linkstream2 microblog

https://ash.confex.com/ash/2015/webprogram/Paper86671.html
https://proxesite.wordpress.com/

Fold [class] recognized by an…[NN] predictor based-on evolutionary & structural info., w/ particle-swarm training
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24232/full

Ngaam J. Cheung,
Xue-Ming Ding,
Hong-Bin Shen

First published: 27 October 2015
DOI: 10.1002/jcc.24232

two papers for journal club:

1. What are super-enhancers? Pott et al., Nature Genetics (2015) http://www.nature.com/ng/journal/v47/n1/full/ng.3167.html

2. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer, Heyn et al., Genome Biology (2016)
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2

#Epigenomic analysis detects aberrant super-enhancer DNA methylation in human #cancer
https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-016-0879-2 hypo-Me of many large blocks

miRNA silencing for…therapy targeted to the [acidic] tumor microenviron., w/ #pHLIP
http://www.nature.com/nature/journal/v518/n7537/abs/nature13905.html miR-155 moves beyond biomarker

DREM…reconstruction of…regulatory #networks from time-series expression http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-104 Classic approach using 3-level IO #HMMs

Yet more thoughts on squeezing in stuff:

Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing:
– 12 pt spacing exactly & 0 before & after + 4 pt before major heads (except for in-line figures, then automatic ‘single spacing’) such as INNOVATION

– no widow/orphan control

– no spaces before paragraphs, just indents

– bullet (*) lists (eg for people)

Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) ****

Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. ****

Titles: Cambria 12 pt looks nice, but flexible.

References: NIH Style EndNote. [1]

QT:{{”
NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}

QT:{{”

11. Descriptive Title of Applicant’s Project

Enter a brief descriptive title of the project. This field is required.

A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.

A “revision” application must have the same title as the currently funded grant.

NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).

“}}

The above is OLD. Now you can go above 81 characters.

QT:{{”
Font

Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}

Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.

QT:{{”
Paper Size and Page Margins

Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.

….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}

http://grants.nih.gov/grants/funding/424

Expanded seq. context model…explains variability in polymorphism[s] http://www.nature.com/NG/journal/vaop/ncurrent/full/ng.3511.html Reminiscent of GOR sec. structure prediction

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.

More thoughts on this. One person’s condensed summary of this for Word:

QT:{{
Margins: 0.5 inches all around
Normal: Arial 11 pt
Spacing: 12 pt exactly (except for in-line figures, then automatic ‘single spacing’)
Hyphenate! (Menu: Page Layout, Page Setup, Hyphenation, Automatic) **** Legends: Arial 8.5 pt, Spacing exactly 8.4 pt. Hyphenated. **** Titles: Cambria 12 pt looks nice, but flexible.
References: NIH Style EndNote. [1]

NIH instructions write: “Use an Arial, Helvetica, Palatino Linotype, or Georgia typeface, a black font color, and a font size of 11 points or larger. (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.). Type density, including characters and spaces, must be no more than 15 characters per inch. Type may be no more than six lines per inch (1 inch = 72 points, six lines/inch = 12 pt exact spacing). Use standard paper size (8 ½” x 11) . Use at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins.”
“}}

QT:{{”

11. Descriptive Title of Applicant’s Project

Enter a brief descriptive title of the project. This field is required.

A “new” application must have a different title from any other PHS project with the same PD/PI. A “resubmission” or “renewal” application should normally have the same title as the previous grant or application. If the specific aims of the project have significantly changed, choose a new title.

A “revision” application must have the same title as the currently funded grant.

NIH and other PHS agencies limit title character length to 81 characters, including the spaces between words and punctuation. Titles in excess of 81 characters will be truncated. Be sure to only use standard characters in the descriptive title: A through Z, a through z, 0 through 9, space ( ), and underscore (_).

“}}

The above is OLD. Now you can go above 81 characters.

QT:{{”
Font

Prepare the application using Arial, Helvetica, Palatino Linotype, or Georgia typeface in black font color. After text attachments are converted to PDF, font size in each final PDF document must be at least 11 points (or larger). (A Symbol font may be used to insert Greek letters or special characters; the font size requirement still applies.) Since some PDF converters may reduce font sizes, it is important to confirm that type density in each final PDF document, including both characters and spaces, is no more than 15
characters+spaces per linear inch and no more than six lines per vertical inch.
“}}

Note: 72 points/inch so 6 lines/inch at 11pt type translates into a line spacing of 11 pts + 1pt per line.

QT:{{”
Paper Size and Page Margins

Final PDF documents should be formatted to be no larger than standard paper size (8 ½” x 11). The final PDF document should have at least one-half inch margins (top, bottom, left, and right) for all pages. No information should appear in the margins, including the PI’s name and page numbers.

….
Figures, Graphs, Diagrams, Charts, Tables, Figure Legends, and Footnotes You may use a smaller type size but it must be in a black font color, readily legible, and follow the font typeface requirement. Color can be used in figures; however, all text must be in a black font color, clear and legible.
“}}

http://grants.nih.gov/grants/funding/424

What’s the EM #algorithm?
http://www.nature.com/nbt/journal/v26/n8/full/nbt1406.html Description of its essence in simple contexts (ie coin toss) & as soft version of kmeans

What is the expectation maximization algorithm? : Article : Nature Biotechnology

Primer
Nature Biotechnology 26, 897 – 899 (2008)
doi:10.1038/nbt1406

Chuong B Do & Serafim Batzoglou

Abstract
The expectation maximization algorithm arises in many computational biology applications that involve probabilistic models. What is it good for, and how does it work?

without too much math