□ Beyond the Genome 2012 - Harvard Medical School, Boston, from 27 - 29 September #btg2012
>> http://www.beyond-the-genome.com
Genome Medicine and Genome Biology are pleased to host the third annual Beyond the Genome conference at Harvard Medical School, Boston, USA from 27 - 29 September 2012.
The aim of the conference is to discuss next-generation sequencing and other new technologies, informatic tools, and how these are being used to identify common and rare disease-causing mutations in the research laboratory and toward the clinic.
Themes will include cancer genomics from discovery sequencing to genome guided therapy, epigenomic technologies and applications, and inherited disease beyond the candidate gene approach. There will also be an informatics workshop.
□ dgmacarthur:
GM: bioinformatics tools shouldn’t be usable only by informaticians. Our target audience should be biologists. #btg2012
□ fiamh:
Ben Raphael on Network and Pathway Analysis of Somatic Mutations in Cancer http://tmblr.co/ZY82CyUBTVZK #BTG2012
□ GenomeBiology:
Speaking of circos plots, make your own along with many other genomics graphics (manhattan plots etc) w ggbio http://bit.ly/SL3Xb3 #BTG2012
□ GenomeMedicine:
MS: made correction pipeline by mapping on short reads http://wgs-assembler.sf.net #BtG2012
□ SahaSurya:
Schatz: Genome mappability score -quantify how reliably reads can be mapped to every position in the genome http://schatzlab.cshl.edu/people/hlee/ #BTG2012
□ fiamh:
Leslie Biesecker on Hypothesis-generating clinical genomics research and predictive medicine http://tmblr.co/ZY82CyUEVEON #btg2012
□ erlichya:
Lynn Jorde shows a comparison of mutation rate estimates from different studies. The average is 1.2x10^-8 mut/bp/gen #BTG2012
□ GenomeMedicine;
SC; comprehensive tool for the analysis of repetitive elements- http://ccmbweb.ccv.brown.edu/repeats.html #BtG2012
□ BlueSEQ:
Tweet archive of the Beyond The Genome 2012 conference (#BTG2012) #NGSeq #genomics http://ngs.is/SYkX7F
□ ICGA 2012 : International Conference on Governance and Accountability #icga2012
>> http://www.waset.org/conferences/2012/copenhagen/icga/
The XXXIII. International Conference on Governance and Accountability aims to bring together academic scientists, leading engineers, industry researchers and scholar students to exchange and share their experiences and research results about all aspects of Governance and Accountability, and discuss the practical challenges encountered and the solutions adopted.
□ appliedgenomics:
NHGRI's Teri Manolio: There had been nearly 1400 GWAS publications since 2005 #icga2012
□ tpolytmus:
#icga2012 LY: #BGI 17PB storage, courier tracking integrated into LIMS, GPUs, mobile apps 4 project tracking, research vs production mode
□ GigaScience:
SH: Noting data compression- esp given rapidity of data generation: going from BAM files (120 Gbytes compressed to CRAM (6 Gb) #icga2012
今日はICGA2012でもBTG2012でも同時多発的にData Storage/Compressionの話題になっていて面白い。
□ State-specific multireference coupled-cluster theory:
>> http://onlinelibrary.wiley.com/doi/10.1002/wcms.1120/abstract;jsessionid=C3151F9D89765FB6A487E0323689F1D9.d03t04 …
Mukherjee’s state-specific multireference coupled-cluster (Mk-MRCC) theory, multireference Brillouin?Wigner coupled-cluster (MR-BWCC) theory, the MRexpT method, and internally contracted multireference coupled-cluster (ic-MRCC) theory. Related methods such as extended single-reference schemes [e.g., the complete active space coupled-cluster (CASCC) theory] and canonical transformation (CT) theory are covered as well
□ Individual RNA Base Recognition in Immobilized Oligonucleotides using a Protein Nanopore http://pubs.acs.org/doi/pdf/10.1021/nl3027873
□ genomigence:
InSequence: ZS Genetics Shows Single Base ID by Electron Microscopy, but Path to Sequencing is Still Long: rea... http://bit.ly/V5OQKx
□ genomicslawyer:
Interesting to see @23andMe name a former eHarmony exec as VP Strategic Alliances: http://www.marketwatch.com/story/23andme-names-christine-castro-neil-rothstein-and-jonathan-ward-to-leadership-positions-2012-10-16 … Signal of future company direction?
