“A Montanha Mágica” é o nome do novo álbum de Rodrigo Leão, a ser editado a 28 de Novembro.
私の最も好きなポルトガルのエレクトロ・アンサンブルの新譜がリリース。
□ RodrigoLMusic: Rodrigo Leão
Primeiro avanço para o novo álbum "A Montanha Mágica". Chama-se "O Fio da Vida" e será uma das canções para ouvir... fb.me/1kSCaSf7g
□ Oceano__: Piotr
Karl Jenkins NEW ALBUM "Peace Makers"/ will be available also as Deluxe Edition Read more about the album : karljenkins.com/news/news-view…
□ Peter Gabriel "games without frontiers" - Massive attack mix
□ RECOT: Read Coordinate Transformer >> http://sesejun.github.com/recot/
RECOT transforms coordinate next-generation sequencer reads from your genome/gene to other species genome. RECOT is useful to compare RNA-seq, ChIP-seq and CLIP-seq sequences between closely-related species.
□ overgeorgoch: Georgia Ochenduszko
Craig Venter Sets X PRIZE for Human Genome Sequencing bit.ly/tv11jG
To goose developers along, Venter?along with the X-Prize Foundation and Medco Health Systems, a health care firm?has put a bounty on the achievement: $10 million to the first team that can meet a standard for accuracy that Venter calls “medical grade.” The task is to sequence the genomes of 100 centenarians, providing a baseline to which other genomes can be compared.
□ 3sat:
Was ist eigentlich "Leben"? Die Frage erhielt eine neue Bedeutung, als der amerikanische Biochemiker Craig Venter... fb.me/18kqQVj3J
Synthetisches Leben
Erkenntnisse und Diskussionen
Die Frage nach dem Leben erhielt eine neue Bedeutung, als der amerikanische Biochemiker Craig Venter ein Bakterium aus künstlich hergestelltem Erbgut schuf. Gert Scobel wird mit seinen Gästen darüber diskutieren, wie bahnbrechend die Forschungen der synthetischen Biologie wirklich sind und welche Gefahren damit einher gehen.
□ Melanie Swan on Genomic Self-Hacking: SNPs series were identified in her own genome relating to cancer, immunity& aging
□ genomera:
Genomera organizer, Melanie Swan, on Genomic Self-Hacking via @diygenomics ow.ly/7Cqke #quantifiedself
Melanie Swan of DIY Genomics describes the results of sequencing her own genome in the hopes of developing her own personalized preventive medicine strategies. She developed a mobile app that permits exporting of personalized sequencing data more easily.
A series of small nucleotide polymorphisms (SNPs) were identified by Melanie in her own genome relating to cancer, immunity and aging. Importantly, she has made available the results of her own deep sequencing results to be combined and compared with those of other individuals.
□ BioMedCentral:
Review: Genetic sequencing technologies and applications for human Genetic History and #Forensics ow.ly/7DRXc #genetics #biology
□ ayrrisbio:
Mass Genomics asks of the clinic: Why not apply whole-genome, or whole-exome to every tumor that comes in the door? bit.ly/uqDJCV
2. For the clinician, it would provide a new avenue of investigation to be taken when all other treatment strategies have failed. A guided shot in the dark is better than no shot in the dark at all.
□ EPFLNews: 量子効果によりエネルギー問題を解決する。
EPFL research in quantum computing to reduce energy consumption 100X bit.ly/t6hnCz #ICT #green Electronics could be 100 times less energy-hungry thanks to a quantum phenomenon known as the tunnel effect - by 2017 in consumer electronics
By 2017, quantum physics will help reduce the energy consumption of our computers and cellular phones by up to a factor of 100. For research and industry, the power consumption of transistors is a key issue.
The next revolution will likely come from tunnel-FET, a technology that takes advantage of a phenomenon referred to as "quantum tunneling." At the EPFL, but also in the laboratories of IBM Zurich and the CEA-Leti in France, research is well underway. As part of a special issue of Nature devoted to silicon, Adrian Ionescu, an EPFL researcher, has written an article on the topic.
