MONET installation

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COST Training School

on Network Modularisation

PLEASE, DO NOT START JUST YET...

IF POSSIBLE, JOIN ME ON:

Friday 20 March 09h00 UCT+1

(registered participants will receive a link just before)
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What's your name? (optional)You will be credited when I will use the information I collect to improve MONET
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Start by installing git

Follow the instructions HERE
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What is your operating system version?
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Look up how to install Docker or Singularity (using command line)

For example, if you are using Ubuntu 18.04, like THIS
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Please, paste here the commands you used to install
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Look up how to start Docker or Singularity

For example, like THIS
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What version of Docker or Singularity was installed?type on the command line: "docker --version" or "singularity --version", to find out
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Let's install MONET!

Type on the command line:

git clone https://github.com/BergmannLab/MONET.git && cd MONET && ./install.sh

Go to NEXT if you feel lost...
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Video tutorial: installation (and running)
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Please, paste any errors here Did you get errors? Did the installer point to any files containing errors? Please paste here...
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In case you are interested in the science......feel free to download the pre-print: https://www.biorxiv.org/content/10.1101/611418v4.full
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DONE installing! Should we try to run some examples together?
YESNO, THNAKS
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First, let's look at MONET's docs. Anything unclear?Please read (what seems interesting): https://github.com/BergmannLab/MONET/blob/master/README.md
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Now, let's look at the --help function. Any questions?Type on the command line: "monet --help"
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MONET is a toolbox containing 3 algorithms: M1, K1 and R1

We will run one examples using each method...
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EXAMPLE (1) - let's run method M1!Given what you have learned from the --help function...Try to modularise the following network using the method "M1" and upload the output files: https://raw.githubusercontent.com/BergmannLab/MONET/master/.test/system_test/input/zachary_karate_club.txt
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EXAMPLE (2) - now, method K1!Try to modularise the same network, zachary_karate_club.txt, using the method "K1" and upload the outputs.
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EXAMPLE (2) - CONTINUED - method K1, try again!I suspect you might have gotten an error... If so, look at the output file: there is a hint regarding a certain K1 parameter you should be using here. [HINT: the reason K1 is getting in trouble is that this network is so very small! Once you figure out the parameter, set it to a small value. Try something below 10]
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EXAMPLE (3) - finally, method R1!As a final exercise, modularise again zachary_karate_club.txt, using the method "R1" and upload the outputs. This time, look at "monet --help": R1 has a lot of options, you could try to use some of them. [the "--c" option, for example, can make computation faster at the price of accuracy in the results... something that could be interesting if you will find yourself working on a big network]
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Before we say GOODBYE... ITS YOUR TURN!

Do you have a Genetic Network you wold like to modularize? Now you know how!

If you have any troubble, please open an issue HERE:

provide the exact monet command you are running

upload the input file you are having trouble with

tell us what error you are getting
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THANK YOU!

if you encoutered ERRORS

or if you have any QUESTIONS

feel free to contact me:

mattia.tomasoni [AT] unil.ch
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