□ russpoldrack:
Most Reported Genetic Associations With General Intelligence Are Probably False Positives http://www.wjh.harvard.edu/~cfc/Chabris2012a-FalsePositivesGenesIQ.pdf …
□ hillaryrosner:
Making sense of overwhelming data--via song: http://bit.ly/QYknXU
□ ConsGenConf:
One week till #CGC12 kicks off! And thanks to our partnership with @CHI_Healthtech, your badge will not be handwritten with a Sharpie. Yay!
□ argonne:
Songs in the key of sea: Argonne biologist turns microbe data from the English Channel into music. http://1.usa.gov/TMrXLm
□ InsideScience:
http://bit.ly/Q7M1CY - 2 Share Nobel Prize for Stem Cell Discoveries Yamanaka, Gurdon share prize for adult stem cell research #Nobel
□ CellPressNews:
Read Nobel Laureate Shinya Yamanaka’s groundbreaking 2006 Cell paper freely http://ow.ly/ejjWe #nobelprize
□ popeetheclown:
指摘1：成熟細胞ではなく分化細胞／終末分化細胞と書くべき．これについては，その方が正しいことを理解した上で，分化という用語が一般常識かどうか疑問が残る，ノーベル賞公式サイトの授賞理由でもmature cellという表現が使われている，の2つの理由で成熟細胞を使いました．
□ AIP_Publishing:
Self-assembled bioinspired quantum dots: Optical properties http://ow.ly/eiCXW #APL_Ed_Pick
□ DSS: Dispersion Shrinkage for Sequencing: a new empirical Bayes shrinkage estimator for dispersion improves DE detection http://m.biostatistics.oxfordjournals.org/content/early/2012/09/22/biostatistics.kxs033.long
□ Chimeric TALE recombinases with programmable DNA sequence specificity:
>> http://m.nar.oxfordjournals.org/content/early/2012/09/26/nar.gks875.full …
The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture.
We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.
□ rnomics:
Massive computing contest won with #RNA-Seq data analysis: The... http://bit.ly/QrMhfZ #CloudingPlatforms #News #amazoncloud #RNAseq @MyEN
□ emmecola:
Economics and genetics meet in uneasy union http://www.nature.com/news/economics-and-genetics-meet-in-uneasy-union-1.11565 …
□ Genoeconomics: Is Our Financial Future in Our Chromosomes?: http://www.science20.com/jon_entine_contrarian/blog/genoeconomics_our_financial_future_our_chromosomes-95173 …
□ CAGS_UAE:
Focus on #Yemen: CTGA Database lists at least 64 #genetic disorders described in the #Yemeni population. http://www.cags.org.ae/ctga_search.html
□ CofactorGenomic:
New blog post up on directional RNA sequencing and how Cofactor helps you fit the best protocols to your project: http://www.cofactorgenomics.com/blog/2012/directional-rna-sequencing …
□ Knome Launches knoSYS 100 Genome Supercomputer to Enhance Interpretation:
>> http://www.bio-itworld.com/news/09/27/12/Knome-launches-knoSYS100-genome-supercomputer-enhance-interpretation.html …
Genomics supercomputer: the knoSYS™100 is optimized for the intensive processing and I/O requirements of whole genome informatics. At nearly 600 lbs. and running at over 1.2 teraFLOPS, it includes four 2.4GHz 8-core/16 thread Intel® Xeon® E5-2665 processors, and 18TB to 54TB of useable disk storage and Gigabit Ethernet?all contained in a secure, sound-proofed enclosure that can be placed in a laboratory environment.