□ PLoSBiology:
Check out the 1st #PLoS podcast! VS Ramachandran & David Brang talk @ synesthesia bit.ly/siQZIt w/#PLoSBiology editor Ruchir Shah
□ linuxfoundation:
NEW paper published today: Understanding the open source development model: bit.ly/tuPYgl #linux #oss
This app creates a tree as the user writes. Letters are placed around a word node, which itself is situated around a sentence node. All sentence nodes are connected at the center. I guess I could have gone for paragraphs, but that seems like it would be pushing it. The particles all repel each other, so even if several sentences wind up on top of one another, they tend to untangle themselves. The mouse has some repulsion force too, so that can be used if they get really caught.
Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.
□ Chris_Evelo:
MT @egonwillighagen: lots of open source bioinformatics software on this Dutch host: ur1.ca/5xmbu #nbic
オランダのバイオインフォマティクス開発環境オープンソースと各デベロッパ数一覧。BioSemanticsのようなサービスが既に欧州/国家プロジェクトで稼働中
The newly updated SOAP suite includes SOAP3 -- a GPU-accelerated short read alignment tool; SOAPindel -- an indel finder; SOAPfusion -- a gene fusion detector; SOAPsplice -- a splice-junction detector; SOAPdenovo-Trans -- a de novo transcriptome assembler; and Metacluster 4.0 -- a binning solving tool for metagenomics data.
Appistry’s new Ayrris Bio offering is poised to make a big impact on life sciences organizations
Appistry is harnessing its experience in clouds, high-performance computing and analytics?FedEx is one of its biggest customers?with its new life sciences offering called Ayrris Bio. Appistry offers its own public service based on its cloud on a per usage basis, including exome, RNA-seq and whole-genome analysis.
But the cloud still raises doubts and concerns. A major issue, discussed below, surrounds security and regulation. Another is whether the cloud can truly handle the masses of next-gen data that is being generated.
□ 何やら凄い自信。readthrough false signalsとやらの原理をお聞かせ願う RT @engineofentropy: OH MY GOD I JUST HAD THE BEST IDEA ON HOW TO IMPROVE NEXT GENERATION DNA SEQUENCING
□ GenesDev: Genes & Development
NEW ISSUE HIGHLIGHTS: Expanding the Drosophila circadian transcriptome - bit.ly/tIlixU Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression
CLOCK (CLK) is a master transcriptional regulator of the circadian clock in Drosophila. To identify CLK direct target genes and address circadian transcriptional regulation in Drosophila, we performed chromatin immunoprecipitation (ChIP) tiling array assays (ChIP?chip) with a number of circadian proteins.
□ WileyNews:
Wiley-Blackwell and The Association of Applied Biologists Launch New Wiley Open Access Journal, Food and Energy ... bit.ly/tpc9P2
□ Cloudscaling:
New blog post: How is AWS Failing to Service Webscale Applications? is.gd/Wxw6Ve
□ loveproblems: Klaus Speidel
"Le rôle des intermédiaires dans le crowdsourcing" @hypios @eyeka @99designs @bluenove bit.ly/tWLiDj
Mal utilisées, les méthodes de crowdsourcing en entreprise peuvent rester sans résultat ou poser d'autres problèmes. Une solution est de passer par des acteurs qui font l'intermédiation.
□ InsideScience:
Researchers perform improved version of faster-than-light neutrino experiment and find same result. Update at bit.ly/ngFyPV
OPERA researchers are the first to emphasize it is too early to speculate on the possible implications. Though the OPERA collaboration has performed thorough analysis of their measurements, the researchers acknowledge the possibility of an overlooked or presently unknown error that would skew the results. They said they are presenting their results to the physics community so that others could check their results and try to duplicate their experiments.
□ Linked Open Data Challenge Japan 2011
- First lecture meeting in Tokyo.
Time lapse sequences of photographs taken with a special low-light 4K-camera
by the crew of expedition 28 & 29 onboard the International Space Station from
August to October, 2011.
HD, refurbished, smoothed, retimed, denoised, deflickered, cut, etc.
