s pick of the ten most important stories in access to medicines in 2011
ow.ly/857lx #10stories
One key fault-line is India, the home of the most quality affordable medicines used in the developing world, but which faces attacks by drug companies and wealthy countries who continue to clamp down on generic production. Other middle-income countries are increasingly finding themselves faced with escalating prices from the pharmaceutical industry. The price of vaccines is a newer source of contention, and will remain so, now that the world’s largest purchasers are openly publishing vaccine prices for the first time.
2011年、『治療薬へのアクセス』医薬品に関連した10の最重要課題: ドーハ宣言、ワクチン価格、途上国疾患対策の資金不足、医療障壁など
□
dominiquebabini:
コロンビアにおけるオープン・アクセス事業の国家戦略。機関レポジトリの推進。ノルウェーと米国との連携。
OpenAccess #OA in Colombia. Summary prepared by #CLACSO for #GOAP Global Open Access Portal #UNESCO
bit.ly/s7GjcZ
The National Academic Network of Advanced Technology (Red Nacional Académica de Tecnología Avanzada-RENATA) -with support from the Ministry of Communication and Information Technologies (Ministerio de Tecnologías de la Información y las Comunicaciones), the Ministry of Education (Ministerio de Educación Nacional) and COLCIENCIAS- is actively promoting open access in Colombia and in the region, and organizing training activities for institutional repositories, and a prize for institutional repositories.
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SpringerSBM:
UNESCO Launches Global Portal to Track Open Access
ow.ly/84WGo (TH) (via @scholarlykitchn) #OA #OpenAccess #publishing
UNESCO has launched a Global Open Access Portal (GOAP). GOAP is an interesting website, designed to summarize the current status of open access to scientific information, especially from a regional and country-specific perspective.
□
MnlimasBio:
JBEI researchers have developed CAD-type tools for engineering RNA components (...)
nanowerk.com/news/newsid=23… Synthetic biology #synbio
The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences.Researchers at the U.S. Department of Energy (DOE)'s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or "RNA devices" for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.
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neilfws:
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments
bit.ly/sZFunM #citeulike
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MITNewsTips:
MIT launches online learning initiative: MITx will offer courses online and make online learning tools freely available-
http://bit.ly/vgJ7Y2
“An open infrastructure will facilitate research on learning technologies and also enable learning content to be easily portable to other educational platforms that will develop. In this way the infrastructure will improve continuously as it is used and adapted.” Agarwal is leading the development of the open platform.
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drkgoto:
世界的にも進化や生態学は受難の時代なんですね。いろんなところで進化や生態学が認知研究にいかに重要かをもっとアピールするべきですね。
dx.doi.org/10.1016/j.cub.…
Funding troubles for evolution and ecology
Some fields, notably molecular and systems biology, frequently deliver little but cost enormous amounts, and I think that many, probably the majority, of evolutionary ecologists would be happy to have more grants funded but the total amount per grant to be capped. This seems to me to be a more intelligent funding scheme too because no one, absolutely no one knows where the next big idea or breakthrough will appear and so spreading the dollars across groups makes sense...
進化・生態学への助成金が、近年の分子・システム生物学にかかる膨大なコスト等によってパイが縮小している問題。フィールドにおける環境保全学術の重要性とは。こういう伝統性と必要性を併せ持ちながら、新興学術分野によって助成金の分配がナローになっている研究の為にこそ、新たな資金調達スキーム（主に民間に向けた）のためのOpen Platformの構築が急務なのではないかと思う。
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systbiol:
Biogeography Revisited with Network Theory: Retracing the History of Hydrothermal Vent Communities
ff.im/OyrcR
生物地理学をネットワーク理論で再構築する
Besides the identification of robust provinces, the network topology allowed us to identify preferential pathways that had hitherto been overlooked. These pathways are consistent with the previously proposed hypothesis of a role of plate tectonics in the biogeographical history of hydrothermal vent communities.
A possible ancestral position of the Western Pacific is also suggested for the first time. Finally, this work provides an innovative example of the potential of network tools to unravel the biogeographic history of faunal assemblages and to supply comprehensive information for the conservation and management of biodiversity.
