October 2014

RT @AllSeq: RT @DaleYuzuki: Submitting an #AGBT15 abstract with @iontorrent data? We have something for you. http://t.co/zOreYiEBtX

9:05am October 3rd 2014 via Hootsuite

RT @iontorrent: Hear Nathan Treff from @RMANJ talk copy number variation at NYC Ion Torrent user meeting (10/7) http://t.co/nQF0zibE2n

8:05am October 3rd 2014 via Hootsuite

RT @usnews: 8 Websites For Free Online Learning: @coursera @duolingo @khanacademy @MITOCW @edXOnline @Codecademy http://t.co/AXM5fYVpIJ

7:05am October 3rd 2014 via Hootsuite

RT @westr: Mayo Clinic Named Most Social Media-Friendly Hospital in U.S. http://t.co/qS4I8z3YKm #mccsm #hcsm

6:05am October 3rd 2014 via Hootsuite

RT @THebertMcGill: How the educational experience has changed...... http://t.co/OOJg3iBgVF

5:05am October 3rd 2014 via Hootsuite

RT @iontorrent: Science/AAAS webinar on exome sequencing in a clinical research lab. Register for this Oct. 15 event http://t.co/4hqMjVFFWR

4:05am October 3rd 2014 via Hootsuite

RT @iontorrent: 16S rRNA profiling on the PGM reveal wild ducks as a potential source of bacterial disease: http://t.co/DrP7eQQWRR

10:30pm October 2nd 2014 via Hootsuite

RT @dgmacarthur: The hot mess that is EHR http://t.co/bNchUwBtYW A warning of what genomics could become without efforts like @GA4GH.

10:05pm October 2nd 2014 via Hootsuite

RT @tracey_423: Boo Carnegie Sci Cntr: boys= Robotics,Chem; girls=Sparkle Sci #womeninscience http://t.co/3KYJuuEn4t

9:05pm October 2nd 2014 via Hootsuite

RT @EricTopol: A Defining Decade in DNA Sequencing http://t.co/xPcXnDP4Pu #genomics @naturemethods http://t.co/RwJJ3Af3dM

8:02pm October 2nd 2014 via Hootsuite

College is ripping you off: Students are cash cows, and schools the predators - http://t.co/MFBUbhe67L http://t.co/wblIvyxRGx

7:35pm October 2nd 2014 via Hootsuite

Yelp Can't Be Trusted | Make Use Of http://t.co/XXDdSUmPQu I personally no longer use Yelp; they filter what you see for their own end.

6:30pm October 2nd 2014 via Hootsuite

AP: Can use multi-factor authentication, restrict individual users, encryption for both S3 and EBS #guinformatics

4:08pm October 2nd 2014 via Hootsuite

AP: Security: shared responsibility model. Together achieve compliance. Diagrammed a virtual private cloud (VPC) #guinformatics

4:06pm October 2nd 2014 via Hootsuite

AP: List of firms that analyze: mentions @stationxinc for genomic data #guinformatics

4:04pm October 2nd 2014 via Hootsuite

AP: 'You need to use the spot market for science; otherwise you are doing it wrong' Ex: $0.13 to $13 #guinformatics

4:01pm October 2nd 2014 via Hootsuite

AP: There is a reserved capacity and an on-demand capacity and a 'spot market' on top of that. Harvard: GATK at 50% discount #guinformatics

4:00pm October 2nd 2014 via Hootsuite

AP: Data up in S3, easily scales (one customer: 156k cores, all 8 regions, $33K in 3d) Otherwise: a 3mo project for cust. #guinformatics

4:00pm October 2nd 2014 via Hootsuite

AP: Flexible sizing of clusters; low cost of failure, can reiterate quickly #guinformatics

3:58pm October 2nd 2014 via Hootsuite

AP: They have EC2 instance families, like a T-shirt size: memory and SSD storage sizes / capability exposed to users #guinformatics

3:56pm October 2nd 2014 via Hootsuite

AP: A region will have several availability zones, split by electrical grids. Customers determine what is where. #guinformatics

3:55pm October 2nd 2014 via Hootsuite

AP: Inception 2008, some 957 new features. 10 regions, 26 'avail. zones', 51 'edge locations' #guinformatics

3:54pm October 2nd 2014 via Hootsuite

Angel Pizarro (Amazon Web Services): "Building secure and scalable genomics services on AWS" #guinformatics

3:52pm October 2nd 2014 via Hootsuite

BL: Great "what if": the kinds of experiments that can be done if computation wasn't limiting #guinformatics

