ISMB/ECCB Conference VIENNA 2011.

□ The ISMB/ECCB 2011 conference.

>> http://www.iscb.org/ismbeccb2011
>> http://bioinformatics.oxfordjournals.org/content/27/13

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past eighteen years the ISMB conference has grown to become the world’s largest bioinformatics/computational biology conference, and ISMB/ECCB 2011 will be the year’s most important computational biology event globally.

□ VIZBI 2011: NIH conference on visualizing biological data

>> http://vimeo.com/album/1640748

As biological data grows rapidly in volume and complexity, biologists rely increasingly on computational visualization to gain insight from data. The VIZBI 2011 conference brought together researchers developing and using computational tools to visualize data from genomes, transcripts, proteins, cells, organisms, and populations. VIZBI 2011 was held March 16-18 at the Broad Institute, Cambridge MA, USA.

□ tweet storage.

□ □ pjacock:
Near complete #bosc2011 tweet archive: twapperkeeper.com/hashtag/bosc20… (thanks @adamhuffman) #bioinformatics #opensource conference (BOSC) pre #ISMB SIG




□ kiharalab:
Kihara, Juan Rodriguez, Meghana Chitale will head to ISMB at Vienna http://bit.ly/g51K5l tomorrow. Attend 3D-SIG, AFP/CAFA, main conf. #ismb




□ GenomeBiology:
Read Genome Biology's take on ISMB 2011 on the BMC blog bit.ly/qfPuYR #genomics #ISMB

Two initiatives to promote data sharing held workshops at the conference: BioSharing and ELIXIR. At the BioSharing workshop, which discussed the bioDBcore database cataloging project, Genome Biology appeared on the panel as a voice of open access publishing and representative of BioMed Central. In addition to Genome Biology, BioMed Central had several other journals represented at the ISMB, including a strong presence from BMC Bioinformatics and GigaScience.

□ bioontology: NCBO
NCBO Web Services and Development of Semantic Applications, bit.ly/nALNgS #ismb




□ GigaScience:
New post in GigaBlog: GigaScience on the road... blogs.openaccesscentral.com/blogs/gigablog/ #ISMB

Despite the advantages of using the enormous user base, the drawback of using a wikipedia based system is the lack of semantic representation. Using semantic media wiki to combine this externally may solve some of this issue, and Ben Good followed this talk showing how genes can be linked to diseases by making a wiki mashup of SNPedia with Gene Wiki.

□ _lrr_: Luis M Rodriguez-R
WikiProject on Computational Biology http://bit.ly/oaXg4K #ismb #eccb11

WikiProject Computational Biology is aimed at improving and organising articles on Computational Biology, Bioinformatics, Computational Systems Biology and related topics.

□ YabiProject: A more complex workflow in Yabi that demonstrates running tasks in parallel.
Almost time for our #ISMB tech talk. New movie of Yabi using @emblebi web services youtu.be/zLCNAqn8nFE?hd…




□ F1000: I still haven’t found what I’m looking for
Sciencenet -- a multidimensional search engine http://bit.ly/nS6xTd

There is a prototype at http://sciencenet.kit.edu/. I’ve had a little play, and think I’m going to put the emphasis on prototype. I ran a search on a protein close to my heart and found the results not quite as useful as if I’d gone directly to some of the more familiar databases. Perhaps Sciencenet will improve with time?I certainly hope so?or maybe we should think about a filtering mechanism on top of this search engine (hey, now that sounds familiar).

□ BiologyOpen:
Biology Open is now accepting papers! Be one of the the 1st to submit! http://open.biologists.com/ http://fb.me/159sI1Muh

Biology Open is an online-only Open Access journal that publishes original research across all aspects of biological science, including cell science, developmental biology and experimental biology. Biology Open aims to provide rapid peer-reviewed publication for good-quality scientifically sound observations in these allied fields.

□ micheldumontier:
#dlab Check out our PLOS One paper on semantic interoperability using relation expansion: plosone.org/article/info%3…
Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning.

We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions.

□ BioMedCentral:
Reading: ‘The Power of Open’ launched by Creative Commons http://ow.ly/5BaOb #oa #open access




□ DailyNewsGW:
LaserGen, National Instruments to Collaborate on Next-gen Sequencing System: The firms aim to have a system deve... http://bit.ly/piarUN




□ BioMedCentral:
‘Beyond the Tree of Life’: a new thematic series from #BiologyDirect http://ow.ly/5DbpX #biology #evolution

The Tree of Life is a powerfully attractive representation of an evolutionary process and pattern that has been severely challenged by the discovery of extensive horizontal gene transfer in bacteria, archaea and other organisms.