□ Mark_Van_Hoen: Mark Van Hoenが自身の曲と関連楽曲をSoundCloudで開放。
Just uploaded loads of tracks of my own, and various productions/projects, enjoy before the labels tell me to remove! bit.ly/sCI11N
<object height="81" width="100%"> <param name="movie" value="http://player.soundcloud.com/player.swf?url=http%3A%2F%2Fapi.soundcloud.com%2Ftracks%2F27883129"></param> <param name="allowscriptaccess" value="always"></param> <embed allowscriptaccess="always" height="81" src="http://player.soundcloud.com/player.swf?url=http%3A%2F%2Fapi.soundcloud.com%2Ftracks%2F27883129" type="application/x-shockwave-flash" width="100%"></embed> </object> Marching Song (Mark Van Hoen Remix).mp3 by markvanhoen
□ dnanexus:
Interesting Video - Stanford and Harvard Researchers discuss the Iranian Genome Project bit.ly/nPwaLF
The Iranian Genome Project aims to provide knowledge to both the scientific and Iranian community by studying and understanding the genetic background of Iranians. Genomics is an emerging field whereby scientists map our genetic code ? the language of life ? and study how differences in this language leads to differences in health and disease.
(Pedigree of the Affected Family and Results of Comparative Genomic Hybridization (CGH) Showing Deletion on Chromosome 12.)
□ GenCounsNews: Leslie Ordal
Noninvasive prenatal diagnosis of a microdeletion syndrome: bit.ly/ve4Lzd Sure to be seeing a lot more of these stories soon.
The definitive diagnosis of fetal aneuploidy and genomic imbalances requires invasive collection of fetal cells through amniocentesis or chorionic villus sampling. These methods are associated with fetal loss and parental anxiety. Analyses of DNA in maternal plasma have shown the potential for noninvasive diagnosis of common aneuploidies.
□ sarahbadr:
20 Hz ? haunting visualisation of data collected from a geo-magnetic storm in the earth's upper atmosphere: is.gd/Dxuy90
20 Hz observes a geo-magnetic storm occurring in the Earth's upper atmosphere. Working with data collected from the CARISMA radio array and interpreted as audio, we hear tweeting and rumbles caused by incoming solar wind, captured at the frequency of 20 Hertz.
Generated directly by the sound, tangible and sculptural forms emerge suggestive of scientific visualisations. As different frequencies interact both visually and aurally, complex patterns emerge to create interference phenomena that probe the limits of our perception.
□ reaktorplayer:
Who Sampled: whosampled.com the ultimate database of sampled music, remixes and cover songs
□ GenomeBiology: GAIIxとHiSeqのエラー/バイアス比較
Comparing the errors/biases of the GAIIx & HiSeq Illumina sequencing platforms bit.ly/s5SoM9 #genomics Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
We provide quantifications and evidence for GC bias, error rates, error sequence context, effects of quality filtering, and the reliability of quality values. By combining different filtering criteria we reduced error rates 7-fold at the expense of discarding 12.5% of alignable bases. While overall error rates are low in HiSeq data we observed regions of accumulated wrong base calls. Only 3% of all error positions accounted for 24.7% of all substitution errors.
Analyzing the forward and reverse strand separately revealed error rates of up to 18.7%. Insertions and deletions occurred at very low rates on average but increased to up to 2% in homopolymers. A positive correlation between read coverage and GC content was found depending on the GC content range.
□ appliedgenomics:
Very happy to announce a partnership between CAG and BGI to conduct large-scale genome sequencing and bioinformatics! prn.to/vzvnas
□ The Children's Hospital of Philadelphia & BGI Announce Partnership New Joint Genome Center to Target Pediatric Diseases http://t.co/3qwTzlhY
The BGI@CHOP partnership will bring together the unique strengths of two world-class institutions. BGI's capabilities and expertise in whole genome sequencing and analysis, combined with Children's Hospital's extensive biobank and expertise in clinical phenotyping, will allow scientists and clinicians to harness the power of large, detailed data sets to improve the lives of patients and families.
□ PLoS: . Rockethubによる個別の研究内容に応じたユーザ参加型の投資イベント
Scientific research funded by and for the public on #SciFund j.mp/tK03vz #crowdfunding
Crowdfunding contest for individual research projects on internet platform.
Can scientists raise money for their research by convincing the general public to open their wallets for small-amount donations? The process is called crowdfunding. You can think of it as the model charities have always used (bundling lots of donations to do good works), with an internet/social media twist.
