BioHackathon 2011 - Public symposium. (8/27 updated.)

□ BioHackathon 2011　公開シンポジウム

Public symposium of the BioHackathon 2011 will be held at Campus Plaza Kyoto (next to the Kyoto station) on Aug 21.

>> http://2011.biohackathon.org/documents/symposium
>> http://www.ustream.tv/channel/biohackathon


・Symposium: Aug 21 (Sun) @ Campus Plaza Kyoto, Kyoto, Japan
・Hackathon: Aug 22 (Mon) - 26 (Fri) @ Bioinformatics Center, Kyoto University



BioHackathon 2011、部外に紹介出来るような形で、たとえばSlide Shareをもっと公開してくれたら嬉しいな。




□ dbcls: ライフサイエンス統合データベースセンター
BioHackathon2011公開シンポジウムをUstream配信します bit.ly/oi0r9G #biohack11

BioHackathon Symposium 2011 　 8/21 10:00-
http://2011.biohackathon.org/documents/symposium




□ pjacock:
Archiving #BioHack11 tweets here twapperkeeper.com/hashtag/BioHac… (giving up on #bh11 for #BioHackathon 2011), see 2011.BioHackathon.org




□ jervenbolleman:
#biohack2011 some slides coming up on github.com/dbcls/bh11/wik…




□ chapmanb: Brad Chapman
Distributed exome analysis pipeline with CloudBioLinux and CloudMan is.gd/gJiICg #ngs #aws




□ ogishima:
Blog: "BioHackathon 2011 シンポジウム" - Ogishima Blog sysbioevo.org/ogishima/blog/…

Tree of Life

View more presentations from Rutger Vos

□ rvosa:
#biohack11, projects in my talk: tolweb.org, ubio.org, treebase.org, timetree.org, gbif.org - slides here: slidesha.re/p0pr9G


□ dbcls:
Rutger Vos The Tree of Life as central unifying concept for the integration of phylogenetic ...




□ biosharing:
BioSharing attends the BioHackathon 2011 - Focus on Linked Data in life science: blog.biosharing.org/2011/08/biohac…

During this first live streamed open symposium day, a series of short presentations set the scene for the hands-on hackaton event that runs for the whole week (Aug 22-26). Presentations include:
- SPARQLing UniProt RDF (Jerven Bolleman)
- BioMart and semantic-web querying (Joachim Baran)
- SADI and semantic-web services (Mark Wilkinson)
Also BioSharing (Susanna-A Sansone) and the ISA infrastructure (Philippe Rocca-Serra) are also introduced, along with NCBO BioPortal (Trish Whetzel), MIRIAM Registry (Camille Laibe) and many others.

□ kozo2:
phenomeblast - Comparative phenomics tools for aligning and analyzing phenotypes across species - Google Project Hosting bit.ly/qWpgCX

PhenomeNet: PhenomeNet is a cross-species phenotype network in which nodes are compared based on phenotypic similarity.
PhenomeBrowser: The PhenomeBrowser is a web-interface to explore the PhenomeNet.
PhenomeBLAST: PhenomeBLAST is an ontology-based tool that provides a practical implementation of cross-species alignments of phenotypes using ontologies. We make both a command-line tool and a web-server available.

□ c_z:

BioHackathonで生まれたPSICQUICも広く普及した。分子間相互作用に関してはもう個別クライアントは書かなくていいかな。次は他のデータセットとの容易な結合ができるようにSWの方向へ。　#BioHack11

□ pjacock:
Bruno Aranda #BioHack11: #PSICQUIC code.google.com/p/psicquic/ aims to standardise the access to molecular interaction databases programmatically


□ Japanese Society for Bioinformatics (JSBi) http://t.co/0Jso5dB announced call for papers for their journal "Genome Informatics" #BioHack11


□ Joachim Barb: 35 DBs in #BioMart Central Portal, 20 DBs in International Cancer Genome Consortium: leads to 900,000,000 triples! #BioHack11




□ dbcls:
Open Bio* projects Interoperable libraries for the Semantic Web






□ apaf:
PDB identifiers in TOPSAN (Peter's question): As an example, here is the TOPSAN entry for PDB id 2Q9K: topsan.org/Proteins/JCSG/… #biohack11
Crystal structure of conserved uncharacterized protein (ZP_00539648.1) from Exiguobacterium sp. 255-15 at 1.59 A resolution. To be published




□ takechan2000:
SADI (Semantic Automated Discovery and Integration) is a framework to create SW services using OWL classes as a service IO #biohack11