□ DailyNewsGW: GenomeWeb News
Coriell Using IBM for Biosample Management: read more http://bit.ly/nuhmVW






□ ReaderMeter: Dario Taraborelli
Wikimedia joining forces with open science: bit.ly/nV03IT #OA #opendata //cc: @PLoS @sciencecommons




□ NatureJapan:「ポスト光」時代のゲノム塩基配列解読チップ
An integrated semiconductor device enabling non-optical genome sequencing http://nature.asia/qLHZgW

より安価でよりコンパクトなDNAシーケンサーをめざす技術的進展は、画像化技術の必要性などいくつかの要因が足かせとなっている。今回、光学的読み取りを行わず、代わりに、鋳型指示DNA合成反応で生成される水素イオンを直接検知して塩基配列データを集める新規のDNAシーケンシング技術が報告された。この手法は、大規模並列処理半導体検出装置（イオンチップ）を用いた、廉価で拡張性の高い塩基配列解読法への道を開くものだ。

□ NatureJapan: 新たなるバイオ医薬品開発 - 最前線レポート
http://nature.asia/nVTMPc

「バイオ医薬品」の開発に新たな波がおしよせている。最初の波は1980年代。遺伝子組み換え技術を用いたヒト成長ホルモンやインスリンなどの、いわゆる第1世代のバイオ医薬品が上市された。その後、抗体や改変タンパク質の技術、トランスジェニック動物、RNAなどの核酸を用いた創薬研究がさかんになり、2000年以降、ヒト型抗EGF受容体抗体（トラスツズマブ）をはじめとするさまざまな抗体医薬品が承認されるようになっている。

さらに、RNAなどの核酸を利用する試みも進んでいる。こうした、第2、第3世代のバイオ医薬品開発について、研究開発の現状から、成功の鍵、安全性の検証、今後の予測まで、最前線を多角的にレポートする。

□ celldna: Cell DNA
New Virus Jumps From Monkeys to Lab Worker - Study shows for the first time that an adenovirus can cross the species... http://ow.ly/1dPdDw




□ appliedgenomics:
Very interesting Harvard/MIT study turns the entire genome of a bacterium into an “editable and evolvable template": bit.ly/n3KVSc




□ portablegenomic:
FDA won’t regulate these apps, for now mobihealthnews.com/11978/fda-wont… but will regulate these mobihealthnews.com/11980/types-of… via mobihealthnews




□ rnomics: Fabrice Leclerc
Immunovirological and Biochemical Changes in Nigerian Patients with Hepatitis B Coinfection on... http://bit.ly/puzAgV #WWS




□ DivaBiotech: Ruby Gadelrab
Africans are seriously underrepresented in GWAS! Genome Revolution Is Skipping Non-Whites | Wired Science | Wired.com bit.ly/rqxJlv




□ DivaBiotec:
Spotlight on Nigeria, Kenya, Ghana - Africa's vast new tech opportunity (Wired UK): bit.ly/os2YLv




□ PLoSMedicine:
World’s first “home grown” African first-aid guidelines: http://bit.ly/qO8pa9
Evidence-Based African First Aid Guidelines and Training Materials

In sub-Saharan Africa, much disease and injury can be addressed by emergency care. First aid training has been promoted as an inexpensive way to save lives. However, first aid training in sub-Saharan Africa is often based on handbooks prepared outside of the continent that are not adapted to the African context.

We formulated evidence-based guidelines that comprehensively address how basic first responders should be trained to manage emergency situations in an African context. The guidelines focussed on first aid interventions requiring minimal or no equipment.

□ reliefweb:
New openaccess publication for disaster management research calls for papers bit.ly/qjXoWG @PLoS Currents: Disasters




□ Chem_Central:
New research in #JCheminf 'PubChem3D: Biologically relevant 3-D similarity' http://goo.gl/SRwrW




□ MissouriCures: MissouriCures.org
#Stemcell treatment may improve functional learning and memory loss in #braincancer patients http://bit.ly/nra8lU #stemcells #cancer






□ PLoSCompBiol:
Chaotic Behavior in the Xenopus laevis Embryo ploscompbiol.org/article/info%3…
Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?

By extending a cell-cycle model previously developed for embryos of the frog Xenopus laevis to include the spatial dimensions of the embryo, we establish a novel role for the rapid, fertilization-initiated calcium wave that triggers cell-cycle oscillations.