□ Cloudera Lands $40 Million From Ignition, Accel Launches $100 Million Big Data Fund
A day after teaming up with the storage concern NetApp, Cloudera announced today that it has landed a $40 million series D round of venture capital funding from Ignition Partners, in a round led by its partner, Frank Artale. Previous investors include Accel Partners, Greylock Partners, Meritech Capital Partners and In-Q-Tel. Cloudera says it will use the funds to expand its marketing and sales operations. By my count, the round brings Cloudera’s total capital raised so far to $76 million.
Accel Partners, which led Cloudera’s last round, is launching a $100 million “Big Data Fund,” with Cloudera as a partner. / in infrastructure like storage or security or management, or building applications that run on Hadoop. And the opportunities for that are multiplying
□ Cloudera Raises $40 Million In Series D Funding; Partners With NetApp For Hadoop Distribution huffingtonpost.com
GigaOm reports that one of the key attributes of the NetApp Open Solution is its separation of the compute and storage layers of a Cloudera Hadoop installation. Separating the compute and storage layers enables enhanced performance, scalability and reduced downtime in the event of the failure of a disk within either the compute or storage layer.
□ emblebi: EMBL-EBI
"RNAcentral": a vision for an international database of RNA sequences by EMBL-EBI leaders and colleagues - bit.ly/tx6w5A
We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource.
Constructing the Microbial Biomap for Planet Earth
The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe.
The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe.
We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.
□ OpenHelix:
Interesting, want to see paper MT @bradpotts: Article Find - First clinical trial of point-of-care DNA testing bit.ly/syKWzj
Spartan Bioscience today announced data from the RAPID GENE study showing that point-of-care DNA testing successfully identified patients carrying the CYP2C19*2 gene at the time of cardiac catheterization. Cardiologists were then able to prescribe antiplatelet therapy according to the patient's genotype. This personalized medicine approach completely eliminated high on-treatment platelet reactivity (HPR) in CYP2C19*2 carriers.
RAPID GENE is the first randomized prospective clinical trial to demonstrate the utility of point-of-care DNA testing for personalized medicine.
□ ayrrisbio:
How much has exome sequencing been driven by cost alone? bit.ly/tw6nut / via @Bioinfo
In the paper, LGB and JCM make the point that an exome costs about 1/6th what a whole genome costs. That seems pretty accurate to me. And that does demonstrate how much more valuable we consider the exome compared to the other regions. Because of that I would not say that exome-seq has been driven by cost alone, but also because it is considered more valuable per base than whole genome.
Fischer Journal Archives on SciVerse ScienceDirect: bit.ly/udLoLT
Elsevier, a world-leading provider of scientific, technical and medical information products and services, today announced the availability of Elsevier Urban & Fischer Journal Archives, three new backfile collections in the life and health sciences, on SciVerse ScienceDirect.
The new backfiles, published in English under the renowned German imprint Urban & Fischer, contain journals concerning immunology and microbiology, medicine, and biochemistry
□ elsevierjp:
RT @pta277: Where do the poor live? bit.ly/vbiBLA 1990年頃は世界の貧困層の95％が低所得国に住んでいたが、今は4分の3が中所得国に住んでいる。貧困対策のための援助はどこをターゲットとすべきか。
This paper argues that the distribution of global poverty has changed and that most of the world’s poor no longer live in countries officially classified as low-income countries (LICs). It is estimated that the majority of the world’s poor, or up to a billion people, live in middle-income countries (MICs).
□ yeastcolloquium:
「網羅性の陰に精度を犠牲にする（バーコードシーケンス） by トロント大・谷内江」をアップしました。 wp.me/p1WcMD-1W #yeastcolloquium #ngsfield @ngsfield
In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons.
Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling.
We describe a statistical framework for QTL mapping using bulk segregant analysis (BSA) based on high throughput, short-read sequencing. Our proposed approach is based on a smoothed version of the standard statistic, and takes into account variation in allele frequency estimates due to sampling of segregants to form bulks as well as variation introduced during the sequencing of bulks.
Visa has filed a patent application for a process that would use, among other sources, DNA databases to identify potential customers.
