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https://github.com/amamory/seriation

An efficient implementation of the Seriation 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.
https://github.com/amamory/seriation

bioinformatics-algorithms protein-interaction seriation

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An efficient implementation of the Seriation 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.

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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.



[![Build Status](https://travis-ci.org/amamory/seriation.svg?branch=master)](https://travis-ci.org/amamory/seriation)

[![DOI](https://zenodo.org/badge/92440644.svg)](https://zenodo.org/badge/latestdoi/92440644)



## 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 (*amamory @ gmail com*)



## Inputs



The input file is a textual file describing an undirected network of nodes (in our examples the nodes are protein names). Example:


L7007 L7008

L7008 L7007

L7010 L7011

L7011 L7010

L7014 L7015

L7015 L7014

L7017 Z1275




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:




Protein	dim1

Z5822	0

Z5823	1

Z2911	2

Z2910	3

Z2909	4

Z4123	5

Z4124	6

Z3105	7

Z3106	8

...




The following image represents the Homo sapiens network with a *random ordering*.



![initial](initial.png)



The next image represents the Homo sapiens network **'seriated'**.



![final](final.png)



## Download and Instalation



The Seriation Package is developed in C and tested on Ubuntu 14.04.

* Download the [package](https://github.com/amamory/seriation/releases/latest) .

* 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




/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




## Download and Compilation



> sudo apt-get install git



> git clone https://github.com/amamory/seriation.git



> cd seriation



> gcc cfm-seriation.c -lm -lpthread -lrt -o cfm-seriation



## How to Use



type 'cfm-seriation' to show the options:




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




type to execute the seriation. This process can take about 12 minutes, depending on the CPU.



> ./cfm-seriation f=data/Homo_sapiens.dat m=3000 P



In case you want a video of the process, type to execute the seriation. 



> ./cfm-seriation f=/usr/share/cfm-seriation/data/Homo_sapiens.dat m=3000 P v



This will consume some extra time.




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% [====================================================================================================]




For a quicker test you can execute smaller dataset, like the Escherichia Coli.



> ./cfm-seriation f=Escherichia_coli.dat




Reading file...

	Proteins: 3598

	Interactions: 13687

Applying random order...

Saving initial order...

INITIAL Energy: 129449102

Ordering...

100% [====================================================================================================]

FINAL Energy: 129025784

Saving final order...

Done!




The results are save in a different directory for each execution. 



## Further Information



* [Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks](http://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](http://ieeexplore.ieee.org/document/7033586/)




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.




## 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.