□ Topographic modelling and the global search for ring species
>> http://ow.ly/9CAZy
>> http://www.biomedcentral.com/1741-7007/10/20
Ring species’ or ‘circular overlaps’ present a unique opportunity to reconstruct the history of speciation. They occur when a chain of gradually diverging populations encircles a geographic barrier.
BMC Biology William Monahan and colleagues suggest a way to discover new examples of ring species, through a global topographic model that utilises information on the geographic barriers involved in the formation of known ring species to predict where other candidate barriers might be found.
生物の輪状種における地理的分散プロセスをグローバルな地形モデリング（凝集障壁・複合障壁）から追跡する知見。
生物多様性研究の地理指向アプローチの議論も展開されている。リングよりもバリアに着目する。単変量・多変量の環境変数が大規模な潜在障壁に有用なケース。
輪状種の分化・発散パターンと命名規則を、より定量的に関連づけるシステムがあったら分類学上便利かもね。輪状種の進化的変異パターンと分布をグラデーションで記述できるなら、その色彩の変量に応じた、何らかの地理的障壁の潜在的影響のスペシエーションも可能。生物種発見の数理アプローチでもある。
□ ChronoZoom (beta):
Zoomable timeline of the cosmos puts us in our place
>> http://www.chronozoomproject.org/
>> http://t.co/fDvtVVIo
Manipulating the slider, zooming in from the big bang through to the Mesozoic era for example, you get an intuitive sense of how our own existence on Earth occupies such a tiny portion of the scale. Each segment of time is packed with extras, like video clips or personal stories, or extra data about the period.
"might one day help visualise all the information in Wikipedia or all the world's libraries".
宇宙137億年のタイムラインを、地球・生命・人間の各々のセグメント・スケールでズームするインタラクティブ年表。将来的にはWikipediaや世界中のライブラリ視覚化に有用なタイムラインの概念とのこと。アカシック・レコードみたいなイメージ。
□ iPOP: integrative personal omits profile
>> http://www.cell.com/fulltext/S0092-8674(12)00166-3
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes
integrative personal omics profile (iPOP), an analysis that combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period.
Our iPOP analysis revealed various medical risks, including type 2 diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. Extremely high-coverage genomic and transcriptomic data, which provide the basis of our iPOP, revealed extensive heteroallelic changes during healthy and diseased states and an unexpected RNA editing mechanism.
iPOP:統合的な個人オミクス・プロファイリング：ゲノム情報と複数のハイスループット法モニタリングの組合せによる分子医療で表現型の動態を明らかに。
>> http://www.cell.com/fulltext/S0092-8674(12)00166-3#Data (上図）
iPOP概観のCircosによる可視化。動的オミクスとゲノムデータを接続・参照し、RNA編集機構を解釈する。トランスクリプトームは黄、プロテオームは紫のリング。
□ Conceptualizing a Genomics Software Institute (GSI):
“data centric architecture” cyberinfrastructure for NGS data
>> http://t.co/zplJXupx
Despite the fragmentation of data and tools, the community itself has developed a remarkably strong foundation of integrative collaborations and shared resources.A key development has been the Genomic Standards Consortium (GSC), which has acted as community-glue, providing a valuable forum for interaction between biologist and computational researchers, and the development of many new software and standards solution products via community consensus.
Other community-led informatics efforts including the many data sharing activities now unified under the BioSharing banner large software efforts that are advancing the field of microbial ecology and efforts to bring suites of software together provide a growing framework on which to build a Genomics Software Institute (GSI). Such an institute is needed and required by the community to reduce the hurdles individual researchers must leap to access data, reformat data, and generate ecosystem and organism level models.
The biological community has many hubs, which are beginning to self-organize under the auspices of community-led initiatives. These initiatives will act as conduits to enable interaction within the proposed conceptualization stage.