The application, published in April, is titled "Systems and Methods to Deliver Targeted Advertisements to Audience," and covers generating transaction profiles based on the transaction data, the account data, and/or other data, such as non-transactional data, wish lists, merchant provided information, address information, information from social network websites, information from credit bureaus, information from search engines, information about insurance claims, information from DNA databanks, and other examples.
What's needed, the report says, is for patient's health records to be combined with layers of genomic and other molecular measurements, such as blood proteins and the microbes in a patient's gut. Like the GPS data used to make Google maps, these data could be plumbed in detail by researchers and used more superficially by others, such as doctors to treat patients, the report says. Separate databases would be combined to form a single network.
□ portablegenomic:
The time for healthcare tech startups is now...If you’re into technology, biology, social media and nano technology... gigaom.com/2011/11/10/mit…
We present a method for gene expression profiling called EDGE, or EcoP15I-tagged Digital Gene Expression, based on ultra-high-throughput sequencing of 27-bp cDNA fragments that uniquely tag the corresponding gene, thereby allowing direct quantification of transcript abundance.
□ FASEBopa:
Check out our federal science budget resources for updates about the budget process as it pertains to biomed. research. bit.ly/qrxpwC
□ NCBI:
dbVar has a new look - cleaner presentation and all data is remapped to current assemblies: http://www.ncbi.nlm.nih.gov/dbvar/
. #bioinformatics
□ PLoSCompBiol:
Call for papers RT @PLoSBlogs Altmetrics: Tracking scholarly impact on the social Web ? PLoS ONE Collection bit.ly/rBbbVe
Increasing scholarly use of Web 2.0 tools like CiteULike, Mendeley, Twitter, and blogs presents an opportunity to create new filters. Metrics based on a diverse set of social sources could yield broader, richer, and timelier assessments of current and potential scholarly impact.
Realizing this, many authors have begun to call for investigation of these metrics under the banner of “altmetrics.” Specifically, altmetrics is the creation and study of new metrics based on the Social Web for analyzing and informing scholarship.
□ sc_k: S.C. Kavassalis
My favourite non academic Marie Curie story is definitely the one about her scandalous affair with young Paul Langevin aip.org/history/curie/…
Il travailla avec ENIGMA pendant 10 ans & est connu aussi sous le nom d'emprunt "ACHILLEA". Il a composé spécialement pour DKN FRANCE cinq morceaux que nous avons le plaisir de vous faire partager.
□ Jens Gad - "Achillea" New Exclusive EP Full Length available on DKN Technology France.
♪ <script type="text/javascript" src="http://mediaplayer.yahoo.com/js"></script>Donde Estes Tu
□ OxfordJournals:
Free in the Review of Economic Studies: oxford.ly/vm9A5x "Bayesian Learning in Social Networks" #socialnetworks #socialmedia Bayesian equilibrium of a sequential learning model over a general social network.
The stochastic process generating the neighbourhoods defines the network topology. We characterize pure strategy equilibria for arbitrary stochastic and deterministic social networks and characterize the conditions under which there will be asymptotic learning?convergence (in probability) to the right action as the social network becomes large.
The graphic, which pulled some of its data directly from TechStars and Y Combinator, gives a sense of just how powerful those programs can be in helping startups stay out of the dead pool.
And according to the stats here, TechStars has a better success rate, with about 7 percent of companies going under, vs. roughly 22 percent for Y Combinator alums.
I was personally a little surprised that such a high percentage?nearly half?of startup founders would have postgraduate degrees, according to the data Gist consulted.
□ foresightnano: 人工ナノシステムを制御する為の人工分子時計。
Controlling artificial molecular machines with an artificial molecular clock of RNA and DNA. goo.gl/AHmTW
In the current work, the authors use such a transcriptional oscillator as a molecular clock to time two other molecular processes. One of these is a DNA nanomechanical device, a DNA tweezers that gives different fluorescent signals when open and when closed. Different RNA molecules produced by the transcriptional oscillator act to either open or close the tweezers. The other process is the synthesis by the transcriptional oscillator of an RNA molecule that binds the dye molecule Malachite Green, changing its fluorescence.