□ elmccarthy:
"Need a fast-booting computer to record dreams before you forget" "Or a notebook" "Ah… sleep mode" "No, a notebook: pen & paper" #biohack11




*****************************************************************

□ synobu:
Biohackathon 2011 開発会議二日目. 成果はこちらに集約中. github.com/dbcls/bh11/wiki #biohack11




□ pjacock:
SADI have some stylish faux wood USB keys with a virtual machine on them - thanks @elmccarthy #BioHack11 sadiframework.org



□ pjacock:
#BioHack11 BioMart tutorial with text-mining data example by @joachimbaran has just started in main room biomart.org


□ joachimbaran:
BioMart tutorial/demo: set-up of customised REACTOME pathways mart with text-mining data within 10 minutes. SPARQL enabled. #biohack11




□ pjacock:
#BioHack11 Mitsuteru Nakao (@32nm) giving quick introduction to google-refine code.google.com/p/google-refin… for cleaning, transforming, & to freebase




□ tkwsm:
BioMed Central Blog : Towards interoperable bioinformatics web services for integrated applications bit.ly/mWzuQs




□ biohack11: BioHackathon 2011
OK Go meets The Muppets OK Go and The Muppets - Muppet Show Theme Song http tinyurl.com/3zsu956 by Jan Aerts - Google+ User Feed




□ apaf1:
Working on RDF output for HMMER3 output (first for 'domtblout') in #bioruby, see: github.com/cmzmasek/bioru… #biohack11


*****************************************************************



□ PLoSCompBiol:
Are There Laws of Genome Evolution? Join the discussion dx.plos.org/10.1371/journa…
ゲノム進化を統計物理的な数理モデルで記述することは可能か。定性進化か、あるいは普遍な創発性か。生物学的ネットワークのノード次数分布、進化速度の対数正規分布など

The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles.

Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as “laws of evolutionary genomics” in the same sense “law” is understood in modern physics.

□ PLoSCompBiol:
New Collection: The Roots of Bioinformatics ploscollections.org/article/browse…




□ rnomics: http://shar.es/HUW2X 確率モデルによるRNA二次構造予測
phylogenomics: Cryptogenomicon ? #RNA secondary structure prediction with probability models... bit.ly/mSGo96 #rnomics-bioinfo #OpenScience

TLでSean Eddy氏のブログcryptogenomiconでのRNA二次構造の確率予測モデルの記事が目に付く一方、#BioHack11 には同開発者によるHMMER3（隠れマルコフモデルを用いた相同性検索ツール）を利用したRDF出力の紹介が




□ emblebi: EMBL-EBI
Applications are being accepted for the EMBL PhD programme (EMBL sites are in France, Germany, Italy and the UK) - www.embl.org/PhDProgramme




□ EurekAlertAAAS: 生物が時間として感じる離散的な経験を、一連のイベントとしてシーケンシャル的にエンコードするニューロンのプロセスを発見
'Time cells' bridge the gap in memories of event sequences : http://eurekalert.org/e/44Jb




□ PLoS:
Bobe: Personal Genome Project seeking 100,000 volunteers for DNA sequencing, wants to forge pathway to personalized medicine. #SciBarSpace



□ PLoS:
Bobe: Bioweathermap is a global environmental sensing effort using genomic sequencing technologies. #SciBarSpace




□ ICSB_2011: ICSB 2011 Orga Team
Less than 48h to start of @ICSB_2011 in Mannheim, tomorrow workshops start already in Heidelberg. Excitement is rising... #systemsbiology




□ BioInfo:
AWS Genomics Event, September 22nd, 2011 aws.amazon.com/genomicsevent

Genomics is increasingly becoming a cloud computing play. More and more researchers and practitioners are turning to cloud computing to solve big data challenges, scale, improve time-to-market, and better manage cost efficiencies.

Reasons to attend

・Hear how genome sequencing customers of AWS have successfully built and migrated large scale projects to the cloud.
・Gain a deeper understanding of Amazon Web Services, including best practices for developing, architecting, and securing applications in the cloud. Gain a deeper understanding of doing large scale, big data analysis with AWS.

