Runxt Life ? Introduction from Firma 103 on Vimeo.
□ Runxt Life
>> http://www.runxt.be/
Runxt Life is a generative music application created for the iOS® platform based on the cellular automaton theory “Conway’s Game of Life” by John Horton Conway.
The ‘game’ is a zero-player game, meaning that its evolution is determined by its initial state, requiring no further input from humans. One interacts with the Game of Life by creating an initial configuration and observing how it evolves.
□ Osciple - sound ripples
>> http://vaetxh.com/osciple/
□ emblebi:
Big science teams up with big business to kickstart European cloud computing: EMBL, CERN, ESA and the 'Helix Nebula' - bit.ly/zW3bTp
Today a consortium of leading IT providers and three of Europe’s biggest research centres (CERN, EMBL and ESA) announced a partnership to launch a European cloud computing platform. ‘Helix Nebula ‐ the Science Cloud’, will support the massive IT requirements of European scientists, and become available to governmental organisations and industry after an initial pilot phase.
Helix Nebula: the Science Cloud: CERN, EMBL, ESAなどの大型欧州研究機関が大規模計算を要する多分野科学研究に開かれたクラウド・プラットフォームを設立。用途は量子科学・ゲノム解析から宇宙開発まで。最初の2年間のパイロットフェーズではヒッグス粒子の探索と大規模ゲノム解析、自然災害研究の三分野に割当て。EMBLの全ゲノム・アセンブリとアノテーション・パイプラインをオンデマンドで世界中から利用出来るインフラ・ニーズとのこと。
Helix Nebula along with the Cloud Security Alliance, OpenNebula Project and the European Grid Infrastructure (EGI.eu), The commercial partners in this platform are Atos, Capgemini, CloudSigma, Interoute, Logica, Orange Business Services, SAP, SixSq, Telefonica, Terradue, Thales, The Server Labs and T‐Systems, They are working together to establish a federated and secure high‐performance computing cloud platform.
□ portablegenomic:
DNAnexus to Launch ‘Operating System’ for Genomics this Year medgadget.com/?p=35134
Sundquist explained that he had the above challenges in mind when he started DNAnexus. “We founded the company with a mission to unlock what we believe is a huge potential for DNA-based medicine and biotechnology.” The company is seeking to do that by building a collaborative and scalable platform. The firm has attracted financial support from Google Ventures and TPG Biotech.
DNAnexusが構築しているGenomicsの為のオペレーティング・システム。 Google VenturesとTPG Biotechから財政支援。エクサバイト・スケールのストレージ・スキームには、コミュニティ主導型のデータ運用が必要。
□ ICSUnews:
New Framework paper sets #FutureEarth in context of global environmental change and grand challenges for science pdf:bit.ly/wXJIit
Conceptual framework for an integrated platform
One of the key tasks of the Transition Team is to develop the conceptual framework for an integrated platform that links major research traditions with critical policy and human development concerns and can be used to identify priority research questions for Future Earth.
地球規模の持続可能性研究。環境変動と開発・施策をリンクする統合プラットフォームの概念的枠組み。
(Schematic diagram showing how producers and consumers of species distribution in...)
□ Trends_Ecol_Evo:
Free to download in TREE this month: The cyber-infrastructure needed to map global biodiversity effectively. bit.ly/xcRrnA
The geography of life on earth lies at the heart of ecology, evolution and the interaction of nature with human society. The spatiotemporal context of individual organisms, populations and species defines their environmental and biotic setting.
<fot size=1>This setting, in turn, drives ecological processes and provides the arena for micro- and macro-evolutionary mechanisms. Geographic data on the distribution of species are also vital for governments, agencies, and companies seeking to develop effective policies, and make sound decisions, regarding land management, health, climate change and biodiversity conservation.
生物多様性グローバルマップに有効なインフラ構築。
生物集団と環境定義の地理生態学的時空間コンテクストの統合。
・Map of Life:
>> http://www.mappinglife.org/
By bringing together all types of information about species distributions, providing model-based integration, and providing a system for users to build upon our knowledge, the Map of Life project hopes to support our community in understanding and saving the world's biodiversity.
□ EurekAlertAAAS:
Cutting-edge science creating solutions for African #agriculture. eurekalert.org/e/4dwr #AAASmtg
A re-invigorated effort to boost African science know-how to solve Africa's challenges has begun. With international funding, the Biosciences eastern and central Africa Hub (BecA-ILRI Hub) based in Nairobi, Kenya and managed by the International Livestock Research Institute (ILRI) is enabling African and international scientists to partner on a wide range of new and exciting research programs. Most of these research programs focus on both animal and crop health for better productivity under challenges including diseases and abiotic stresses.
