linkstream2 microblog

Swift Playgrounds (https://itunes.apple.com/us/app/swift-playgrounds/id908519492?mt=8)

• Drag simple blocks of code
• Very gentle introduction to coding
• Begin with controlling a video game character
• iPad only

Scratch Jr (https://itunes.apple.com/us/app/scratchjr/id895485086?mt=8)

• Drag icons that represent code blocks
• Tablet only (iPad & Android)

Blockly (https://blockly-games.appspot.com/)

• Similar to Swift Playgrounds in its introduction
• Begin with controlling a video game character
• Gentle introduction to coding
• Exposure to basic programming syntax
• Runs in browser
• Tablet version in beta

Scratch (https://scratch.mit.edu/)

• More complex desktop version
• Exposure to basic programming syntax
• Also runs in browser

Hopscotch (https://itunes.apple.com/us/app/hopscotch-learn-to-code-creatively-and-make-games/id617098629?mt=8)

• Nice video tutorials
• Considers a broader range of applications than the other ones
• Slightly less gentle introduction to coding
• Tablet only (iPad & Android)

R Datacamp (https://www.datacamp.com/courses/free-introduction-to-r)

• Browser-based introduction to R
• Video tutorials
• Guided interactive coding exercises
• Full programming syntax

Naldi, A. et al. Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PLOS Computational Biology 13, e1005432 (2017).

Reconstruction & signal propagation analysis of the Syk signaling #network http://journals.PLoS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005432 Inferring potential targets of the kinase

The $AMZN Echo’s always-listening feature entangles it in a murder
case http://www.pcworld.com/article/3152899/smart-appliance/the-amazon-echos-always-listening-feature-entangles-it-in-a-murder-case.html Did the victim say “#Alexa, call the cops”

http://dx.doi.org/10.1093/bioinformatics/btw120

http://AlgoRun.org, #Docker-based packaging [w/ web GUI & workflow mgt] for platform-agnostic implement[ations]
http://Bioinformatics.Oxfordjournals.org/content/early/2016/03/02/bioinformatics.btw120

Hosny, A. et al. AlgoRun, a Docker-based packaging system for platform-agnostic implemented algorithms. Bioinformatics Advance Access, Mar 2, 2016.

“this has got to be a record… imported this into Zotero to find the total author count. It’s 1,014”
http://www.g3journal.org/content/5/5/719.abstract

The Yale graduate school regulations governing dissertations includes a paragraph that indicates that only two dissertation committee members need Yale appointments:

QT:{{
“Registered doctoral candidates must have a principal adviser with an appointment on the Graduate School faculty. The Graduate School requires that each dissertation be read by at least three persons but not more than five, at least two of whom are ladder or ladder-track faculty members at Yale. All readers must hold the Ph.D. degree as well as a faculty position or be considered otherwise qualified to evaluate the dissertation…”
}}

http://www.yale.edu/printer/bulletin/htmlfiles/grad/policies-and-regulations.html#dissertation

Pixelmator (photoshop Mac alternative): http://www.pixelmator.com Has a vector mode:
http://www.pixelmator.com/blog/2013/05/14/introducing-vectormator/

Latest version of GIMP for Mac OS X does not require X11:
http://www.gimp.org/downloads/

Dreamweaver & Illustrator alternatives:
http://www.onextrapixel.com/2013/06/18/10-best-alternatives-to-adobe-dreamweaver/ http://www.onextrapixel.com/2011/03/15/10-best-alternatives-to-adobe-illustrator

http://pikimal.com/html-editor

It’s sort of like Dreamweaver for $130
http://www.artisteer.com/

Summary for:

“Epigenomic Alterations in Localized and Advanced Prostate Cancer” Lin PC, Giannopoulou E, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA*, Elemento O*. 2013. Epigenomic alterations in localized and advanced prostate cancer. Neoplasia

http://www.ncbi.nlm.nih.gov/pubmed/23555183

In this paper, the authors take advantage of new advances in reduced representation bisulfite sequencing, a method for measuring DNA methylation patterns genome-wide, with high coverage and
single-nucleotide resolution, to study methylation patterns in prostate cancer. Working with a prostate cancer cohort already studied with DNA-Seq and RNA-Seq analyses, the authors identified
differentially methylated regions (DMRs), comparing the methylation of prostate cancer samples to benign prostate samples. The analysis found an increase in DNA methylation in prostate cancer samples, and that the methylation was more diverse and heterogeneous compared to the patterns of benign samples. Furthermore, it was found that genes near hypermethylated DMRs tended to have decreased expression, while genes near hypomethylated DMRs tended to have increased expression. Additional analyses revealed that breakpoints associated with prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue. Finally, a study of CpG islands at different stages of prostate cancer (benign vs. PCa vs. CRPC (castration-resistant prostate cancer)) revealed that certain islands become increasingly methylated with disease severity. The authors used this data as the basis for two classification models: one to discriminate between benign prostate tissue and PCa tissue, and another to discriminate between PCa tissue and CRPC tissue. Both models demonstrated high sensitivity and specificity, indicating that CpG islands with high discriminatory power could serve as a diagnostic basis for predicting disease aggressiveness. Finally, additional analyses revealed that breakpoints associated with
prostate-cancer-specific deletions, duplications, and translocations tended to be highly methylated in benign prostate tissue.

A little prettier than before, but still quite blue.
http://www.digitaltrends.com/wp-content/uploads/2011/09/windows-8-blue-screen-of-death.jpg