3:51pm October 2nd 2014 via Hootsuite

BL: Now trying to do with splicing what they did with Myrna - ongoing work #guinformatics

3:50pm October 2nd 2014 via Hootsuite

BL: Using ReCount 2011 pub: http://t.co/g1GAv5L3pE normalizing many RNA-Seq datasets: 18 studies, 475 samples, >8B reads #guinformatics

3:49pm October 2nd 2014 via Hootsuite

BL: Next his tool Myrna, 2010 publication: http://t.co/lLUGzdshu5 eQTL calcuation - 465 at $0.34 per sample 'close to free' #guinformatics

3:48pm October 2nd 2014 via Hootsuite

BL: So the 'same SW runs on the same HW' 'and all you need is a credit card' #guinformatics

3:46pm October 2nd 2014 via Hootsuite

BL: Hadoop is open-source MapReduce, for huge clusters (like AWS). Reproducibility: a complex pipeline scales #guinformatics

3:45pm October 2nd 2014 via Hootsuite

BL: Mentions work with GEUVADIS (website http://t.co/w4F0IfgkXw ), introducing MapReduce to aggregate & compute #guinformatics

3:44pm October 2nd 2014 via Hootsuite

BL: Why study big datasets? May make new insight; may combine datasets; can add power to smaller expt #guinformatics

3:39pm October 2nd 2014 via Hootsuite

Ben Langmead (Hopkins) "Scalable software for analyzing many sequencing datasets at once" #guinformatics @benlangmead

3:36pm October 2nd 2014 via Hootsuite

IF: Costs: WES $5-30; WGS $20-100; RNA-Seq $5-10 http://t.co/K0LOYzTvM7 With: est. compute, 1mo storage, platform, support #guinformatics

3:34pm October 2nd 2014 via Hootsuite

IF:Madhavan group at GU: 78 exomes, 2TB data, 125K core-h in 1.7d All Amazon cloud-based 'at modest cost' #guinformatics

3:31pm October 2nd 2014 via Hootsuite

IF: Olopade lab: 200 exomes, 200GB data, 76K core-h in 1.25d #guinformatics

3:31pm October 2nd 2014 via Hootsuite

IF: Globus uses galaxy-based workflow mgmt. With Nancy Cox: 134 samples, 4TB data, 2200 core-h in 6d http://t.co/mCgC91xu87 #guinformatics

3:30pm October 2nd 2014 via Hootsuite

IF: He did early work on grid computing - 3rd-party outsourcing. Does every lab need a haystack sorting machine? #guinformatics

3:25pm October 2nd 2014 via Hootsuite

Ian Foster (U Chicago, Argonne N.L.) "Finding needles in haystacks: large-scale NGS analysis using Globus Genomics" #guinformatics

3:22pm October 2nd 2014 via Hootsuite

DK: Illustrated with chart of heart failure in-pt mortality rate by date. Area to comment, attach, similar to an intranet #guinformatics

3:16pm October 2nd 2014 via Hootsuite

(Mayo named most social-media friendly hospital: http://t.co/1C2j8kXjwb h/t @westr) #guinformatics

3:13pm October 2nd 2014 via Hootsuite

DK: Dabo, a social media platform in a healthcare environment. Getting engagement at point-of-service #guinformatics

3:12pm October 2nd 2014 via Hootsuite

Dawn Knight (Mayo Clinic, Dabo) "Making quality metrics actionable" #guinformatics

3:10pm October 2nd 2014 via Hootsuite

RT @lrasmus: @atulbutte - "the best knowledge bases today don't track if we were right or not". Great point! #GCDS2014

3:02pm October 2nd 2014 via Hootsuite

JM:Q:n of 1 trials? A:We do believe it will be multi-omics when the time comes. Schilsky (ASCO) ref: http://t.co/magNHTuH9n #guinformatics

2:43pm October 2nd 2014 via Hootsuite

JM: Putting together a center; mainly around GI cancers. "A shift from 'pay for consumption'" to "pay for outcomes" #guinformatics

2:40pm October 2nd 2014 via Hootsuite

JM: Theranostics: Two indiv's with same profile; but phosphoprotein analysis shows differences. Could be at this level #guinformatics

2:34pm October 2nd 2014 via Hootsuite

JM: 1B people w/ cancer care; "what about the rest of people worldwide?" Prospective profiling for cancer care is the future #guinformatics

2:33pm October 2nd 2014 via Hootsuite