Why the Cloud does not solve the computational scaling problem in biology.

□ Why the Cloud does not solve the computational scaling problem in biology?

>> http://ivory.idyll.org/blog/aug-11/cloud-not-the-solution.html

クラウドが計算生物学におけるスケーリングの問題を解決出来ない理由:　クラウドが総体的な計算コストの低減に寄与しない現象： 本年初旬にNHGRIの出したグラフも引用されています。

To see why, consider the following model. Take two log-linear plots, one for cost per unit of compute power (CPU cycles, disk space, RAM, what have you), and one for cost per unit of sequence ($$ per bp of DNA). Now suppose that sequence cost is decreasing faster than compute cost, so you have two nice, diverging linear lines when you plot these trends over time on a log-linear plot (see Figure 2).

It's also worth noting that de novo assembly (my current focus...) remains one of the biggest challenges. It requires gobs of the most expensive computational resource (RAM, which is not scaling as fast as disk and CPU), and there are no good solutions on the horizon for making it scale faster. Neither mRNAseq nor metagenomics are well-bounded problems (you always want more sequence!), and assembly will remain a critical approach for many people for many years. Moreover, cloud assembly approaches like Contrail are (sooner or later) doomed by the same logic as above.

□ ctitusbrown: 次世代シーケシング戦略の議論において重要な三つのコンポーネント。商業的弊害/アセンブラ/ゲノム自体の反復構造
Assembling genomes with modern sequencing (blog post) ivory.idyll.org/blog/aug-11/as… #bioinformatics

A key component of any sequencing strategy discussion nowadays is that sequencing has become very commercial.While this drives down costs (pretty dramatically!), you also can't trust a damn thing that sequencing companies say, because the market is very competitive and there's very little percentage in straight-up honesty, much less full disclosure.

□ articlescouk: バイオインフォマティクス市場の巨大な成長。アプリケーションの需要拡大により2013年までに62億ドル市場に。データベース分野ではDDBJなどの日本がリードする機能強化の寄与も。
Global Bioinformatics Market to Witness Stupendous Growth http://goo.gl/fb/bVWs7

We have found that Japan has effectively strengthened its capabilities to be a worldwide player in the field of bioinformatics databases. With an estimated revenue of Yen 38 Billion (US$ 0.46 Billion) in 2010, the market is likely to attract more players in the years to come. The country has one of the largest databases for bioinformatics across the globe known as DDBJ, in comparison to USA (GenBank) and Europe (EMBL-Bank).

□ BlowtheMind:
Is Electronic Music 'Real Music?' RL talks to Songify-creator Parag Chordia (@indianmusic) and IDM artist @RichardDevine http://is.gd/q72Exe




□ この記事はマジで必見。DiscoveryNewsのRichard Devineへのインタビュー。アルゴリズム作曲とソフトウェア、Autechreにも言及してます / The Alien Sounds of Richard Devine : http://t.co/VSVHUHA




□ IKnowledgeBlog:
Presenting 'The Beat of the Scientific Drum' blogs.plos.org/thestudentblog…. Melodies made from sounds, meaning made from data...




□ cdmblogs:
Music: Not a Turntable, Not a Knob - A New Inertial Sensor Music Controller, as Artists Explore http://cdm.fm/qF6aCY
円盤状の慣性センサーを利用した、全く新しい概念の音響ツール。今までは複雑なアルゴリズムを要したエフェクトも、どんどん物理化・可触化して行くのかも




□ techno_id_com:
For those interested in Generative Music have a look at this VST http://www.techno-id.com/vst_plug-ins.htm#sunra #aleatoire #generative




□ timprebble:
Tuning In ? A Film about Karlheinz Stockhausen BBC (1981) http://rootstrata.com/rootblog/?p=5816






□ OxfordJNLsJapan:　世界の芸術的な天井。　http://bit.ly/rlb7IK




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




□ OA_Africa: Open Access Africa
@BiomedCentral are bringing #OpenAccess #Africa #publishing initiative to West Africa http://ow.ly/5VfOP #opendata #openscience #OA




□ DailyNewsGW:
Pronto Diagnostics to Distribute Vermillion's OVA Test in Israel, Palestinian Territories: Pronto will begin off... http://bit.ly/roW8Yh




