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DRUGraph README

Last changed: 2013/09/30

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This package includes the source code for the network algorithm for
the identification of drug-drug interactions (REF).

For the code to compile, you will NEED TO INSTALL, first:

1) The GNU Scientific Libraries (GSL), available from
http://www.gnu.org/software/gsl/


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INSTALLATION
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---- Unix ----

In a Unix-like system (including MacOS), you can install the DRUGraph
software by uncompressing the tarball (tar -xzvf
drugraph-version.tar.gz) and running the usual stuff from the
drugraph-version directory:

cd drugraph-version

./configure

./make

./make install

This will install the software in your/default/bin/directory. To
install in a different directory run

./configure --prefix=path_to_install_directory

instead of just "./configure". For other configure options run:

./configure -h


You can uninstall the whole thing by running

./make uninstall

from the installation directory.


---- Windows (MinGW) ----


1) First of all, you have to download and install MinGW
(http://sourceforce.net/projects/mingw/files/latest/download?source=files)

During the installation, when it prompts you which packages to
install, select gcc, msys and mingw base. The other default options
are OK.


2) Download GNU Scientific Libraries (GSL), available from
http://www.gnu.org/software/gsl/. In my installation, I've used
version 1.15.


3) Launch MinGW console (Programs -> MinGW -> MinGW Shell or
C:\MinGW\msys\1.0\msys).


4) Unzip the contents of the GSL downloaded file under your msys home
which is at C:\MinGW\msys\1.0\home\user\ (it's important to perform
step 3 or you won't have the home directory).


5) In your msys console, cd into the gsl-15 folder and type the following:

./configure --prefix=/MinGW

make

make install

All these steps may take a while.


6) Untar the contents of rgraph under your msys home and type the following:

./configure 

make

[make install]


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USING DRUGraph
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The program takes as input a file containing a list of drug-drug
interactions with the following format:

d1 d2 0
d1 d3 1
d1 d4 1
...

This corresponds to a situation in which drug 1 (d1) and drug 2 (d2)
have an interaction of type 0, d1 and d3 have an interaction of type
1, and so on. Interaction types must be integer between 0 and K-1,
where K is the number of interaction types.

The program outputs a file predictions.dat with the following format:

d2 d3 0.50 0.20 0.30
d2 d4 0.15 0.55 0.30
...

This corresponds to a situation with three types of interactions
(K=3), and indicates that: drugs 2 and 3 have an interaction of type 0
with probability 0.50, of type 1 with probability 0.20, and of type 2
with probability 0.30; drugs 2 and 4 have an interaction of type 0
with probability 0.15, of type 1 with probability 0.55, and of type 2
with probability 0.30; and so on.

To see how everything works with a practical example, you can change
to the directory main/ in the installation directory and run drugraph
on the test network ddi_cokol_TRAIN.dat.

Command line parameters
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To run the program, type the following in the command line:

drugraph K net_file niterations seed

where:

* K is the number of types of interactions (for example, if
  interactions can be antagonistic, additive or synergistic, then
  K=3).

* net_file is the file containing the known interactions, and has the
  format described above.

* niterations is the number of sampling iterations carried out by the
  Metropolis algorithm.

* seed is the seed for the random number generator, and can be any
  positive integer.


Running output
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After starting the program, the algorithm proceeds by: (i) determining
a convenient thinning step; (ii) thermalizing the sampler; (iii)
sampling. Please, be aware that each of these processes can take a
long time (even days) in networks larger than a few hundreds of drugs.

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CONTACT
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sees.lab@gmail.com