Posts Tagged ‘cbb752’

Education in Computational Biology Today and Tomorrow

March 25, 2017

Education in #CompBio, by @bffo & @joannealisonfox
http://journals.PLOS.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003391 Keeping up in a rapidly changing field. Will implement some @Yale

QT:{{”
“These initiatives help to extend computational biology beyond the domain of specialized laboratories. Researchers, at all levels, need to keep themselves up-to-date with the quickly changing world of computational biology, and trainees need programs where bioinformatics skills are embedded so they can have comprehensive training. New bioinformatics workflows can be adopted more widely if education efforts keep pace. As previously pointed out , starting early is also very important. There is still room for programs that capture the excitement and enthusiasm of secondary school students and convey the potential of computational biology to the public. We welcome additions to the PLOS Computational Biology “Bioinformatics: Starting Early” collection (www.ploscollections.org/cbstartingearly).

We would like to involve the community in this endeavor. With this editorial, we are calling out to educators and researchers who have experience in teaching, specifically, those keen to raise the expectations and the inquisitiveness of the next generation of biologists. The Education collection will continue to publish leading edge education materials in the form of tutorials that can be used in a “classroom” setting (whatever that may mean nowadays: stated more generically, “the places where people learn”). We will continue to encourage articles set in the context of addressing a particular biological question and, as mentioned above, we welcome new “primers” and “quick guides.” We will also be inviting tutorials from the various computational meetings. A new category of papers that is in the pipeline for the Education collection is the “Quick Tips” format, the first of which was just published . The “Quick Tips” articles address specific tools or databases that are in wide use in the community.
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Explore Erudite – BD2K Training Coordinating Center

December 6, 2016

http://bigdatau.org/explore_erudite

Needleman–Wunsch algorithm – Wikipedia

November 11, 2016

https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm

relates to

https://en.wikipedia.org/wiki/Wagner%E2%80%93Fischer_algorithm

https://en.wikipedia.org/wiki/Michael_J._Fischer

QT:{{"

Historical notes and algorithm development[edit]

The original purpose of the algorithm described by Needleman and Wunsch was to find similarities in the amino acid sequences of two proteins.[1]

Needleman and Wunsch describe their algorithm explicitly for the case when the alignment is penalized solely by the matches and mismatches, and gaps have no penalty (d=0). The original publication from 1970 suggests the recursion

A better dynamic programming algorithm with quadratic running time for the same problem (no gap penalty) was first introduced[3] by David Sankoff in 1972. Similar quadratic-time algorithms were discovered independently by T. K. Vintsyuk[4] in 1968 for speech processing ("time warping"), and by Robert A. Wagner and Michael J. Fischer[5] in 1974 for string matching.

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Visualization of Statistical Power Analysis

July 28, 2016

Visualization of Power Analysis http://amarder.GITHUB.io/power-analysis/ Useful sliders giving one a feel of the #statistics

How does multiple testing correction work?

June 13, 2016

How does multiple-testing correction work
http://www.nature.com/nbt/journal/v27/n12/abs/nbt1209-1135.html Intuition for teaching: genome-wide error rate on a single gene v family

The role of regulatory variation in complex traits and disease : Nature Reviews Genetics : Nature Publishing Group

June 12, 2016

Reg. variation in cplx traits by @LeonidKruglyak
http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html nice teaching figure for #eQTLs, showing how mostly cis + hotspots http://www.nature.com/nrg/journal/v16/n4/full/nrg3891.html

Plant endophytes as a platform for discovery-based undergraduate science education : Abstract : Nature Chemical Biology

March 26, 2016

Ex. of extreme project oriented course

http://www.nature.com/nchembio/journal/v3/n7/abs/nchembio0707-356.html

EM algorithm

March 11, 2016

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

SVM movie

March 5, 2016

quick video for visualizing the power of kernels in SVM
https://www.youtube.com/watch?v=3liCbRZPrZA

Visualizing matrix multiplication as a linear combination – Eli Bendersky’s website

February 20, 2016

http://eli.thegreenplace.net/2015/visualizing-matrix-multiplication-as-a-linear-combination/