アフリカの農業バイオイニシアチブ市場に巨大な好機。BecA-ILRI HubといいH3Africaといい、途上国の食糧・医療問題に大規模なBio/Data事業が発足の傾向。
アフリカとかアジアの僻地・経済開発に「今が好機です！」と基金を煽って市場活性を促すのはドンドンやれと思う。金を注ぎ込め。
BecA-ILRI Hubの方針はそこなんだけど、結局サハラ以南の社会経済の貧窮は、世界に出て行った優秀な人材が還流しないことに起因するもので、ここにトップクラスの拠点を置くことで地域の自立性も高める効果も期待される。普遍的だけど、特にアフリカは世界の食糧・防疫モデルの重要な拠点。
ちなみに米NHGRIも、H3Africa Consortiumをハブに、アフリカにおけるバイオリポジトリ開発の為の資金の手配に躍起になっている。失念したのだけど、アフリカで採取された凍結遺伝子サンプルなどは欧州にストレージする方針が何処かの機関で採択されていたような…
□ OA_Africa:
RT @openscience: Why South Africa should care about the Research Works Act education-copyright.org/rwa_in_sa/ #rwa #openaccess #oa #frpaa #openscience
In just 3 pages the Research Works bill seeks to prohibit open access mandates for federally funded research in the USA thus reverting the open access policy of the National Institute of Health (NIH) in the USA. It was introduced by Darrell Issa on 23 December 2011 and has caused major battles between the academic and publishing industries. The bill has the support of Elsevier, Association of American Publishers and the Copyright Alliance:
米国のH.R. 3699法案(研究成果法)が南アフリカの医療・保健環境に与える影響。
HR3699は、NIH等が推進する研究論文へのオープンアクセス性が連邦方針から高まる中、研究分野の著作権利益を制限し産業界の競争力を損なうとの批判から科学出版業界を中心に支持。教育・研究リソースのOpen Access化は、アフリカ等の医療福祉には不可欠なものに違いないのだけど
震災・福島原発事故の直後、NIHの緊急アクセス・イニシアチブによって、コクランライブラリー(Wiley-Blackwellとの共同)、Dynamed、EEP等のリソースから、被災地・被曝医療に関する研究論文へのアクセスが期間限定で開放されたけど、成果はフィードバックされてるのかな
□ iscb:
Feb 21, 2012 - ISCB Response to Research Works Act HR-3699 tinyurl.com/84q4ynq
HR 3699 will limit American taxpayers in accessing the results of the crucial scientific research they funded. By reversing the growing trend for cooperation and collaboration made possible by the open and rapid sharing of information and research results, this bill will inhibit our ability to exploit scientific discoveries, stifle critical advances in life-saving scientific research, and impede the pace of innovation in all scientific disciplines.
HR-3699への計算生物学会の応答。多数の学術誌団体・機関と同調し反対表明。NIH/PubMedデータベースの蓄積を無に帰す法案との批判。公共の保健医療におけるアクセシビリティの重要性
□ cc_jp:
世界中の図書館で次々とCCライセンスの採用が広まっています。「ドイツ国立図書館(DNB)、書誌データをパブリックドメインライセンス(CC0)のLinked Data形式で公開開始」 current.ndl.go.jp/node/20043 (森本)
□ PLoSCompBiol:
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report dx.plos.org/10.1371/journa…
Our results underscore two general considerations for researchers proposing novel types of analysis based on the GO: 1) that GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and 2) that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis.
遺伝子オントロジー・アノテーションから得られたオルソログとパラログ間の機能的類似性評価メトリック。統計解析依存を脱却。
「オーソログ遺伝子の統計的差異は、実験手法の相補性を反映していないと結論づけた」GOアノテーションを『開世界仮説』に属する物とし、時間とリソースの制約に基づき、統計分析に依存するのは公平性を欠くという洞察から、バイアスの適切な解釈を呈示する寸法。
□ Exploring Rational Drug Design
>> http://t.co/ETh1q0HK
Selectivity Strategies for Rational Design: 薬剤の合理的設計の選択戦略
Affinity Optimization: drug designers must account for explicit water molecules
□ mfenner:
New blog post: Crowdsourcing the analysis of scholarly tweets. Please help analyze the dataset via github repository blogs.plos.org/mfenner/2012/0…
Euan Adie and I started the CrowdoMeter project, an analysis of the semantic content of tweets linking to scholarly papers. Because classifying almost 500 tweets is a lot of work, we turned this into a crowdsourcing project.