Specifically, in our simulations a fast calcium wave results in synchronized cell cycles, while a slow wave results in full-blown spatio-temporal chaos. We show that such chaos would ultimately lead to an unpredictable patchwork of cell divisions across the embryo. Given this potential for chaos, our results indicate a novel design principle whereby the fast calcium-wave trigger following embryo fertilization synchronizes cell divisions.

□ Cascading dynamics in complex quantum networks

>> http://chaos.aip.org/resource/1/chaoeh/v21/i2/p025107_s1

量子情報の長距離移送: 外部摂動下ネットワークのカスケードダイナミクスにおける光子損失の最小化

Recently, small-scale quantum communication has been realized by transporting entangled photons, rendering potentially feasible quantum networks on large scales. We propose a class of quantum networks comprising quantum repeaters for long-distance information transport and local networks of fibers and switches.

As the transmitting capability is limited by the node bandwidth, photon loss can occur through the dynamical process of cascading when the network is under external perturbations. We obtain results that can be used to guide quantum network design to minimize the photon loss.

□ AIP_Publishing:
Asymptotic evolution of quantum walks with random coin http://ow.ly/5ElGH #AIP_JMP




□ OxfordJNLsJapan:
【生物学・植物】Plant Ecologyから無料アクセス論文：植物種が豊富なことが林分構造と生産性に与える影響について http://oxford.ly/q9Getw #plants
Effects of plant species richness on stand structure and productivity.




□ OxfordJNLsJapan:
【ライフサイエンス】魚類と哺乳類の噛み方の違いは顎と舌骨の形の違いhttp://bit.ly/jtfqrG 原著論文はこちらから http://oxford.ly/jVpFGH #fish #animals #mammals
Evolution of Muscle Activity Patterns Driving Motions of the Jaw and Hyoid during Chewing in Gnathostomes




□ Hypios:
Michael Bonner and Klaus-Peter Speidel debunk the myth that solutions are the only benefit of open... http://fb.me/DDPyOQEU
Sometimes the Solution is not the Solution.

If companies only focus on the solution, if they construe this as the only valuable thing that can come from Open Problem-Solving or Open Innovation, they will be disappointed if this solution does not come. Similarly, if a solution is found but discarded, the company will seem to have wasted its time and money. It is better to think of Open Innovation as a process of development or maturation within R&D: a fundamental cultural shift in a company’s approach to thinking about problems.

□ RichardDevine:
Björk: Biophilia: multimedia exploration of music, nature and technology, for iOS http://bit.ly/q3Pbfo

Biophilia is an extraordinary and innovative multimedia exploration of music, nature and technology by the musician Björk. Comprising a suite of original music and interactive, educational artworks and musical artifacts, Biophilia is released as ten in-app experiences that are accessed as you fly through a three-dimensional galaxy

□ gaou_ak:

ソフトウェアと違い、データは一般的にはファクトなので知的財産ではない。ただし、キュレートされたデータの集合は知的財産となる場合がある（ドイツではそうらしい）。これを明確に回避するには、CC0 ( http://bit.ly/qncham )を選ぶ必要がある。 #BOSC2011

□ tenapi:

超算術的直線と交わらない 平面の 空でない \Pi^0_2 部分集合があるか。

単位円と超算術的直線の交点や接点はかならず超算術的点になるから単位円から超算術的要素をもたない \Pi^0_2 部分集合をとりだせばよいのでした。ちゃんちゃん!!

□ tri_iro:

「超算術的直線と交わらない」という条件だと、必ず全不連結になってしまうけど、ちょっと条件を変えて、「超算術的点を含まない」に変えると、平面の空でない連結Pi^0_2部分集合の存在も自明で、実は単連結にも、更に言えば可縮にも出来るけれど、こういう問題で何か発展形は無いかなあ。

超適当なイメージ：Δ^0_1→その辺の地面。ジャンプ→地道に階段をのぼる。超算術的階層→登山。ハイパージャンプ→宇宙に飛び出す。とすると、深海には何がいるのか気になるところである。

□ tri_iro:

そういや「RT(2)→WKL問題」がついに解かれたという噂が流れているらしい。4年前からずっと追っかけてた問題だから感慨深い。ちなみに RT(2) とは、集合論とかの記号を使えば、 ω→(ω)^2_2 のことです。

2007年（4年前）から現在までの「RT(2)→WKL問題」の研究の流れは、ジャファロフのサイトの図表 (pdf) http://www.math.uchicago.edu/~damir/files/diag_rm_strong.pdf のカオスさが物語っているような