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.
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.
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.
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.
WikiProject Computational Biology is aimed at improving and organising articles on Computational Biology, Bioinformatics, Computational Systems Biology and related topics.
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).
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.
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.
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.
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。
「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。
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.
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.
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.
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.
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
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
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!!
「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。
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
The first single off the album, "Promises," is scheduled for release on Black Hole Recordings in June.
their second full-length album would have to wait. Much to their fans' relief, Mavie and Josh decided to reform as a duo, and the resulting full-length record is due for release in Winter 2011.
8000 lanterns were released by Poznan in Poland June 21st, 2011 for the first day of summer. The 8000+ lanterns are a world record and the city plans on beating that record again next year.
LONDON--For 80 years, Abbey Road Studios has been one of the most important places in the music business.
CNET got a chance to visit and see some of the most impressive studio rooms and equipment in the industry. Including a microphone that both McCartney and Lennon often sung into.
Fractal geometry apparently also appears in the human body. The pattern of heartbeats over long intervals looks fractal. How about the geometry of cells? And could the observation of fractal geometry be used to identify cancer cells?
On May 11, 1944, a warm and cloudless spring day, U.S. Army Air Force B-24 Liberators, B-17 Flying fortresses and their fighter escorts lifted off from airfields across southeast England. They climbed, circled, and then formed into one huge formation before heading out to bomb targets in Nazi-occupied Europe.
The bombers and hundreds of fighters flying escort, forming two missions four hours apart, filled the sky with contrails. Researchers from Lancaster University and the Environmental Agency in the U.K. combed through military and meteorological records and determined that the vast cloud cover created by aircraft condensation trails -- or contrails -- slowed the rise of temperatures on the ground that morning.
We investigate consensus formation and the asymptotic consensus times in stylized individual- or agent-based models, in which global agreement is achieved through pairwise negotiations with or without a bias.
Considering a class of individual-based models on finite complete graphs, we introduce a coarse-graining approach (lumping microscopic variables into macrostates) to analyze the ordering dynamics in an associated random-walk framework.
Network modeling based on ensemble averages tacitly assumes that the networks meant to be modeled are typical in the ensemble. Previous research on network eigenvalues, which govern a range of dynamical phenomena, has shown that this is indeed the case for uncorrelated networks with minimum degree ??3.
Here, we focus on real networks, which generally have both structural correlations and low-degree nodes. We show that: (i) the ensemble distribution of the dynamically most important eigenvalues can be not only broad and far apart from the real eigenvalue but also highly structured, often with a multimodal rather than a bell-shaped form; (ii) these interesting properties are found to be due to low-degree nodes, mainly those with degree ??3, and network communities, which is a common form of structural correlation found in real networks.
In addition to having implications for ensemble-based approaches, this shows that low-degree nodes may have a stronger influence on collective dynamics than previously anticipated from the study of computer-generated networks.
The largest digital camera ever built for a space mission has been painstakingly mosaicked together from 106 separate electronic detectors. The resulting "billion-pixel array" will serve as the super-sensitive 'eye' of ESA's Galaxy-mapping Gaia mission.
While the naked human eye can see several thousand stars on a clear night, Gaia will map a billion stars within our own Milky Way Galaxy and its neighbours over the course of its five-year mission from 2013, charting their brightness and spectral characteristics along with their three-dimensional positions and motions.
On 9 July the Republic of South Sudan becomes the earth's newest country - instantly making the world's atlases completely out of date. So here's your new guide to the globe to download and explore. Just click 'play' below and use Prezi's pan and zoom buttons by mousing over the right of the screen
In this humanitarian emergency, MSF will continue to provide essential medical aid where the needs are greatest, and where we can be of most relevance and benefit to the population. Improving access to healthcare and improving its emergency response has to be a priority for this new country.
However, the government of South Sudan has allocated just 3.7 percent of its budget to health in 2011, a decrease from 7.9 percent in 2006. It is essential that emergency humanitarian needs are adequately prioritized by the South Sudanese government, by donor governments and by international humanitarian NGOs.
It was in 1972 when Elisabeth Noelle-Neumann first outlined the main fea- tures of the theory of the spiral of silence at the 20th International Congress of Psychology in Tokyo. Forty years later, in the year 2012, the International Journal of Public Opinion Research is planning to publish a special edition of the Journal focusing on the theory. Guest editor is Dr. Thomas Petersen.
