For the beginner: Advice for applyingMachine Learning (Andrew Ng) Related blog (Jan Hendrik Metzen): Trying to go through Advice for applyingMachine Learning using Python IPython notebook.
Google released Tensor Flow 1.0 on Feb. 15. 2017.
According to this post, Tensor Flow is one of the top choice neural network tools, and used the most in GitHub.
Therefore, it aroused my interests to start to learn to use Tensor Flow.
Hopefully, I will keep updating my learning process here.
[Bioinfo] GATK ERROR: attempting to calculate the mismatch count against a reference string that is smaller than the read
Before variant calling process, the local realignment at indel regions is known to reduce false positives of variant calls (ref1). There are a few types of errors.
ERROR MESSAGE: attempting to calculate the mismatch count against a reference string that is smaller than the read
options: -evalue 1e-10 (E value threshold) -num_threads 8 (Number of threads (CPUs) to use in blast search.) -perc_identity 97 (% identity cutoff) -num_descriptions 5 (hit # threshold)
[Linux] Delete/Remove files before certain days with certain extension
1. Find files under current directory (maximum 4 subdirectories) at least 1 day ago | select files with ‘.bam’ | select files with ‘variant’ | output file list to variant_bam_removed.txt
When we culture the bacteria, sometimes we can observe some bacteria may become resistant to antibiotics. How to predict the emergence of drug resistance? What is the growth state of bacteria in the presence of drugs? One Science article from UCSD Physics investigates the issue using both bulk and single-cell techniques, and further builds up a model to predict the growth rate of the resistant bacteria strain under different drug concentration.
Summary
They observed that the resistant bacteria either grow or do not grow (i.e., growth bistability) when the drug concentration is less than minimum inhibitory concentration (MIC). In addition, their model is able to predict the growth rate of bacteria under different concentration, and the concentration range in which the growth bistability occurs. They suggested that the model can be used to further study the evolution of drug resistance.
Opinion
As Chang-Ting Jason Lin said, the paper combines the quantitative model in system biology and the single-cell method to study the drug resistance, which may be a hot issue.
Science. 2013 Nov 29;342(6162):1237435. doi: 10.1126/science.1237435.
The innategrowthbistability and fitnesslandscapes of antibiotic-resistantbacteria.