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bhaapgh:
tool browsing funding :
app.nihmaps.org/nih/browser/#c…;>
#grantfunding
Grants from fiscal year 2011 are still being awarded. Currently there are 52,093 projects and 16,608 subprojects in the database, which includes grants awarded through the month of November. We anticipate adding grants to the database as they are made available on the NIH ExPORTER website (http://exporter.nih.gov/).
NIHによって助成金が給付された研究セクションのマップビューアー。約80,000回に及ぶ投資先を、トピック共有頻度の解析によって近接的に配置されたドットと、その部門ごとにカラーリングして可視化。
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carninci:
Finally our comprehensive map of mouse olfactory receptors promoters using nanoCAGE came out in Genome Research. This …
t.co/yg7Wvkak
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bhaapgh:
The ontology of clinical research, useful for annotating biomed studies of all
sorts code.google.com/p/ontology-of-… #semanticweb
The Ontology of Clinical Research (OCRe) is a formal ontology for describing human studies that provides methods for binding to external information standards (e.g. BRIDG) and clinical terminologies (e.g. SNOMED CT). It allows the indexing of research studies across multiple study designs, interventions/exposures, outcomes, and health conditions.
With such indexing, investigators interested in the evidence pertaining to a particular question (e.g., what is the effect of A on B in people with C) will be able to locate relevant research studies more easily across disparate data sources. The ontology was developed using Protégé 4 beta.
OCRe: 臨床研究オントロジー - BRIDGなどの外部標準と、SNOMED CTなどの医学用語を組み合わせたメソッドで、より多数の異種データソース間に股がった研究を可能にする。オントロジーはProtégé 4 betaで開発。
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MishaAngrist:
"incorporating WGS data [into] an electronic medical record, that is not something we envision at this point. "
bit.ly/tkVmRJ
Q&A: Mt. Sinai's Erwin Bottinger on Linking Patient Sequence Data with Electronic Medical Records
Mount Sinai Hospital is looking to become one of the first hospitals to make patients' genomic sequence linkable to their electronic medical records for clinical use. If successful, it plans to scale up to exome and eventually whole-genome sequencing for these patients.
臨床インフォマティクス: 患者のゲノム配列を電子カルテにリンク。 exomeデータまで拡張を視野。臨床意思決定支援モジュールの為のインターフェースをテストへ。
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creativecommons:
Help shape the future data/research infrastructure for Wikimedia:
bit.ly/WikimediaData #opendata #bigdata #wikipedia
We are working to create a public repository of open data to allow researchers and third-party services to access, share and remix data from our projects and communities and accelerate discovery.
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GenePoolNews:
GenePool acknowledged in "Post-Transcriptional Trans-acting Regulator Co-ordinates Transmission-Stage Enriched mRNAs"
nar.oxfordjournals.org/content/early/…
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PLoSGenetics:
The history and geography of genomes in @DiscoverMag:
bit.ly/sUhLfx
Mexicans and people of Mexican descent predominantly derive from an admixture event(s) between Europeans and Amerindians, with a minor African component.
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DailyNewsGW:
Study Links Elevated De Novo CNV Rate to Bipolar Disorder: read more
bit.ly/uHFg1S
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GenomeBiology:
Tavazoie lab: user-friendly tool performs rapid, accurate protein quantification from 15N MS data
bit.ly/rP4urp #genomics #proteomics
In quantitative mass spectrometry based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach.
We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.
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BioMedCentral:
Biophysical & structural considerations for protein sequence evolution
ow.ly/8433f #research from #BMCEvolBiol @BMC_series...
Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.
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rnomics:
DeepBlockAlign: a tool for aligning #RNA-seq profiles of read block patterns: High-throughput...
bit.ly/t2NAsc
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druvus:
Secrets of the deep for transcriptomes uncovered
bit.ly/vPB0P9 #ngs #rna-seq
The low abundance of many transcripts has limited the analysis of transcriptome complexity.