As biological data is now produced faster than it can easily be handled and stored, the dissemination of this data has become a major bottleneck. GigaScience: a new type of journal from BioMed Central and BGI ? no stranger to these issues being the world’s largest Genomics center ? starts taking submissions today with the goal of addressing many of the issues surrounding “big-data”.
Scientists claim to have identified markers that enable the segregation of rare, truly pluripotent human hematopoietic stem cells (HSCs) from multipotent progenitors (MPPS). They identified CD49f as a specific marker for pluripotent HSCs, enabling their isolation using flow cytometry.
Washington, DC?The DOE Office of Science (SC) announced today the selection of a collaboration of top scientists from across the Nation to lead development of a computer-based Systems Biology Knowledgebase (http://genomicscience.energy.gov/compbio/index.shtml#page=news) for the scientific community that is designed to advance understanding of microbes and plants for energy and environmental solutions.
The shiny new Scientific American blog network is now live! We are excited to announce that 39 new blogs joined the network
Open Biology is a fast, open access journal covering biology at the molecular and cellular level.
Open Biology will publish original, high quality research in cell biology, developmental and structural biology, molecular biology, biochemistry, neuroscience, immunology, microbiology and genetics.
This workshop will bring together developers, curators, journal editors and researchers to discuss on the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.
The focus on the workshop is a strawman uniform system for describing these bio-resources, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement.
DBアーカイブの英語版が出来てた http://dbarchive.biosciencedbc.jp/index-e.html
The Life Science Database Archive maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata (description of datasets) in a unified format, and to access and download the datasets with clear terms of use
「新着論文レビュー」 前川桃子・山中伸弥，転写因子Glis1による体細胞初期化の促進（Nature 6月9日号）が公開されました．first.lifesciencedb.jp/archives/3079
The first in a series of reworkings of Sohrab material by artists showing solidarity to his cause... all label and artist money goes towards the fund for his appeal against the refusal to be granted political asylum in Germany...
This release is a fund-raiser to help pay for a lawyer to help with his appeal against the ruling. 100% of Artist and Label money from this release will be donated directly to the appeal fund.
Soundworks Collection: The Sound of Transformers: Dark of the Moon from Michael Coleman on Vimeo.
The amazing visual effects in this film are complimented by the talented efforts of the sound team including Re-recording Mixers Greg Russell and Jeff Haboush, and Supervising Sound Editor and Sound Designers Ethan Van der Ryn, and Erik Aadahl.
The interpretation of the gene as DNA and the deciphering of the genetic code then gave rise to molecular interpretations of mutation, views that also impacted evolutionary biology, population genetics, commercial development of plants and animals, and human genetics.
This book shows how generational definitions or assessments of mutation have responded to the technologies added to science and the experiments that abounded with the inquiries of each successive generation.
Staff at an Australia library have been stunned after first edition copy of Charles Darwin's Insectivorous Plants book was returned 122 years late. http://tgr.ph/jG7Fr1
形態の進化ではたいてい発生遺伝子の変化が起こっているが、原因となった変異がいくつあって、どんな影響を与えたのかについてはほとんどわかっていない。Frankelたちはセイシェルショウジョウバエ（Drosophila sechellia）のshavenbaby遺伝子をモデル系として用いて、この現象の遺伝学的特性を調べた。そして、shavenbabyの5つのシス調節エンハンサーの1つに見られる進化的変化が、この遺伝子の発現の時期と量の両方を変化させた多数の単塩基置換によって生じたことが明らかになった。
したがって、ショウジョウバエでこうした無毛の幼虫が進化するには、大きな影響を及ぼす単一の変異ではなく、小さな影響を及ぼす多数の突然変異が必要だったことになる。この研究は、ダーウィンが提唱した「漸進的」進化説に対する単塩基置換レベルでの定量的裏付けとなる。
ソングバード（スズメ目の鳴き鳥）は人工の文法体系の規則を学習する能力があることが、Nature Neuroscience（電子版）に発表された研究で報告されている。この種の階層的言語構造を処理する能力は、これまではヒト独自のものと考えられていた。
ソングバードはヒトの言語の前駆的機能の基礎になる神経回路のモデルとして昔から利用されているが、この研究はソングバードがそれほど高度な能力をもつことを示唆する最初の研究の1つである。
京都大学の安部健太郎らは、ソングバードが野生の鳥のさえずりを聞き分けるためにその音節群のシンタックス（系統的配列）に関する情報を利用できるかどうか調べた。さらに彼らは、自作のさえずりによって鳥に人工的な文法規則を教えた。どちらの場合も、鳥はさえずりの構造に鋭敏になったようにみえた。
The diversity of avian plumage colors occupies only a portion (26?30%, using violet-sensitive and ultraviolet-sensitive models, respectively) of the total available avian color space, which represents all colors birds can theoretically see and discriminate.