□ AIP_Publishing:
Decentralized Energy in Nigeria http://ow.ly/5U9fN


□ AIP_Publishing:
The relationship between climate change and famine in Africa http://ow.ly/5Y8jw




□ ongenetics: Steve Mount
All 4096 hexamers evaluated for their effect on splicing (when placed in an internal exon). Ke et al. @GenomeResearch bit.ly/GeneNews




□ rnomics:
Biogenic mechanisms and utilization of small #RNAs derived from human protein-coding genes: The nature... http://bit.ly/nq9J5F #nature


□ rnomics:
Top story: Metaxa - Microbiology, Metagenomics and Bioinformatics http://goo.gl/xwHhq, see more http://goo.gl/4keaa




□ rnomics:
Merck Shuts Down RNAi Research Center in SF Cutting 50 Jobs: Merck has decided to close down the... http://bit.ly/nyBwjd #bioportfolio




□ Xconomy:
Merck shuts down RNAi center in SF, the fmr Sirna Therapeutics. A late-breaker from last Fri pm http://bit.ly/mUtfdK




□ IPTVeducation:
Check out "Science Bytes"-series of short videos, based on studies from @PLoS, highlighting science discoveries http://bit.ly/qVXrUx #STEM




□ chilhalprit:
New Products: The Malaysian Genomics Resource Center Berhad has updated its free online bioinformatics analysis ... http://bit.ly/nUSIBr




□ AdamKraut:
Bioinformatics challenges for personalized medicine - bioinformatics.oxfordjournals.org/cgi/content/sh…




□ dgmacarthur:
Very interesting. RT @bachinsky: Assumptions, not data, dictate opinions about predictive genetic testing in youth: bit.ly/pzc4B4




□ BerkeleyLabTABL:
Lab Scientist to Direct Bioinformatics at CREA: Steve Garan, a long-time guest scientist at the Physical Bioscie... http://bit.ly/oLtDaF




□ blaue_fuchs:
流れで発見。雪豹でも SciPy 入れれてない罠を思い出した。＞ Python for Bioinformatics: SciPy on Lion (1) - http://bit.ly/qtCocJ




□ PLoSCompBiol:
#PLoS: From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs dx.plos.org/10.1371/journa…




□ genomigence:
GenomeResearch: Synthetic spike-in standards for RNA-seq experiments [RESOURCES]: High-throughput sequencing of ... http://bit.ly/nMwkRg




□ TriLinkBioTech:
Transcription Factor Beacons for the Quantitative Detection of DNA Binding Activity http://bit.ly/pi8YIg




□ RainDanceTech:
Genome Research and PLoS ONE publish studies from Scripps & Christian-Albrechts validating RainDance’s MethylSeq: goo.gl/ZqGGm




□ CellPressNews:
Today we launched Cell Reports, our first all open-access journal. Find out more and submit your papers here http://ow.ly/5SpQx #science




□ PLoS:
Keep those great #binarybattle app ideas coming! We at @PLoS and @mendeley_com love what's been shared so far! mendeley.com/blog/developer…




□ SpringerJapan: http://springerquotes.heroku.com/

Springer API Challengeで1位を獲得したアプリSpringerQuotes. 検索した論文の引用文を共有できるアプリです。Springerのオープンアクセス論文約8万件から、簡単な操作で引用文が作れます。#API #Developers #Mashery

□ NatureJapan:
特集記事： 地球や地球型惑星の深部構造を理論計算で解明 http://nature.asia/ruanmh （愛媛大学地球深部ダイナミクス研究センター）




□ NatureJapan: Decoherence in crystals of quantum molecular magnets
Nature Highlights: 解読されたデコヒーレンス http://nature.asia/pVFxhP

脆弱な量子情報が環境へと失われる基礎的な過程である量子デコヒーレンスは、量子力学で想定される多数のエキゾチックな応用に対する主要な制限となっている。

しかしながら、実用上の関心が寄せられている多くの系においては、まだ理論によっても、実験によっても十分に明らかにされていない。Takahashiたちは、そのような系の1つである量子分子磁石の結晶について、量子情報が失われる原因となる主要なデコヒーレンス過程は定量的に予測可能で、実験により確かめられることを示している。