{"id":21297966,"url":"https://github.com/amamory/seriation","last_synced_at":"2025-10-18T14:33:58.167Z","repository":{"id":55580729,"uuid":"92440644","full_name":"amamory/seriation","owner":"amamory","description":"An efficient implementation of the Seriation problem which 'finds a suitable linear order for a set of objects'. 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It has been used to order a network of proteins such that 'related' nodes are closer in the other.\n\n[![Build Status](https://travis-ci.org/amamory/seriation.svg?branch=master)](https://travis-ci.org/amamory/seriation)\n[![DOI](https://zenodo.org/badge/92440644.svg)](https://zenodo.org/badge/latestdoi/92440644)\n\n\n## Authors\n\nThe Seriation Package was developed by [Felipe Kuentzer](http://lattes.cnpq.br/1979213773480902), in collaboration with \nDouglas 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).\n\n**Contact information**: Alexandre Amory (*amamory @ gmail com*)\n\n## Inputs\n\nThe input file is a textual file describing an undirected network of nodes (in our examples the nodes are protein names). Example:\n\u003cpre\u003e\nL7007 L7008\nL7008 L7007\nL7010 L7011\nL7011 L7010\nL7014 L7015\nL7015 L7014\nL7017 Z1275\n\u003c/pre\u003e\n\nIn 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.\n\n## Outputs\n\nThe output is a text file with the order of the network nodes. Example:\n\n\u003cpre\u003e\nProtein\tdim1\nZ5822\t0\nZ5823\t1\nZ2911\t2\nZ2910\t3\nZ2909\t4\nZ4123\t5\nZ4124\t6\nZ3105\t7\nZ3106\t8\n...\n\u003c/pre\u003e\n\nThe following image represents the Homo sapiens network with a *random ordering*.\n\n![initial](initial.png)\n\nThe next image represents the Homo sapiens network **'seriated'**.\n\n![final](final.png)\n\n\n## Download and Instalation\n\nThe Seriation Package is developed in C and tested on Ubuntu 14.04.\n* Download the [package](https://github.com/amamory/seriation/releases/latest) .\n* Is recommended to update your packages before the instalation:\n\u003e sudo apt-get install update\n* To install, you can double-click it or execute:\n\u003e sudo dpkg -i cfm-seriation_1.0-1_amd64.deb\n* In case of missing dependencies, try: \n\u003e sudo apt-get install -f\n* To unistall:\n\u003e sudo dpkg -r cfm-seriation\n\n* this distribution has the following files\n\n\u003cpre\u003e\n/usr/share/cfm-seriation/bin/             Executable file\n/usr/share/cfm-seriation/etc/             Auxiliar used to plot charts with GNUPLOT\n/usr/share/cfm-seriation/data/            Biological input networks\n/usr/share/cfm-seriation/src/             Source code in C\n\u003c/pre\u003e\n\n\n## Download and Compilation\n\n\u003e sudo apt-get install git\n\n\u003e git clone https://github.com/amamory/seriation.git\n\n\u003e cd seriation\n\n\u003e gcc cfm-seriation.c -lm -lpthread -lrt -o cfm-seriation\n\n\n## How to Use\n\ntype 'cfm-seriation' to show the options:\n\n\u003cpre\u003e\ncfm-seriation\n\nUsage: cfm-seriation [OPTION...]\n\n Seriation Parameters:\n   f=[NETWORK FILE].dat       Network file path name\n   o=[ORDER FILE].dat         Apply initial order\n   i=[INTERVAL]               Number of isothermal steps\n   m=[STEPS]                  Number of steps\n   c=[FACTOR]                 Cooling factor\n   a=[ALPHA]                  Alpha value\n   p=[PERCENTUAL]             Percentual energy for initial temperature\n   s=[SEDD]                   Random seed\n   P                          Plot graphs\n   v                          Generate video\n\u003c/pre\u003e\n\ntype to execute the seriation. This process can take about 12 minutes, depending on the CPU.\n\n\u003e ./cfm-seriation f=data/Homo_sapiens.dat m=3000 P\n\nIn case you want a video of the process, type to execute the seriation. \n\n\u003e ./cfm-seriation f=/usr/share/cfm-seriation/data/Homo_sapiens.dat m=3000 P v\n\nThis will consume some extra time.\n\n\u003cpre\u003e\nUsage: cfm-seriation [OPTION...]\n\n Seriation Parameters:\n   f=[NETWORK FILE].dat       Network file path name\n   o=[ORDER FILE].dat         Apply initial order\n   i=[INTERVAL]               Number of isothermal steps\n   m=[STEPS]                  Number of steps\n   c=[FACTOR]                 Cooling factor\n   a=[ALPHA]                  Alpha value\n   p=[PERCENTUAL]             Percentual energy for initial temperature\n   s=[SEDD]                   Random seed\n   P                          Plot graphs\n   v                          Generate video\n\nReading file...\n\tProteins: 9684\n\tInteractions: 163509\nApplying random order...\nSaving and plotting initial order...\nINITIAL Energy: 4123514310\nOrdering...\n100% [====================================================================================================]\n\u003c/pre\u003e\n\nFor a quicker test you can execute smaller dataset, like the Escherichia Coli.\n\n\u003e ./cfm-seriation f=Escherichia_coli.dat\n\n\u003cpre\u003e\nReading file...\n\tProteins: 3598\n\tInteractions: 13687\nApplying random order...\nSaving initial order...\nINITIAL Energy: 129449102\nOrdering...\n100% [====================================================================================================]\nFINAL Energy: 129025784\nSaving final order...\nDone!\n\u003c/pre\u003e\n\nThe results are save in a different directory for each execution. \n\n## Further Information\n\n\n* [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.\n\n\n* 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).\n\n## License\n\nThe source code is distributed under the terms of the GNU General Public License v3 [GPL](http://www.gnu.org/copyleft/gpl.html).\n\n## How to Cite this Package\n\nIf you are using this package on your research, please cite our paper:\n* [Optimization and Analysis of Seriation Algorithm for Ordering Protein Networks](http://ieeexplore.ieee.org/document/7033586/)\n\n\u003cpre\u003e\nKUENTZER, Felipe A. et al. Optimization and analysis of seriation algorithm for ordering protein networks. \nIn: IEEE International Conference on Bioinformatics and Bioengineering (BIBE), 2014. p. 231-237.\n\u003c/pre\u003e\n\n## Where Seriation is Used\n\nIf you are using the Seriation Package, please send an email to *alexandre.amory at pucrs.br* so we can update this list of users:\n* [Transcriptogrammer](http://lief.if.ufrgs.br/pub/biosoftwares/transcriptogramer/)\n\n## Similar Packages\n\n* [R Package seriation](http://www.jstatsoft.org/v25/i03), available at http://cran.r-project.org/web/packages/seriation/index.html.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Famamory%2Fseriation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Famamory%2Fseriation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Famamory%2Fseriation/lists"}