□ nygenome: あら素敵なショッピングモール。いいえ、遺伝子研究所です。 NYの街角に溶け込んだオシャレな佇まい
We are officially launching today! nygenome.org/media #nygenome
New York Genome Center (“NYGC”) is an independent, non-profit organization ? leveraging the collaborative resources of leading academic medical centers, research universities, and commercial organizations. Our vision is to transform medical research and clinical care in New York through the creation of what will become one of the largest genomics and bioinformatics facilities in North America.
□ GenCounsNews: Leslie Ordal
American College of Medical Genetics adds "Genomics" to its name bit.ly/vt79Yi
□ rnomics: Fabrice Leclerc
A two-dimensional mutate-and-map strategy for non-coding #RNA structure: Wipapat Kladwang,... bit.ly/rpRPnB #chemfeeds @MyEN
Non-coding RNAs fold into precise base-pairing patterns to carry out critical roles in genetic regulation and protein synthesis, but determining RNA structure remains difficult. Here, we show that coupling systematic mutagenesis with high-throughput chemical mapping enables accurate base-pair inference of domains from ribosomal RNA, ribozymes and riboswitches.
□ AppliedBio: Applied Biosystems
Learn the basic principles of Real-time PCR with this free digital handbook. ow.ly/7etuc #new2qPCR
□ NCBI:
New YouTube Videos: An explanation of BLAST E-values (pt.1) bit.ly/w0r4jH & Answers to a few E-value FAQs (pt.2) bit.ly/v4zh44
□ PublicHealth: APHA
Another study looks at using Twitter to track disease outbreaks, this time in the UK: goo.gl/1eTlf
Over several months, the researchers were able to gather a database of over 50 million geo-located tweets, which could then be compared to official data from the UK's National Health Service on flu incidence by region.
The researchers deployed state-of-the art machine learning algorithms that automatically figured out which keywords in the database of tweets were associated with elevated levels of flu. In this way they were able to create a predictive model that transformed keyword incidence in tweets into an estimate of the severity of flu in that area.
□ portablegenomic:
Steve Jobs: iCloud may even store medical data - shar.es/bIwFv
ジョブスが病床で流体モニタとx線装置の新設計をスケッチした話も凄い。医療現場をデジタルハブに依存させるのはリスキーだけど、アナログとの冗長性システムを確立が課題。
緊急手術を要する患者さんが運び込まれた時、一刻も早くカルテをiCloudと同期させなきゃいけないのに、突然バックアップとか取り出したりアップデートを落とし始めたら嫌だよね。
One of the passages in Walter Isaacson’s recently published biography of Steve Jobs quotes the former CEO as envisioning Apple’s iCloud as a place where people might store their medical data:
□ PLoSCompBiol:
On @Quora: How valid is Giulio Tononi's mathematical formula for consciousness? Answer: qr.ae/7bw9o
□ DailyNewsGW:
Affymetrix, Broad Institute Collaborate for The Cancer Genome Atlas: read more bit.ly/v56Ssl
About 13,500 cancer samples will be processed on the Affymetrix Genome-wide Human SNP 6.0 Array as part of the partnership. Copy number variation and somatic events will also be studied using the array, as will determining the loss of heterozygosity.
Financial terms of the deal were not disclosed.
□ OpenHelix:
:) MT @dullhunk: Why can't people just say what they mean? bit.ly/sIhWkv new blog post @ O'Really? inspired by @OpenHelix @stephenfry
□ bio_insilico: GoogleとDNAnexusがcloud storageを利用した最大規模のDNAデータベースを公開ヘ。SRAのミラーリング他、$10/1GBでのダウンロード利用が可能。
Google to preserve free DNA database - BioNews: Google to preserve free DNA databaseBioNews'D... bit.ly/v6QXJl #biotech #genomics
□ planetrdf: Planet RDF
CumulusRDF - RDF triple store on top of Apache Cassandra lists.w3.org/Archives/Publi… via Andreas Harth @aharth and Günter Ladwig
□ DailyNewsGW:
Cofactor Genomics Collaborates with Kentucky Network on Sequencing Data: read more bit.ly/t1XwSL
KBRIN's collaboration with Cofactor has resulted in bringing next-gen sequencing design and analysis to Kentucky's research community, KBRIN Project Director Nigel Cooper said, adding that the KBRIN-INBRE program's goal is to build collaborative research and develop a statewide bioinformatics structure.
