http://bioinformatics.oxfordjournals.org/content/early/2013/12/12/bioinformatics.btt719.short
Posts Tagged ‘bioinformatics’
BETASEQ: A Powerful Novel Method to Control Type-I Error Inflation in Partially Sequenced Data for Rare Variant Association Testing
December 23, 2013Genomics Researchers Imagine their Ideal Computer
December 9, 2013http://chronicle.com/article/Still-Hunting-Medical/143221/
Paul Basken
The Chronicle of Higher Education
CCLE WGS dataset
December 9, 2013This is the URL for ccle with WGS data:
https://cghub.ucsc.edu/datasets/ccle.html
They have an XML describe all the datasets and there are WGS as well. (This should be publicly available WGS.)
QT:{{”
The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, the Novartis Institutes for Biomedical Research, and the Genomics Institute of the Novartis Research Foundation. CCLE will conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, develop an integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and translate cell line
integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.
NOTE: these data sets do NOT require any special access or authorization status. However, you will need to use the public access token/key URL, or your secure key file that you may have downloaded for projects like TCGA that use a secure key file.
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TCGA Toolbox and Roadmap Dashboard
October 13, 2013Encouraging citation of software – introducing CITATION files | Software Sustainability Institute
September 8, 2013Machine Learning Resources
September 1, 2013Comprehensive list
http://www.sciencemag.org/site/feature/data/compsci/machine_learning.xhtml
Potential Classes for an Undergraduate Major in Bioinformatics
August 5, 2013I list below a number of courses that I think should be
included/excluded from the undergrad bioinformatics program. This is based on a discussion with a student who did an undergraduate double major in CS and Biology.
The courses that I think essential for the program are:
– Algorithms, Data structures, Cell & Molecular biology, and Genetics
The courses that I think should be included in the program are:
– Discrete mathematics, Algorithms on strings, Computational complexity, Statistics, Data mining and Databases, Machine Learning, Biochemistry, Unix/Linux operating system, Scripting Languages (Perl and/or Python), and Scientific writing
The courses that I think might less important are:
– Computer architecture, Compiler theory, Circuit design, Inorganic chemistry, and Chemical engineering
Curious to get people’s thoughts on this. Feel free to comment or email me (http://contact.gerstein.info).
Potential Classes for an Undergraduate Major in Bioinformatics
August 4, 2013I list below a number of courses that I think should be
included/excluded from the undergrad bioinformatics program. This is based on a discussion with a student who did an undergraduate double major in CS and Biology.
The courses that I think essential for the program are:
-Algorithms, Data structure, Cell and Molecular biology, and Genetics
The courses that I think should be included in the program are:
-Discrete mathematics, Algorithms on strings, Computational
complexity, Statistics, Data mining and Databases, Machine Learning, Biochemistry, Unix/Linux operating system, Scripting Languages (Perl and/or Python), and Scientific wirtting
The courses that I think might less important are:
-Computer architecture, Compiler theory, Circuit design, Inorganic chemistry, and Chemical engineering
Curious to get people’s thoughts on this. Feel free to comment or email me.
The Graduate School of Biomedical Sciences at Houston – Program in Biomathematics and Biostatistics Course Requirements
July 20, 2013Bioinformatics and Genomics — Huck Institutes of the Life Sciences – PhD in bioinformatics
July 16, 2013IBIOS Bioinformatics and Genomics Program – PhD in bioinformatics at PSU http://www.huck.psu.edu/education/bioinformatics-and-genomics
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