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<script src="https://bits.csb.pitt.edu/asker.js/lib/asker.js"></script>
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.reveal pre { font-size: 100%; overflow-x: auto; overflow-y: auto;}
.reveal h1 { font-size: 2em}
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.reveal ul {display: block;}
.reveal .slides>section>section.present { max-height: 100%; overflow-y: auto;}
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<script>
$3Dmolpromise = new Promise((resolve, reject) => {
require(['https://3Dmol.org/build/3Dmol.js'], function(){
resolve();});
});
require(['https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.2.2/Chart.js'], function(Ch){
Chart = Ch;
});
$('head').append('<link rel="stylesheet" href="https://bits.csb.pitt.edu/asker.js/themes/asker.default.css" />');
//the callback is provided a canvas object and data
var chartmaker = function(canvas, labels, data) {
var ctx = $(canvas).get(0).getContext("2d");
var dataset = {labels: labels,
datasets:[{
data: data,
backgroundColor: "rgba(150,64,150,0.5)",
fillColor: "rgba(150,64,150,0.8)",
}]};
var myBarChart = new Chart(ctx,{type:'bar',data:dataset,options:{legend: {display:false},
scales: {
yAxes: [{
ticks: {
min: 0,
}
}]}}});
};
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Linux¶
Happy Birthday Linux! Here's your cake:
%%html
<div id="prepared" style="width: 500px"></div>
<script>
jQuery("#prepared").asker({
id: "prepared",
question: "Have you used the Linux commandline before?",
answers: ["Yes","No"],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
Installing (Linux)¶
For this class we expect you to do your work on your own computing resources.
Your code will be evaluated using Ubuntu 22.04. You use the system package manager (apt) and the python package manager (pip) to install additional software needed for the course. sudo runs a command with super user privileges.
sudo apt install git vim wget python-pip ipython-notebook python-tk clustalw libcairo2 libcairo2-dev libxml2 libxml2-dev cmake libeigen3-dev swig graphviz python-pygraphviz imagemagick python3-openbabel
sudo pip3 install pysb matplotlib biopython prody MDAnalysis cython sklearn Pillow py3Dmol pandas pydotplus pydot bionetgen
macOS¶
Macs also have a built-in commandline (Terminal.app). Many of the packages we use are also available of OS X. However, keep in mind your assignments must run properly on Ubuntu 22.04.
MacPorts is most convenient for installing software (https://www.macports.org), but not all packages that we use are readily available.
Windows¶
As of Windows 10, can install Linux Subsystem. In theory should work just like Ubuntu and is much less cumbersome to use than the Windows shell.
Colab¶
Google Colab provides a cloud-based solution from running python. You can run bash commands by prefixing them with !.
Since your colab runtime will eventually timeout, we strongly recommend install Jupyter notebook locally on your own machine rather than using cloud resources.
Commands¶
The first word you type is the program you want to run. bash will search PATH environment variable for an appropriately named executable and run it with the specified arguments.
- ipython - start interactive python shell (more later)
- ssh hostname - connect to hostname
- passwd - change your password
- nano - a user-friendly text editor
A BASH cheatsheet¶
ls - directory listing¶
$ ls -l
total 8
-rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt
drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture
$ pwd
/home/dkoes/intro
$ cd lecture/../..
$ pwd
%%html
<div id="question1" style="width: 500px"></div>
<script>
jQuery('#question1').asker({
id: "cdquestion",
question: "What prints out?",
answers: ["~/","/home/dkoes", "/home/dkoes/intro","/home/dkoes/intro/lecture","An Error"],
extra: ["","","","","",""],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
$ ls -l
total 8
-rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt
drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture
$ ls *.txt
%%html
<div id="question2" style="width: 500px"></div>
<script>
jQuery('#question2').asker({
id: "lsquestion",
question: "What prints out?",
answers: ["hello.txt","*.txt", "hello.txt lecture", "An Error"],
extra: ["","","","","",""],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
Spacing Out¶
du - disk usage of files/directores
[dkoes@n052 tmp]$ du -s
146564 .
[dkoes@n052 tmp]$ du -sh
144M .
[dkoes@n052 tmp]$ du -sh intro
4.0K intro
df - usage of full disk
[dkoes@n052 tmp]$ df -h .
Filesystem Size Used Avail Use% Mounted on
pulsar:/home 37T 28T 9.3T 75% /net/pulsar/home
Dude, where's my stuff?¶
locate find a file system wide find search directory tree which print location of a command man print manual page of a command
Save the Environment¶
NAME=value set NAME equal to value No spaces around equals
export NAME=value set NAME equal to value and make it stick
$ dereference variable
user@python$ X=3
user@python$ echo $X
3
user@python$ X=hello
user@python$ echo $X
hello
user@python$ echo X
X
Getting at your variables¶
%%html
<div id="questionvarprint" style="width: 500px; "></div>
<script>
jQuery('#questionvarprint').asker({
id: "varquestion",
question: "Which does <b>not</b> print the value of X?",
answers: ["echo $X","echo ${X}","echo '$X'","echo \"$X\""],
extra: ["","","","","",""],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
$ ls -l
total 8
-rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt
drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture
$ ls '*.txt'
%%html
<div id="questionls2" style="width: 500px"></div>
<script>
jQuery('#questionls2').asker({
id: "ls2question",
question: "What prints out?",
answers: ["hello.txt","*.txt", "hello.txt lecture", "An Error"],
extra: ["","","","","",""],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
Your Environment¶
env list all set environment variables
PATH where shell searches for commands
LD_LIBRARY_PATH library search path
PYTHONPATH where python searches for modules
.bashrc initialization file for bash - set PATH etc here
History¶
history show commands previously issued
up arrow cycle through previous commands
Ctrl-R search through history for command AWESOME
.bash_history file that stores the history
HISTCONTROL environment variable that sets history options: ignoredups
HISTSIZE size of history buffer
Shortcuts¶
Tab autocomplete
Ctrl-D EOF/logout/exit
Ctrl-A go to beginning of line
Ctrl-E go to end of line
alias new=cmd
make a nickname for a command
$ alias l='ls -l'
$ alias
$ l
%%html
<div id="stringm" style="width: 500px"></div>
<script>
jQuery('#stringm').asker({
id: "stringm",
question: "What prints out?",
answers: ["ovolo","volo", "ovol","vl","An Error"],
server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi",
charter: chartmaker})
$(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide();
</script>
Batch processing files¶
for file in *.png
do
convert $file ${file%.png}.tif
done
Assignment 1¶
- Due in a week
- Use GradeScope to hand-in
- Test your code before submitting