微生物メタゲノム等の生態系予測モデルの為のシーケンスデータ・ツールをコミュニティ主導で運用する統合フレームワークとサイバーインフラ。
微生物メタゲノムは若い分野。相互接続する多様性の代謝動態の予測モデルと解析は、人間の開発が生態系システムに齎す影響の計量に重要。でも、次世代シーケシングで生成されるデータのキュレーションやアクセシビリティは断片化、運用が阻害されてる。これらを統合運用するフレームワークを概念化する。
これら微生物メタゲノムのコミュニティ運用には、ISAのメタデータ追跡フレームワークと共有ソリューションを介しBioSharingにカタログ。データコモンズに準じ、異種のデータセットに有用なツールとリソースを提供する。
□ Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues:
microDNA in brain are somatically mosaic
>> http://t.co/Xv7fiBkN
□ jyasuda1:
miRNAの話と思ったが、全然違うもの。これはこれで驚き。哺乳類の細胞の中に多種多様な輪状のDNA（マイクロDNAと書いてある）が存在するという論文
さっき紹介した論文を恐れおののきながら読んでいる。どうしてこんなことを誰も指摘しなかったのか。本当なのか？ゲノムから数万もの短い配列が輪っかになって切り出されているのだ。しかもヒトの細胞で。
正常組織のDNAの0.1～0.2％にも上る量で取れてくると。1つ200bpとして、1細胞あたりでも数万近くあるはず。電顕写真もある。ヒトの体のDNAはいっぱいちぎれているということで、体全体がモザイクだということだ。
Junk DNAにリング状のものがあることは既知のことだったけれど、輪であることで正常の遺伝子を制御する機構が働いている例があるとしたら面白いね。
マイクロDNAの微小欠失のモザイク化が複雑になればなるほど生命現象の反復性の確率的維持が難しくなるんじゃないかとか。進化の壁を規定するのが体細胞生成における不確実性の定量と、その振る舞いのカオスの縁にあるのだとしたら、『ヒト遺伝子』と他の哺乳類との比較は重要性を帯びてくるのかも。
□ iGenomics:
Ruper Yip: Amazon cloud is now HIPAA compliant (medical data). FISMA certified (government data) & EU Safe Harbor compliant. #abrf
Ruper Yip: Demoing DesignStudio that can stream data in real time to BaseSpace , ILMN's cloud solution. #abrf
□ ISUGenomics:
Illumina's new technology is WOW! Single cell RNA-Seq. No PCR library prep, can't wait to try that out! #ABRF
□ Researchers Develop Permanent DNA-Based Data-Storage Device:
>> http://t.co/w1oW4ELA (Robotics Trends)
DNA-Light data encode system (AIP Applied Physics Letters)
DNAフィルムと紫外線の光トリガ合成プロセスを応用した恒久的なデータ・ストレージ。
□ Bioinformatics curriculum
>> http://sciblogs.co.nz/code-for-life/2012/03/13/bioinformatics-curriculum/
They show a graph of responses to the question “What are the most important topics that someone should understand in order to work in the field of computational biology / bioinformatics?” I have to admit I don’t quite agree that programming and then statistics are the most important.
A key element missing though, that I’ve touched on before, is the theoretical biology that is used in and underpins computational biology. To me that is the most important background. It is not necessarily taught much in ‘straight’ biology courses.
バイオインフォマティクス領域で最も重要なトピックとは何か→統計プログラミングという結果。でも筆者は理論生物学の教育背景が依然として最重要であると主張。ICSB教育委員会への提言。
□ The Biodiversity Heritage Library for Europe:
>> http://www.bhl-europe.eu/
The EU-project ‘Bio?di?ver?sity Her?itage Library for Europe’ is ded?i?cated to solv?ing this prob?lem by mak?ing this type of con?tent easy to find. It aims to make the exist?ing dig?i?tal col?lec?tions of Euro?pean bio?di?ver?sity lit?er?a?ture freely acces?si?ble to any?one online. Both BHL-Europe’s mul?ti?lin?gual por?tal (com?ing soon) and the Euro?peana por?tal pro?vide instant access to this type of lit?er?a?ture, with over 100,000 objects now already avail?able through Euro?peana.
http://t.co/JxDQVaqe
□ MrPrudence:
John Cage's Atlas Eclipticalis performance of 1964 - the conductor was replaced by a clock with baton attached to it http://t.co/MKIAlxul
□ reaktorplayer:
The Wolfram Atlas of Simple Programs: http://atlas.wolfram.com/
□ fabmass:
a must read: In Defence of the Virtual: A Secret History of Ballardian Film Adaptations (via Ballardian) http://t.co/pxuRJid1
□ Sagebio:
“a rite of passage..after 244 years, Encyclopaedia Britannica is going out of print" http://nyti.ms/AqCzSm #longlivetheking
□ dgmacarthur:
Fantastic response by @johnhawks on that "bioengineer humans to fight climate change" article: http://t.co/uNyiUFXr
□ Doctors Believe Using Health Apps Will Cut Down on Visits [INFOGRAPHIC]
>> http://mashable.com/2012/03/12/mobile-health/
□ nutrigenomics:
ELIXIR: a distributed infrastructure for European biological data http://t.co/q5sFDdkx http://www.elixir-europe.org/
□ DailyNewsGW:
FTC Requests Additional Information From Roche Related to Illumina Bid: http://t.co/axglL5Q0
□ DailyNewsGW:
Recent CDx, NGS Deals Signal Siemens' Increasing Interest in Genomics Arena: http://bit.ly/xFQHLm
独・シーメンス社のゲノミクス領域の臨床応用戦略。illumina MiSeqプラットフォームとの連携など。共同診断・医療インフォマティクスへ。
□ FASEBopa:
FASEB responded to @NIHforHealth request for information on data and informatics. Check out our comments. >>> http://bit.ly/FO7Ky9
□ SAMSCOPE:
>> http://www.ncbi.nlm.nih.gov/pubmed/22419785
An OpenGL based real-time interactive scale-free SAM viewer.
visualize complex ChIP-Seq and RNA-Seq features such as polarity as well as coverage across whole 3Gbp genomes such as Human. SAMSCOPE provides instantaneous and intuitive browsing of complex data at all levels of detail across multiple experiments.
