I need a name too
Watching some extremely helpful youtube videos, I become interested in this project. There are a few questions I want to ask, and answering those questions will ultimately lead me to a greener pasture. Here they are the source I want to give credit to:
BioinformagicianBioinformagician
chatomicschatomics
Genomics guruGenomics Guru
BiostatsquidBiostatsquid
LiquidBrain bioinformatics
SingleCell Genomics
SanbomicsSanbomics
Jensen Teaching
Fun Genomics
No one likes your personal life or story
You need a good name
People like to know the sincere reason why you are doing this
You have to be persistent, there will be some (or a lot) bumpy roads, this is sure; there might not be success in the end, this is not sure. the question becomes how you want to define “success”, lol.
Expert bioinformatics
I start to collect “solid”, bullet-proof bioinformatics protocols.
CUT-and-Tag protocol
I have to give credit to Dr. Zheng for her great effort to make her protocol available.
Building a website with wordpress
My friend gives me an extremely useful video, which I can follow to build a website.
JDK for Mac OS
step 1: download the installer 15.0.1 for mac
step 2: where is it installed: /Library/Java/JavaVirtualMachines/
step 3: to remove it, use the command: sudo rm -rf jdk-15.0.1.jdk
Now, to match the version, I am downloading Java8, and it turns out that I need to accept the license and log in oracle.
Mount an external hard disk with CentOS7
My linux currently runs on my laptop with only 250 GB diskspace, I need to extend to an additional hard disk and mount it properly.
I am following this link as a starting point.
Manage and administration for MacBookPro MacOS MacAdmin
I have my own page on configuring configuring the MacBook Pro.
Scenario 1: a historical post Rstudio in Mac
I downloaded and install Rstudio, when I tried to launch it, it could not find R executable. It seems that I need to have R installed first.
On the source machine,
##Help post deserves the credit # store_packages.R # # stores a list of your currently installed packages tmp = installed.packages() installedpackages = as.vector(tmp[is.na(tmp[,"Priority"]), 1]) save(installedpackages, file="~/Desktop/installed_packages.rda") # restore_packages.R
On the designation machine
## The most straightforward way
# installs each package from the stored list of packages load("~/Desktop/installed_packages.rda") for (count in 1:length(installedpackages)) install.packages(installedpackages[count])
## Or, here is more careful way
# installs each package from the stored list of packages load("~/Desktop/installed_packages.rda") ## These codes are used for installing packages # function for installing needed packages installpkg <- function(x){ if(x %in% rownames(installed.packages())==FALSE) { if(x %in% rownames(available.packages())==FALSE) { paste(x,"is not a valid package - please check again...") } else { install.packages(x) } } else { paste(x,"package already installed...") } } # install necessary packages required_packages <- installedpackages lapply(required_packages,installpkg)
Installing caret package
When I tried to install the “caret” package, it depends on “ModelMetrics”. To install this package causes quite a lot effort.
People had similar problem when they tried to install "ModelMetrics", omp.h is missing, To install this, I need (1) become admin account (2) use the command "brew install libomp" But, it fails to install "libomp" due to the homebrew error So, I followed "brew doctor" suggestion and made it work!! sudo mkdir -p /usr/local/Cellar /usr/local/Frameworks /usr/local/opt /usr/local/sbin sudo chown -R $(whoami) /usr/local/Cellar /usr/local/Frameworks /usr/local/opt /usr/local/sbin
Scenario 2: working with GPU and GPU management in Mac
I am gradually collecting the information about MacOS GPU related information.
On support from Apple explains some basics. First help doc on the allocating GPU under MacOS
Scenario 3: installation as an admin in MacOS
1. Become admin: su li11-admin with correct password 2. sudo -H "whatever installation command" 3. Enter the same password as admin
Scenario 4: how to make a screen shot
- Hold "command" + "shift" + 4
- A selection window pops up for selection
- Drag and release the choice, a screen shot is taken and saved on desktop
Scenario 5: how to connect network drive via the samba drive
- Click "Go" --> choose "Connect to Server
- Choose the connect "server address" and hit connect
- After authentication, it is good to go
Scenario 6: Basic installation
Scenario 7: I want to access network drive from the command line
Find this post very helpful!. After I go through the VPN and connected to the network drvie, using the /Volumnes/whateverDrive/
Scenario 8: Install jupyter on my MacBookPro
Initially, I found this
But, why don’t I start with jupyter.org??
This link seems more legit!
Scenario 9: Install JDK (for eclipse) on my MacBookPro
A very bad documentation from oracle
Deep Learning with Python
A great and popular book on deep learning, and a good course using this book with.
Case 1 Set up profile and GPU on Tiguar
# standard setup for Python 3.5 # (switches to the environment that has also MXNet) export PATH=/ddn/gs1/home/klimczakl/miniconda2/bin:$PATH source activate mxnet3 # on bioinfoX export CUDA_VISIBLE_DEVICES='' # on tiguar - your preferred GPU for multiple processes #export CUDA_VISIBLE_DEVICES='1' #Since Lez logs in as me, I can't use export CUDA_VISIBLE_DEVICES='1' # use this to evaluate GPU memory nvidia-smi # use next available GPU for if your preferred GPU close to full export CUDA_VISIBLE_DEVICES='2' export CUDA_ROOT=/ddn/gs1/home/klimczakl/miniconda2/envs/mxnet3 python # now in Python interpreter # alternatively include in your script from keras import backend as K import tensorflow as tf config = tf.ConfigProto() config.gpu_options.allow_growth=True sess = tf.Session(config=config) # this will give you base GPU memory allocation nvidia-smi
Special setup for Python 2.7
# special setup for Python 2.7 (use based environment) # only for legacy Keras 0.3.3, Theano 0.8.2 # requires "backend": "theano" in .keras/keras.json export PATH=/ddn/gs1/home/klimczakl/miniconda2/bin:$PATH export CUDA_VISIBLE_DEVICES='1' export CUDA_ROOT=/ddn/gs1/home/klimczakl/miniconda2 python -s # now in Python interpreter import theano
Learning Python with muver
muver is developed by my former colleague Dr. Christopher Andrew Lavender, and currently hosted on github. While learning programming in python, I wanted to follow the muver developing path and get my first project done in python, I name it as “RNAseqEnsemble”.
First thing first, muver requires four major open source software. I need to make sure they are all properly installed.
Bowtie2 GATK, version 3.7-0 picard samtools
Python related note
Since I have lost the wordpress pages at Duke University hosting, I have to use this temporarily page to keep track of python related note.
I wanted to run python3 on my windows 10 machine, just to streamline the coding convention. So, at this moment:
I am accumulating python help websites
Machine Learning vs. AI
I have joined a few ML/AI teams to learn together, keep up with the field, and once in a while attend some kind of ML/AI related competitions.
ImageRecognitionMaster
ShenZhou
RushHour
Good ML/AI webportals
This cheat sheet is called ML-CheatSheet.
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