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SAGRudd:
Computational Techniques for Genome Resequencing Using @CompleteGenomic Reads. #awesome review; @MGRC pipeline better!
liebertonline.com/doi/abs/10.108…
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DailyNewsGW:
NHGRI Expands PhenX Project with Standards, Measures Initiative: read more
bit.ly/vyox5k
The new grants will provide $1 million to support researchers who evaluating the current standards of the National Institutes of Health-funded Consensus Measures for Phenotype and Exposures (PhenX) Toolkit program. The investigators will incorporate PhenX measures into their ongoing GWAS or large population studies and make recommendations on fine tuning the PhenX Toolkit, said NHGRI.
NHRGIが表現型と曝露(PhenX)研究を主要プロジェクト基準に拡張。GWASと連動し大規模な人口調査へ
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Genome10K:
"Very cool! The Human Epigenome Browser at Washington University : Nature Methods : Nature Publishing Group"(
twitthis.com/dzldse )
Advances in next-generation sequencing have reshaped the landscape of genomic and epigenomic research. Large consortia such as the Encyclopedia of DNA Elements, the Roadmap Epigenomics Mapping Consortium and The Cancer Genome Atlas have generated tens of thousands of sequencing-based genome-wide datasets, creating a reference and resource for the scientific community.
Small groups of researchers now can rapidly obtain huge volumes of genomic data, which need to be placed in the context of the consortium data for comparison. These data are often accompanied by rich metadata describing the sample and experiment, which is critical for their interpretation. Visualizing, navigating and interpreting such data in a meaningful way is a daunting challenge.
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visualisingdata:
New on visualisingdata.com | 10 significant visualisation developments: July to December 2011
bit.ly/ulX7Rh
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PLoSCompBiol:
CrowdoMeter ? or trying to understand tweets about journal papers
blogs.plos.org/mfenner/2011/1…
This is a great study because it shows empirically what many of us felt already: Twitter is one of the fastest tools to discover newly published scholarly papers, and the number of tweets is an important measure of scholarly impact. This is an important paper for the altmetrics movement, even though Gunther Eysenbach in the paper says that he doesn’t like the term.
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Chavach:
MIT Synthetic Biology Center - “Genetic Programming
Our goal is to create a programming language for living cells that is similar to languages used to program computers and robots. This requires the development of a high-level language that allows a programmer to describe a desired function and computational methods that convert this language into a linear DNA sequence.
□ Unified Medical Language System(UMLS):
>>
http://www.nlm.nih.gov/research/umls/
Metathesaurus and semantic network with lexical applications that can be used to overcome problems caused by differences in terminology and scattering of related information across databases
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ayrrisbio:
Full sequences of falconry birds will contribute to ways to protect the species
bit.ly/t1VI7r
ファルコン・ゲノム・プロジェクト:ハヤブサとセイカーハヤブサ2種のゲノム完全配列決定。英国と中国(BGI)、UAEの連携で実現
Abu Dhabi's Falcon Hospital (ADFH) provided the blood samples collected from male specimens of peregrine and saker falcons, and BGI were responsible for sequencing these samples on its large-scale next-generation sequencing platforms and producing high-quality data output. The bioinformatics analysis is conducted by the scientists from the School of Biosciences, Cardiff University (UK) and BGI.
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gedankenstuecke:
For all data miners: Got a genome and transcriptome. Now what?
j.mp/sqMMnr
I thought this was pretty much the list of things I’d want to see with a new genome on a new browser. And the reason I think this is especially key is because there’s only going to be more and more of this. With the new sequencing technologies and the data deluge, more groups are going to find themselves with important sequence data for their labs or their local researchers. Could be patients, could be model organisms, could be species. How to proceed with this data is important.
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genomicsnetwork:
Read a synthesis of ESRC Innogen's work on legal & bioethical regulatory mechanisms -
bit.ly/tb09u0
Health research, (bio)technology, regulation & values: Operationalising socio-moral values in the legal setting
The research that these papers represent relies on both desktop-based critical analysis (case-studies) and fieldwork- based empirical research (qualitative interviews). This Working Paper summarises and integrates the Work, but also deepens the ideas, justifies the undertaking, and further develops the argument.