□ BiosecurityCntr:
Annals of Emergency Medicine: Allocating Scarce Resources in Disasters: Emergency Department Princip http://fb.me/VHkM7Krv
□ eurogene:
Mapping gene-environment interactions at regulatory polymorphisms...mechanisms of phenotypic variation http://1.usa.gov/zawH1f
遺伝子の調節多型と環境相互作用のマッピング。グルココルチコイド影響下の表現型変異メカニズムの洞察
□ BioMedCentral:
Discovering opinion leaders for medical topics using news articles http://ow.ly/9FBpE from #JournalofBiomedicalSemantics #openaccess
□ keyboardrobot:
Please give your comment on “BioDBEntry” proposal for extensions to “http://schema.org” vocabularies. http://t.co/iF1fh5sC
□ Chembl:
ChEMBL Schema & SQL Querying Webinar: This is a call for people wanting to sign up for the "Schema & SQL Queryi... http://bit.ly/wih1zE
□ rnomics:
Dynamic Architecture of a Minimal #RNA Polymerase II Open Promoter Complex: Barbara Treutlein, Adam... http://bit.ly/zfCyHF #cell @MyEN
□ GenCounsNews:
Brandeis researchers receive NINDS grant to examine psychosocial impact of genetic testing for epilepsy http://t.co/Ggi3Zkb9
□ EarthOpenSource:
Why current risk assessment methods for chemicals / #pesticides cannot work: http://edrv.endojournals.org/content/early/2012/03/14/er.2011-1050.short
□ JoDesignHistory:
New issue of the Journal of Design History out now vol. 25, no. 1 (March 2012) See contents incl. hover-over abstracts http://jdh.oxfordjournals.org/content/current
>> The History of Advertising Design in Kuwait: Post-Oil Cultural Shifts 1947-1959
http://m.jdh.oxfordjournals.org/content/25/1/55
□ ImplementSci:
Review | Sustaining new programmes and practices in health care: recommendations for future research | http://t.co/5q8ZcoSn
□ TrueSight:
Self-training Algorithm for Splice Junction Detection using RNA-seq
>> http://bioen-compbio.bioen.illinois.edu/%7Eyangli9/TrueSight/
□ NCIcaBIG:
See the newest community-contributed #opensource tool: PAIS - Pathology Analytical Imaging Standards from Emory #caBIG http://t.co/FjYPJvAb
□ RNAimmuno:
>> http://t.co/UcQd5IGq
A database of the nonspecific immunological effects of RNA interference and microRNA reagents
□ ??? ▼ :
How world's smallest DNA virus evolved in rare parakeets: http://t.co/NDIC1EuX
□ IDSAInfo:
"Pass it on: Social media can be useful in monitoring and dispelling health misinformation and myths." http://fb.me/1pF4jUGTt
Europeana Portal Features from europeana on Vimeo.
□ cc_jp:
デジタル図書館“Europeana”の便利な機能(マップ検索・ディスプレイ、Wikipediaでの引用、画像のライトボックス表示)についてまとめられたムービーです。 http://t.co/1Lb1NIEI (森本)
□ dritoshi:
既存のウェブアプリ用 framework は、ユーザからの入力を直接、受けることなく、計算・解析によって、データやモデルが自動的に生成されることが考慮されていない。ここをコードジェネレータ側でなんとかしたらいいのかも。
□ greatpunkin:
日本植物生理学会のiPhoneアプリが便利すぎる。もうこれだけあれば、重い要旨集持たなくて良さそう。動作がもっさりなのが少し残念だけど、充分使えます。http://t.co/NBaHKtSM
□ _shk:
検索結果をわかりやすくするRich Snippetsのため, htmlマークアップのバイオDB拡張をNBDCと医薬基盤研でW3Cに提案しました。Microdata形式でhttp://Schema.orgのpropertyを拡張. http://t.co/q4b9GHv9
□ synobu:
TogoAnnotation: ソーシャルブックマークでゲノム注釈を行なうプロジェクト. 遺伝子, 文献, ゲノムごとのサマリや各種JSON APIが付け加わりました. http://t.co/WtGKVZO7
□ cc_jp:
イタリア文部省ーUniversity and ResearchがCCライセンス(CC BY)を採用し、オープンデータ・ポータルを開始しました。 http://archivio.pubblica.istruzione.it/scuola_in_chiaro/open_data/index.html (森本)