For this purpose I have created a public repository on Github which contains not only the source code for the CrowdoMeter website, but also all data ? the same dataset made available on figshare.
□ Four Ways to Slice Obama’s 2013 Budget Proposal
・Explore every nook and cranny of President Obama's federal budget proposal.
>> goo.gl/waIx3
Chart shows $3.7 trillion authorized to be spent in 2013. (Total spending is estimated to be $3.8 trillion, including funds authorized in other years). Negative budget authority, which results from fees or other collections, is shown only on the department totals tab, but is included in other totals.
□ fumi1:
USの2013 budget proposalをd3.jsで可視化 by NYT goo.gl/waIx3
DNA nanorobot from Wyss Institute on Vimeo.
□ DNA Nanorobot Developed for Future Immune Responses Programming http://t.co/hDE8EhTw | Harvard announcement: http://t.co/vzDPjBy4
<fon tize=1>This programmable nanotherapeutic approach was modeled on the body's own immune system in which white blood cells patrol the bloodstream for any signs of trouble. These infection fighters are able to home in on specific cells in distress, bind to them, and transmit comprehensible signals to them to self-destruct.
The DNA nanorobot emulates this level of specificity through the use of modular components in which different hinges and molecular messages can be switched in and out of the underlying delivery system, much as different engines and tires can be placed on the same chassis. The programmable power of this type of modularity means the system has the potential to one day be used to treat a variety of diseases.
トリガーターゲット治療反応へのDNAナノロボット応用。プログラマブルな白血球細胞の免疫系近似モデル。標的治療への新アプローチ。
□ biomol_info:
"Open Source" Drug Development Company Launched ow.ly/9gnng
□ portablegenomic:
Want to see your genome on a smartphone? Portable Genomics in the San Diego Union Tribune. m.utsandiego.com/news/2012/feb/…
□ OKFN:
The Open Data Handbook v.1.0 is here - the why, what and how of open data! Read all about it: bit.ly/Ahqo2R #opendata
>> http://opendatahandbook.org/
We are also aware of the need to tailor general advice about open government data to the legislative frameworks and requirements of different countries. If you would like to be involved in writing a country specific adaptation of the Open Data Handbook, please do get in touch via the mailing list.
Open Data Handbookがリリース。より多言語への翻訳は、途上国の社会インフラ、経済開発の為のオープン・データ開発に不可欠。
Open Dataの指向するところの、国家単位の立法フレームワークと、オープン・ガバメント要件については、もっと民間の意見を汲み上げる必要性。その草の根としてのハンドブックでもある。
□ irynakuchma:
Species data from biodiversity hotspots in the developing world to go #openaccess bit.ly/xGTUpz (HT @SciDevNet) #Pensoft #EOL #EOASP
Research on new species from biodiversity hotspots in the developing world, published in a range of journals, may soon become freely available online as soon as they are published, thanks to a project launched last week.
生物種データのオープン・アクセス・イニシアチブで、ブルガリアのPensfot出版がEOLと提携。EOASPはコスト確保のためパイロット・ファンド設置
Linked Open Data from europeana on Vimeo.
□ greenharr:
JISC and Europeana video on Linked Open Data: bit.ly/xlJgSd
Simple animation to explain what Linked Open Data is and why it's a good thing, both for users and for data providers.
□ FrancoisBelleau:
OpenData.qc: Drug Product Database in a Virtuoso triplestore to play at #hackinghealth, have fun. opendataqc.blogspot.com/2012/02/drug-p…
I will be bringing the Canadian Drug Product Database to the Hacking Health Hackhaton to play with in RDF format and store in a Virtuoso triplestore. The same technology used to publish Wikipedia according to the Semantic Web standard, the software used by DBpedia project.
□ BrainCatalog:
Making your database available via Wikipedia: the pros and cons: j.mp/Az1cBe
The Rfam database is a collection of RNA families: http://j.mp/AorvCJ
For Pfam and Rfam we adopted the use of Wikipedia as the wiki model.
Are wikis the future of biological databases? Well, the answer is yes, and no. They help bridge the vast gap between the amount of human-annotated data compared to unannotated data. Where annotations do exist, the use of wikis can help to improve the annotation and keep it relevant. But, wikis are extremely simple and are unlikely to replace the complex relational organisation of many biological databases.
生物学的データベースをWikiモデルで構築することの課題。Rfamなどの先行例。資金調達リスクに果たすBiocuratorの役割。
□ Biofab Data Access API
>> http://www.programmableweb.com/api/biofab-data-access
Datasets are or will be in compliance with the Synthetic Biology Open Language (SBOL) standard.
□ RNA-Seq Atlas -
A reference database for gene expression profiling in normal tis