Part I addresses the issues of scope and methodology. Part II explores the nature of the analytical touchstones relied on throughout the Work (ie: what is meant by ‘values’?). Parts III and IV go on to tell two stories which are related in that both rest on two primary premises:
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ayrrisbio:
Next-generation sequencing of viral genomes and viral diagnostics.
bit.ly/rVGR46
Novel DNA sequencing techniques, referred to as "next-generation" sequencing (NGS), provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology.
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Dev_journal:
New model for topographical axonal mapping relies solely on balance of forward and reverse ephrin/Eph signalling.
bit.ly/t2q2Gh
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Dev_journal:
Shaping sound in space: the regulation of inner ear patterning
bit.ly/uM0ubo Review by Andrew Groves and Donna Fekete
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PLoSCompBiol:
Predictability of Evolutionary Trajectories in Fitness Landscapes
dx.plos.org/10.1371/journa… Last week's most-viewed new research!
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PLoSCompBiol:
bit.ly/uEvQE6 RT @NeuroscienceNew Do You See What I See? computational #neuroscience
neurosciencenews.com/neural-simulat…
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VBCtweets:
VBC: US asks journals not to publish details of controversial bird flu studies
winnipegfreepress.com/world/breaking…
米政府が鳥インフル研究の論文の公表を差し止め要求。話には聞いたことあったけど酷いな…
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BioMickWatson:
BBC News - Hong Kong orders chicken cull as bird flu alert raised
bbc.in/vkTfwY
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AIP_Publishing:
Photoinduced write-once read-many-times memory device based on DNA biopolymer nanocomposite
ow.ly/858C2 #AIP_APL
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GenCounsNews:
Study participants at risk for developing Alzheimer's share their thoughts about being tested for APOE gene
bit.ly/u7Vp80
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EsterLBarle:
Many faces of endocrine disruptors: BPA Sends False Signals To Female Hearts - Science News
sciencenews.org/view/generic/i… via @sciencenewsorg
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TheScientistLLC:
The results from our 2011 Life Sciences Salary Survey are here!
bit.ly/vUwb4z
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PopInstitute:
Congress Rejects Large Cuts in International Family Planning Assistance
ow.ly/85JGr
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EurekAlertAAAS:
Plant-eating #dinosaur discovered in #Antarctica :
eurekalert.org/e/4bJX
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YusukeKomiyama:
2nd Global COE Workshop between Beijing Genomics Institute and University of Tokyo―Perspectives for Personal Genomics
bit.ly/t4oUN8
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YusukeKomiyama:
次世代生命体統合シ ミュレーションソフトウェアの研究開発 報告会
ISLiM成果報告会2011 DAY2 bit.ly/uWpHs8
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synobu:
CyanoBaseがNARのデータベース論文Top 5に. oxfordjournals.org/our_journals/n…
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tri_iro:
ALC2011・4日目7 ユーリ・アンドリューズ『強極小群の計算可能性』 モデル理論におけるBaldwin-Lachlanの定理は、任意のアレフ1-範疇的な理論に対し、素モデルから飽和モデルへの長さω+1の初等鎖が存在することを主張するけれど、これに対するスペクトル問題がある（続
まず、分解/局所モジュラー/体ライク（Zilberの三者択一）な理論で実現可能なスペクトルには限りがあり、フルショフスキ構成が必要であることを述べ、これを用いて、目的のスペクトルに対応するモデルの列を構成するという、今、計算可能モデル理論で最も熱い（たぶん）トピックの話
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eisula:
Ten Simple Rules for Making Good Oral Presentations
ploscompbiol.org/article/info:d… via @PLoSCompBiol
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OxfordJNLsJapan:
【音楽学】OUP音楽系ジャーナルからオペラ、古楽、ガーシュウィンなどに関連する論文をご案内。３月１日まで無料でアクセスいただけます。
oxford.ly/vbKDKr #opera #operatic #music
Music & Letters publishes articles on topics ranging from antiquity to the present day and embracing musics from classical, popular, and world traditions. It is renowned for its long and lively reviews sections, the most comprehensive and thought-provoking in any musicological journal.