□ Cofactor Genomics Collaborates with Kentucky Biomedical Research Infrastructure Network to Expand Genomics Research Throughout State >> http://t.co/uZM0l2T7
The KBRIN-INBRE program seeks to expand biomedical research activities across the state by developing Kentucky’s next generation of biomedical researchers. The network funds student training and career development in the primarily undergraduate universities (PUI)’s.
In addition to scientific workforce development, the INBRE award also builds critically important bioinformatics infrastructure to assist researchers in quantifying large volumes of data produced through genomic techniques. Currently, the institutions in the network that benefit from the collaboration include Morehead State University, Northern Kentucky University, Western Kentucky University, Eastern Kentucky University, the University of Louisville, and the University of Kentucky.
UK genotoxicity assay firm Gentronix and French personalized medicine company BioQuanta SA recently announced a deal for the commercialization of services based on BioQuanta's Mitoxis functional metabolomics platform.
The winner of the Pistoia Alliance Sequence Squeeze Competition stands to win a $15,000 prize.
The competition aims to encourage a diverse group of scientists -- including bioinformaticians, mathematicians, physicists, and computer scientists -- to address a thorny problem in the management of NGS data. The Alliance notes that with sequencing costs plummeting faster than the data storage and processing rates predicted by Moore's Law, current NGS instruments can generate more data in a day than any one machine could have produced during the whole of 2005.
Using whole-animal bioassays, we demonstrate through inhibition by verapamil that the widely used organophosphate and pyrethroid acaricides coumaphos and τ-fluvalinate, and three neonicotinoid insecticides: imidacloprid, acetamiprid and thiacloprid are substrates of one or more MDR transporters.
Among the candidate inhibitors of honey bee MDR transporters is the in-hive antibiotic oxytetracycline. Bees prefed oxytetracycline were significantly sensitized to the acaricides coumaphos and τ-fluvalinate, suggesting that the antibiotic may interfere with the normal excretion or metabolism of these pesticides.
□ InsideScience:
Chemical elements once known as 110, 111 and 112 will be called darmstadtium (Ds), roentgenium (Rg) and copernicium (Cn), IUPAP announces.
The focus for this conference is large-scale genome informatics. Biology is an experimental science that is experiencing an explosion of new data. This requires biologists to increase the scale and sophistication in the information technology used for their research.
The conference scope encompasses the management and the analysis of these data, such as whole genome comparisons within and among species and strains, the analysis of results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify regulatory sequence motifs.
□ genetics_blog:
Flux simulator for simulating RNA-seq data bit.ly/thFQDa #gi2011
□ Cain: CloVR - cloud virtual resource automated pipeline for sequence analysis from the desktop http://clovr.org/
□ byuhobbes:
Fiume: less than 2% of genetics software has GUI; not a problem for geeks, but definitely a problem in the delivery of medical care #gi2011
The project is run as part of the "Sequence Mapping and Assembly Assessment Project (SMAAP)", a collaborative effort to compare and evaluate methods and strategies for de novo genome assembly (dnGASP)and RNASeq read alignment(RGASP3) using data from second generation sequencing platforms.
□ genetics_blog:
Now speaking at #gi2011: Mark Gerstein on genomic variation in ENCODE TFBSs and transcribed RNAs. Slides here: lectures.gersteinlab.org
In this paper we provide a complete and novel formulation to discover both loci and classes of transposons inserted into genomes sequenced with high-throughput sequencing technologies.
In addition, we also present “conflict resolution” improvements to our earlier combinatorial SV detection algorithm (VariationHunter) by taking the diploid nature of the human genome into consideration.
We test our algorithms with simulated data from the Venter genome (HuRef) and are able to discover > 85% of transposon insertion events with precision of > 90%. We also demonstrate that our conflict resolution algorithm (denoted as VariationHunter-CR) outperforms current state of the art (such as original VariationHunter, BreakDancer and MoDIL) algorithms when tested on the genome of the Yoruba African individual (NA18507).
- "human brain or the evolution of weather systems can, in principle, compute the same things"
- "Computation is therefore simply a question of translating inputs and outputs from one system to another."