A new study focused on a single gene, the one coding for the cannabinoid receptor 1 (CNR1) in brain cells. Participants with certain mutations in this gene spent more time looking at happy faces than others did.
With the increase of automated discovery and large-scale data collection, eurekometric research has the potential to explode. First, automated science will necessarily have the property of creating large amounts of discovery data.
Illustrative examples of automated science include the Sloan Digital Sky Survey, Lincoln Near-Earth Asteroid Program, Gordon and Betty Moore Foundation Marine Microbial Genome Sequencing Project, and the Census of Marine Life. The initial output of these projects will not be publications, but findings. Each object, such as a newly discovered asteroid, need not have its own publication, but each object can be examined separately from a eurekometric perspective.
In addition, there is the potential in such areas as automated drug discovery, automated chemical synthesis path discovery, and automated theorem proving.
By integrating the front line medical expertise of physicians with the artistry of moviemakers, we are trying to shift the focus toward scaling health apps worldwide: We would like to develop a mobile health app that can help kids, from Los Angeles to Mumbai, make better food choices. We want to create compelling solutions to global health problems.
Africa's nations are achieving some success in building their science capacity, but the foundations remain unsteady.
For blazing a new trail in open-access journals, inspiring broader change in scholarly publishing, and thriving along the way, SPARC (the Scholarly Publishing and Academic Resources Coalition) has named the Public Library of Science’s (PLoS) PLoS ONE as the SPARC Innovator for June 2011.
Researchers from the Center for Biomedical Informatics (CBMi) at The Children’s Hospital of Philadelphia have created a free iPad app called Genome Wowser, which provides a mobile interface to data from the UC Santa Cruz genome browser, one of the three major portals to the reference genome sequence established in 2000.
Three major life science funders, the Howard Hughes Medical Institute, the Wellcome Trust, and the Max Planck Society today announced that they intend to fund the launch of what they hope will become a top-tier biomedical and life science journal to rival the likes of Nature and the New England Journal of Medicine -- and it might seem the Public Library of Sciences' (PLoS] flagship open access biomedical journals.
The journal, which they expect to begin publishing summer 2012, has yet to be given a name, but it would be online-only and open-access, with -- initially at least ? no charges for authors to publish papers, by contrast to most open access journals such as PLoS Biology which charge authors an article fee.
The 2011 Web Server Issue of Nucleic Acids Research is the ninth in a series of annual special issues dedicated to web-based software resources for analysis and visualization of molecular biology data. It is freely available online under NAR's open access policy. The present issue reports on 92 web servers.
In this paper, we present a method for the sensitive detection of microRNAs (miRNAs) utilizing an antibody that specifically recognizes DNA:RNA heteroduplexes and a silicon photonic microring resonator array transduction platform. Microring resonator arrays are covalently functionalized with DNA capture probes that are complementary to solution phase miRNA targets.
Following hybridization on the sensor, the anti-DNA:RNA antibody is introduced and binds selectively to the heteroduplexes, giving a larger signal than the original miRNA hybridization due to the increased mass of the antibody, as compared to the 22-mer oligoribonucleotide.
NBDC / DBCLS BioHackathon 2011 will be held in Kyoto, Japan. Main focus of the BioHackathon is to develop technologies for handling Linked Data in life science. We will discuss, explore and develop SPARQL endpoints, semantic web services, triple stores, ontologies, natural language processing, visualization and Open Bio* tools to utilize RDF data.
LDIF - Linked Data Integration Framework http://bit.ly/jwzLRJ 複数データセットで、同じ対象に異なるURIを与えていたり、同関係を別プロパティで記述しているものを統合するツール。マッピングはR2R、Slikを用いる
今日はルッツの実効的フラクタル次元の話。「フラクタルの理論」の重要なポイントが 『線が １次元を超えることも有り得る（コッホ曲線など）』 なのに対し、「ランダムネスの理論」の重要なポイントは 『点が ０次元を超えることも有り得る』 であるという対比は結構面白いかも。
