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# seriation
This software is an efficient implementation of the [Seriation](http://www.jstatsoft.org/v25/i03) problem which 'finds a suitable linear order for a set of objects'. It has been used to order a network of proteins such that 'related' nodes are closer in the other.
## Authors
The Seriation Package was developed by [Felipe Kuentzer](http://lattes.cnpq.br/1979213773480902), in collaboration with
Douglas G. Ávila, Alexandre Pereira, Gabriel Perrone, Samoel da Silva, [Alexandre Amory](http://lattes.cnpq.br/2609000874577720), and [Rita de Almeida](http://lattes.cnpq.br/4672766298301524).
**Contact information**: Alexandre Amory (*alexandre.amory at pucrs.br*)
## Inputs
The input file is a textual file describing an undirected network of nodes (in our examples the nodes are protein names). Example:
<pre>
L7007 L7008
L7008 L7007
L7010 L7011
L7011 L7010
L7014 L7015
L7015 L7014
L7017 Z1275
</pre>
In the tab Files you can find networks for different species such as [Escherichia coli](data/Escherichia_coli.dat), [Mus musculus](data/Mus_musculus.dat), [Saccharomyces cerevisiae](data/Saccharomyces_cerevisiae.dat), [Homo sapiens](data/Homo_sapiens.dat), among others.
## Outputs
The output is a text file with the order of the network nodes. Example:
<pre>
Protein dim1
Z5822 0
Z5823 1
Z2911 2
Z2910 3
Z2909 4
Z4123 5
Z4124 6
Z3105 7
Z3106 8
...
</pre>
The following image represents the Homo sapiens network with a *random ordering*.
The next image represents the Homo sapiens network **'seriated'**.
## Download and Compilation
The Seriation Package is developed in C and tested on Ubuntu 14.04.
* Download the package ("amd64":/redmine/attachments/download/360/cfm-seriation_1.0-1_amd64.deb) or ("i386":/redmine/attachments/download/361/cfm-seriation_1.0-1_i386.deb).
* Is recommended to update your packages before the instalation:
> * sudo apt-get install update
* To install, you can double-click it or execute:
> * sudo dpkg -i cfm-seriation_1.0-1_amd64.deb
> * In case of missing dependencies, try: sudo apt-get install -f
* To unistall:
> * sudo dpkg -r cfm-seriation
* this distribution has the following files
<pre>
/usr/share/cfm-seriation/bin/ Executable file
/usr/share/cfm-seriation/etc/ Auxiliar used to plot charts with GNUPLOT
/usr/share/cfm-seriation/data/ Biological input networks
/usr/share/cfm-seriation/src/ Source code in C
</pre>
## How to Use
type 'cfm-seriation' to show the options:
<pre>
cfm-seriation
Usage: cfm-seriation [OPTION...]
Seriation Parameters:
f=[NETWORK FILE].dat Network file path name
o=[ORDER FILE].dat Apply initial order
i=[INTERVAL] Number of isothermal steps
m=[STEPS] Number of steps
c=[FACTOR] Cooling factor
a=[ALPHA] Alpha value
p=[PERCENTUAL] Percentual energy for initial temperature
s=[SEDD] Random seed
P Plot graphs
v Generate video
</pre>
type 'cfm-seriation f=/usr/share/cfm-seriation/data/Homo_sapiens.dat m=3000 P' to execute the seriation. This process can take about 12 minutes, depending on the CPU.
In case you want a video of the process, type 'cfm-seriation f=/usr/share/cfm-seriation/data/Homo_sapiens.dat m=3000 P v' to execute the seriation. This will consume some extra time.
<pre>
Usage: cfm-seriation [OPTION...]
Seriation Parameters:
f=[NETWORK FILE].dat Network file path name
o=[ORDER FILE].dat Apply initial order
i=[INTERVAL] Number of isothermal steps
m=[STEPS] Number of steps
c=[FACTOR] Cooling factor
a=[ALPHA] Alpha value
p=[PERCENTUAL] Percentual energy for initial temperature
s=[SEDD] Random seed
P Plot graphs
v Generate video
Reading file...
Proteins: 9684
Interactions: 163509
Applying random order...
Saving and plotting initial order...
INITIAL Energy: 4123514310
Ordering...
100% [====================================================================================================]
</pre>
## Further Information
* [Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks](ieeexplore.ieee.org/document/7033586/). This paper describes the optimizations implemented in this package.
* Felipe's Master Thesis [Otimização e análise de algoritmos de ordenamento de redes proteicas](http://hdl.handle.net/10923/6663). Full description of the optimizations implemented in this package (in Portuguese).
## License
The source code is distributed under the terms of the GNU General Public License v3 [GPL](http://www.gnu.org/copyleft/gpl.html).
## How to Cite this Package
If you are using this package on your research, please cite our paper:
* [Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks](ieeexplore.ieee.org/document/7033586/)
<pre>
KUENTZER, Felipe A. et al. Optimization and analysis of seriation algorithm for ordering protein networks.
In: IEEE International Conference on Bioinformatics and Bioengineering (BIBE), 2014. p. 231-237.
</pre>
## Where Seriation is Used
If you are using the Seriation Package, please send an email to *alexandre.amory at pucrs.br* so we can update this list of users:
* [Transcriptogrammer](http://lief.if.ufrgs.br/pub/biosoftwares/transcriptogramer/)
## Similar Packages
* [R Package seriation](http://www.jstatsoft.org/v25/i03), available at http://cran.r-project.org/web/packages/seriation/index.html.
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