□ Socrates_Logos:
TeselaGen’s DNA construction technology makes genetic engineering cheaper and faster. http://1.usa.gov/P8UGrN
Latest JBEI Startup to Speed Up Biotech Industry: TeselaGen’s DNA construction: DNA Synthesis: $538,000/243 constructs w/ 2.3 months
□ adajane:
The future of consumer genetics, @nygenome reports on #CGC12: http://bit.ly/UmKtdG
□ EricTopol:
Data-driven diabetes care http://tnw.co/QjYp12 good case made, and it will get a lot better #mHealth #digitalhealth
□ crodarte:
SoCal is on the map!! USC Center for Body Computing to create digital health incubator http://shar.es/5VfH2 @DrLeslieSaxon #mhealth
□ SERE: Single-parameter quality control and sample comparison for RNA-Seq
>> http://www.biomedcentral.com/content/pdf/1471-2164-13-524.pdf …
□ DailyNewsGW:
Big Data Program Funds Genome Data Analysis Project http://bit.ly/VwcU6I
□ MandE_NEWS:
Is medical science built on shaky foundations? - http://tinyurl.com/9tjevwj
□ DailyNewsGW:
Two Additional Lawsuits Filed Seeking to Block BGI Buy of Complete Genomics http://bit.ly/Udq9LH
□ Shareholder Lawsuits Seek to Stop BGI's Buy of Complete Genomics:
>> http://www.genomeweb.com/sequencing/shareholder-lawsuits-seek-stop-bgis-buy-complete-genomics …
□ bmahersciwriter:
J.C. Venter, Jon Rothberg embark on the next big genome race: sequencing Mars! http://bit.ly/U8mpKl from @antonioregalado
まさかの火星メタゲノム・シーケシングw さすがJCVさんやでぇ。。
□ GenoCon2:
Next-Generation Digital Information Storage in DNA via @Socrates_Logos | @scoopit http://sco.lt/5ouFEn
□ PhilippBayer:
Interesting approach! "SNP-SNP Interactions Discovered by Logic Regression Explain Crohn's Disease Genetics" http://t.co/2tChrrgj #OA #gwas
□ variomeproj:
HVP Consortium Update - September 2012 - http://eepurl.com/p0jUn
>> http://www.humanvariomeproject.org
The Human Variome Project
The Human Variome Project is all about standardising the way genetic variation information is collected, curated, interpreted and shared. It is the business of the Consortium to discuss and debate the ideas that will eventually become the HVP Standards and Guidelines that underpin routine data sharing. Project Roadmap 2012-2016 sets the goals for our activities, it is now up to each of us to start down the path towards those goals.
□ wilbanks:
If reading our paper on licensing open chemdata, make sure to read supplementary material. Much more work there. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002706 …
Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models
The Open PHACTS project utilizes a semantic web approach to integrate chemistry and biology data across a myriad of data sources, including for chemistry ChEBI, ChEMBL, and DrugBank, and for biology UniProt, Wikipathways, and many others. The chemical structure representations are obtained from ChemSpider, which has previously imported the chemical databases and standardized according to their data model and are making the data available as open data to the project.
In some ways, there are analogous difficulties in the exchange of computational models like quantitative structure activity relationship (QSAR) datasets
□ iNut:
Genome Environment Browser (GEB) http://web.bioinformatics.ic.ac.uk/geb/
□ MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks
>> http://m.bioinformatics.oxfordjournals.org/content/28/19/2412.full
A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib has been used to identify causative single-nucleotide polymorphisms in whole genome sequencing, detect balanced chromosomal rearrangements and compute enrichment of messenger RNAs (mRNAs) on microtubules, typically requiring applications of under 200 lines of code. MolBioLib includes programs to perform a wide variety of analysis tasks, such as computing read coverage, annotating genomic intervals and novel peak calling with a wavelet algorithm.
