Bioengineering & #systemsbiology. Classic def’n in terms of the “4 M’s”—Measurement, #Mining, Modeling & Manipulation
http://www.ncbi.nlm.nih.gov/pubmed/16474915
QT:{{”
Systems Biology can also be defined operationally, as
by the MIT Computational & Systems Biology Initiative,
in terms of the “4 M’s”—Measurement, Mining, Modeling,
and Manipulation—illustrated schematically in Fig. 1 (see
http://csbi.mit.edu/).
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http://www.kdd.org/kdd2014/
8/24-8/27
13th International Workshop on Data Mining in Bioinformatics (BIOKDD’14) August 24, 2014 * New York City, NY, USA
http://home.biokdd.org/biokdd14
What is a support vector machine? A nice overview w/o equations, just pictures. Great for #teaching!
http://www.nature.com/nbt/journal/v24/n12/abs/nbt1206-1565.html #SVM .@GenomeNathan YES, but see
http://noble.gs.washington.edu/papers/noble_what.html …, which has an expanded, “free” version.
http://noble.gs.washington.edu/papers/noble_what.html
http://www.nature.com/nbt/journal/v24/n12/abs/nbt1206-1565.html
.@kdnuggets 77K genres from auto. & manual methods like
gene-classification approaches. How $NFLX Rev. Eng. Hollywood http://theatln.tc/1cKP4gx
http://m.theatlantic.com/technology/archive/2014/01/how-netflix-reverse-engineered-hollywood/282679/
Long-span PET mapping reveals characteristic patterns of #SVs in… cancer [v norm] genomes, but no MEIs or small events
http://genome.cshlp.org/content/early/2011/04/05/gr.113555.110.abstract
The described study used long paired-end-tags (PET) to analyze and compare SVs in cancer and normal genomes. It determined the prevalence of different types of SVs in normal and cancer sample. Overall, the results are interesting and convincing on a qualitative level; however, for the reasons outlined below, more precise and quantitative delineation of the observed effects is highly desirable.
1) Small sample size of normal genomes (only 2 normal genomes)
2) Validation rate was low (< 77%) for everything except deletions, and for singletons it was even lower. .
3) Long PET is not good for finding smaller events (few kbps). Thus, this analysis missed smaller scale SVs and cancer rearrangements.
4) While there is a discussion about breakpoints and associated repeats, it is not very informative as breakpoint locations were not determined to basepair resolution.
5) No MEI were considered — particularly, no cancer MEI were considered in the analysis, while recently it was found that somatic retrotransposition occurs in cancer (Lee et al., PMID: 22745252)..
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes –
Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.
Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.
How a #Gawker Editor Picks the ‘Viral’ Content Readers Can’t Resist: Human intuition trumps data #mining
http://m.us.wsj.com/articles/SB10001424052702304579404579231772007379090
Neetzan Zimmerman is the human intuition between Gawker’s successful shares Sort of like buZz feed….
How a Gawker Editor Picks the ‘Viral’ Content Readers Can’t Resist Sharing
Five Web-based Apps to help you #visualize big data: Many Eyes, ICharts, Visualize Free, Wolfram Alpha, Data Wrangler
http://www.techrepublic.com/blog/five-apps/five-web-based-apps-to-help-you-visualize-big-data ==
Also Visualize Free to complete the 5 MT @KirkDBorne 5 Web-based Apps to help you visualize #BigData
http://www.techrepublic.com/blog/five-apps/five-web-based-apps-to-help-you-visualize-big-data
A REPORTER AT LARGE
AUTO CORRECT
Has the self-driving car at last arrived?
BY BURKHARD BILGER
NOVEMBER 25, 2013
Has the self-driving car at last arrived? Almost, thanks to DARPA challenges, maps & machine learning
http://www.newyorker.com/reporting/2013/11/25/131125fa_fact_bilger via @gigajordan
Might be good for course slides!
MT @sjackman @anshul
http://scikit-learn.org/stable/tutorial/machine_learning_map … is useful for #teaching, providing students a practical way to wade through all the approaches
linkstream2 microblog 