□ PLoSCompBiol:
New Education: Biomedical Cloud Computing With Amazon Web Services dx.plos.org/10.1371/journa…




□ portablegenomic: Portable Genomics
Interview with Biomedical Pioneer, Dr. Leroy Hood medgadget.com/?p=26371




□ mndoci:
@chapmanb will be covering his distributed exome sequencing pipeline bcbio.wordpress.com/2011/08/19/dis… at the #AWS genomics workshop aws.amazon.com/genomicsevent/




□ genetics_blog: Stephen Turner
Estimating Trait Heritability from GWAS Data gettinggeneticsdone.blogspot.com/2011/08/estima…

The basic idea is to use GWAS data to estimate the degree of "genetic sharing" or relatedness among the samples, computing what the authors call a genetic relationship matrix (GRM). The degree of genetic sharing among samples is then related to the amount of phenotypic sharing using restricted maximum likelihood analysis (REML).

□ portablegenomic: Portable Genomics
Mobile devices and emerging technologies are fueling the creation of a $1.3 billion health care WiFi industry soc.li/QogXZVh




□ preferred_jp:
twitterで自然言語処理　research.preferred.jp/2011/08/twitte…　みなさんよむべしです！！




□ Symbiologica: Juliana Mastronunzio
Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. ncbi.nlm.nih.gov/pubmed?term=pr…




□ nutsci:
good comments by Blumberg RT @priti959: Antioxidant vitamins may cut mortality risk: EPIC data nutraingredients-usa.com/Research/Antio… via @NutraUSA




□ nutrigenomics:
I lk #Google+ > #FB but still lk #Twitter much more, its fast & comprehensive => twttr Just Got the Respect it Deserves tnw.co/onURao




□ NatureJapan:
Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia nature.asia/riKzba
ネイチャージオサイエンス掲載論文です。「34億年前の地球最古の化石、火星の生命に期待広がる」国際ニュース : AFPBB News http://t.co/VYksG8b




□ blockagefree:
Last dinosaur before mass extinction discovered bit.ly/paXNzt #science RT @DrSampyRoy




□ cshperspectives: CSH Perspectives Ed.
"When we dissect the genetic basis of real adaptations, they invariably rest on changes in DNA seq" bit.ly/nHJfjg via @carlzimmer

One often hears the suggestion that the neo-Darwinian view of evolution is on the skids, and that that view will be completely changed?if not overturned?by new biological ideas like modularity, genetic assimilation, evolvability, and epigenetics. Epigenetics in particular (I’ll define it in a moment) has been especially touted as a concept that will revolutionize evolutionary biology.

□ AIP_Publishing:
Numerical-simulation and experimental-validation of the largest Egyptian solar process-heat system http://ow.ly/69kBz #AIP_JRSE


□ AIP_Publishing:
Ultra-portable explosives sensor based on a CMOS fluorescence lifetime analysis micro-system http://ow.ly/69frz #AIP_ADV


□ AIP_Publishing: 人体の熱を利用して発電する着衣式エレクトロニクスの展望。
Wearable electronics self-powered by using human body heat: The state of the art and the perspective http://ow.ly/69fAW #AIP_JRSE




□ physorg_physics:
Physicists build first single-photon router tw.physorg.com/233229075




□ OxfordJNLsJapan:
Why Is It So Hard to Find a Suicide Bomber These Days?
【OUP BLOG】自爆テロが少なくなってきたのはなぜか？　bit.ly/oE9jGw




□ wsjtecheurope:
University Not the Only Route to Success on.wsj.com/qcPQuk < the impressive team @gosquared #ALevel #resultsday

<br />


□ PLoSMedicine:
Tobacco companies use corporate social responsibility for political purposes: bit.ly/rl27hm


□ PLoSMedicine: PLoS Medicine
This Week in PLoS Medicine: Tobacco’s corporate responsibility; Health policy & systems research; Smoking in films bit.ly/n2OHoa




□ Erika_Check:
86% of land species, 91% of ocean species yet to be discovered, says study that pegs number of species on earth at 8.7m bit.ly/kDy0K




□ NatureJapan:
Nature Cover Story: 温暖化と紛争のホットスポット：国内紛争とエルニーニョとの結びつき nature.asia/oH158d




□ sangerinstitute:
New genetic variant for osteoarthritis found without DNA sequencing - the power of 1000 Genomes Project data bit.ly/ppxopN




□ NutraEurope:
Early under-nutrition may increase heart disease risk in later life. http://j.mp/pXJyNR




□ AIP_Publishing:
CERN clears the sky on CLOUD formation http://ow.ly/6dta2 #AIP_PT




□ PLoSONE:
We've started our Media Tracking Project | EveryONE bit.ly/n7FHmE