□ BIOENGINEERS INTRODUCE ‘BI-FI’: THE BIOLOGICAL INTERNET:
>> http://engineering.stanford.edu/news/stanford-bioengineers-introduce-biological-internet
M13DNA一本鎖パッケージによる細胞間コミュニケーションプラットフォーム。将来はセルラシステム等に応用。写真のお姉さん綺麗
□ fierceLamb:
introduction to variant calling https://wikis.utexas.edu/download/attachments/33948791/Barrick_IntroToVariantCalling.pdf?version=2&modificationDate=1345564857000 … ( by Bioinformatics Team (BioITeam) at the University of Texas ) samtools etc.
□ ewanbirney:
For genome geeks: the genome reference consortium blog - an excellent read about how the genome reference will evolve http://genomeref.blogspot.com/
□ hmason:
Stack Overflow Data Visualization Contest http://bit.ly/TmSys7 (via @xamat)
□ aprilush:
#ekaw2012 - @Open_PHACTS uses #VoID ( http://vocab.deri.ie/void and http://lab.linkeddata.deri.ie/ve2/ ) by @deri to keep provenance of data sets
□ maxplanckpress:
Video. Why do our brains make biased choices? http://buzz.mw/-cqe_y via @EurekAlertAAAS #brain #memory
□ nervous_jesse:
Continuous version of the Game of Life. Paper here http://arxiv.org/abs/1111.1567 Sexy video here http://www.youtube.com/watch?v=KJe9H6qS82I … via @spot
□ GenomeCruzer:
Next generation 3D Genomic Analysis Software. http://GenomeCruzer.com : discover the biological messages of your genomic data ! #BioInformatics
□ ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing http://www.biomedcentral.com/1471-2105/13/247/abstract …
□ PLOSMedicine:
India’s patent law on trial @MSF_UK @MSF_access http://blogs.plos.org/speakingofmedicine/2012/10/01/indias-patent-law-on-trial/ …
□ BioWireFeed:
$FONR (Fonar) $SNTA (Synta) $ROSG (Rosetta) - 3 Superactive Biotech Stocks of October 1, 2012 http://www.bio-wire.com/archives/95
□ InsideScience:
http://bit.ly/SFpNXy - Terror of Flying Into Alaska's Capital - When a jet flipped over, officials decided to try a better system #airtravel
□ physorg_com:
New antibiotic cures disease by disarming pathogens, not killing them http://phy.so/268332169
□ cairowire:
amnesty calls for urgent action re. alber saber: egyptian arrested for critical internet posts ? http://is.gd/vAyccY #egypt #humanrights
□ Dr_Bik:
De Long: but most small RNAs in environmental data don't map to known sequences. Had to develop criteria to predict putative sRNA
□ GigaScience:
#iGEM2012Asia: UT Tokyo trying to promote scientific literacy by tweeting book reviews from @UT_Tokyo feed & #iGEMbk hashtag
□ MaliciaRogue:
This is so cool :) "Commuting: Steven Strogatz Explains One of the Laws of Multiplication" http://t.co/omLnIv17
□ isatools:
90% of scientists do not use a metadata standard or developed their own in the lab. Leads to interoperability problems. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021101 …
□ InsideScience:
http://bit.ly/PSbTAk - French, American Physicists Share Nobel Prize for Quantum-Physics Research #Nobel
□ IndexCensorship:
Streaming now: Free speech in a hyper-connected world, panel debate feat @sdp + @marietjeD66 http://webcasts.barouhandpartners.com/marietje_schaake/save_the_date_free_speech_in_a_hyper_connected_world … tweet your qu's w/ #FSHCW
□ biochem_fan:
今回ノーベル化学賞を取った Brian Kobilka による、β2アドレナリン受容体-Gs複合体の構造(PDBID: 3SN6) を拙作のWebGL版分子ビューアでご覧ください。http://webglmol.sourceforge.jp/glmol/viewer.html?pdb:3sn6 …
□ htby:
ブラウザ上で論理回路が設計できる『The Logic Lab』が素晴らしい | IDEA*IDEA http://j.mp/WJHsRX (via Instapaper)
□ hacchy:
ちょっと共感してくれた方のために，このツールを（現在投稿中）。ISM: an accurate and fast taxonomic profiling software http://bit.ly/RMvxSj
□ jsports:
高度36,576ｍ！怖すぎ！成層圏からのフリーフォールRed Bull StratosをJ SPORTS3にて10月8日生中継！http://www.jsports.co.jp/notice/121001_red_bull_stratos.html … pic.twitter.com/ZqJwV36e
□ yuifu:
ENCODE Project Reveals Genome as an Information Processing System //ゲノムを情報処理システムと見た時、80％という数字は驚きではない、と。こういう見方もあるんですね。 http://m.spectrum.ieee.org/tech-talk/at-work/test-and-measurement/re-imagining-our-genes-encode-project-reveals-genome-as-an-information-processing-system …
□ tri_iro:
"Strange Functions in Real Analysis" http://www.amazon.co.jp/Strange-Functions-Analysis-Applied-Mathematics/dp/0824703200 … を買った。 counterexample in analysis http://www.amazon.co.jp/Counterexamples-Analysis-Dover-Books-Mathematics/dp/0486428753 … 的な反例図鑑を期待していたけど、殆ど反例載ってなくて残念
□ yuifu:
「forward/reverseにマップされたリードの山をk塩基シフトしたときの相互相関係数を計算．kについてプロットするとfragment長由来のピークが出るが，read長由来の'phantom peak'も出現．」 #encodejp-08
□ acoela:
重要なのは「ウイルスの起源は何か」「どう進化してきたか」で、「ウイルスは生物か」という問題の立て方はあまり良くないよね。もとは独立した生物だったのが退化した、というのが本当ならとても面白い。 / “ウイルスは退化しているもののやはり生…” http://htn.to/2k8ut3
□ celmisia:
PRAGMA biodiversity workshopが始まった。 これ→http://pragma23.pragma-grid.net/dct/page/70009
□ _masaka:
TurtleとMicrodata/RDFの視覚化 http://www.kanzaki.com/works/2009/pub/graph-draw … MDからのRDF抽出／変換機能を追加。もう少し整備してからARC2のモジュールとして公開する予定
□ c_z:
メモ。解析／可視化パッケージの一覧。 Software for social network analysis http://www.gmw.rug.nl/~huisman/sna/software.html …
□ tenapi:
なんと、Følnerの基準とか言う結果によれば、アメナブルな可算群のクラスは \Pi^0_2 にまで降りてくるじゃないか。これは意外だ…では気を取り直して、アメナブルでない可算群にその逆説的分解を対応させるエフェクティブな方法がないか調べてみよう。
□ mixingale:
アブストによればさっきのアセモグルet.al.の論文は一定の仮定の下で世界経済は「不平等だがイノベーションの多い"冷酷な資本主義国"」と「これにタダ乗りして高い厚生を得る"優しい資本主義国"」という非対称なものに必然的に分化してくということを論じたものだそうです。
□ suztomo:
小さい頃は技術の発達して人間の仕事が減れば働かなくても暮らしていける社会がくるものだと思っていたけど、今考えてみると技術に仕事を奪われた人が増えて失業率の高い社会になってしまうのではないか。
もっと言うと、その技術をフランチャイズ化して安く買い叩くようになった結果、開発の末端が誰でも出来る作業に分断されて、低賃金で高負荷を強いられているという歪な構造に。開発者には見返りもあるが、その評価と報酬のバランスが正当とは言えない。金を動かす側の論理と乖離が運命付られてるから