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News

Aug 2013
yoshiko version 2.0

We have released yoshiko version 2.0, a mature version of our cluster editing algorithm. It has been implemented mostly by Emanuel Laude and contains a lot of helpful redcution rules from fixed parameter algorithmics and a powerful heuristic for large data sets.

24 Aug 2011
natalie version 2.0

We have released natalie version 2.0, a mature version of our network alignment algorithm.

27 Jun 2011
side chain placement

scp is a package that contains our code for exact side chain placement as used in a recent paper in Optimization Letters.

5 Mar 2010
heinz and BioNet

heinz now works together with the BioNet package.

17 Dec 2008
yoshiko/charles

The yoshiko/charles code is now online. The tool solves the cluster editing problem as well as its directed "cousin", the transitivity editing problem, to provable optimality.

1 Sep 2008
planet lisa moves to Amsterdam

The planet lisa project is now based at the Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands.

20 Jul 2008
ISMB 2008

Our paper Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach has won the oustanding paper award at ISMB 2008 in Toronto, Canada. See the heinz section for more information on our software to discover optimal subnetworks with respect to our signal-based scoring scheme of p-values.

Jul 2008
ISMB 2008

We will give a presentation at ISMB 2008 on Identifying Functional Modules in Protein-Protein Interaction Data: An Integrated Exact Approach. Our software is available as the heinz package.

Oct 07
Algorithmic Operations Research

Our theoretical lara paper has been accepted for publication in Algorithmic Operations Research.

27 Jul 07
BMC Bioinformatics

The paper describing the lara program has been accepted for publication in BMC Bioinformatics.

28 Jun 07
4SALE support for lara

lara has been integrated into the RNA alignment and editing framework 4SALE. Get the latest lara version that is compatible with 4SALE.

Natalie

The planet LiSA library is now hosted in "Amsterdam"

MOVED To https://github.com/ls-cwi/natalie

Introduction

natalie is a tool for pairwise global network alignment [1]. The current version is capable of reading in graphs in GraphML, GML, LGF (lemon graph format), and STRING format and computes an alignment. Output visualization is still very much neglected, but will be realized in the future. Source code is available upon request.


Usage

Usage:
  ./natalie [--help|-h|-help] [-beta num] [-c num] [-d] [-e num] [-g1 str]
     [-g2 str] [-gm str] [-if1 int] [-if2 int] [-ifm int] [-k int] [-l int]
     [-maxSwitches int] [-n int] [-nd int] [-no int] [-ns int] [-o str]
     [-of str] [-op int] [-phi num] [-s int] [-sf int] [-t int] [-tau num]
     [-v|--verbosity int] [-version] [-w]
Where:
  --help|-h|-help
     Print a short help message
  -beta num
     Parameter used in the objective function (default: 1)
  -c num
     Specifies the correlation threshold 
     (only used in conjunction with -ifm 2, default: 0.9)
  -d
     Force binary edge weights
  -e num
     Specifies e value cutoff 
     (only used in conjunction with -ifm 1 and -ifm 2, default: 10)
  -g1 str
     File name of input graph G_1
  -g2 str
     File name of input graph G_2
  -gm str
     File name in which matching edges of G_m are defined;
     if omitted, the complete graph is used
  -if1 int
     Specifies the input file format for G_1:
     0 - GML format
     1 - GraphML format
     2 - STRING format (default)
     3 - LGF format
     4 - CSV format
     5 - LEDA format
  -if2 int
     Specifies the input file format for G_2:
     0 - GML format
     1 - GraphML format
     2 - STRING format (default)
     3 - LGF format
     4 - CSV format
     5 - LEDA format
  -ifm int
     Specifies the input file format for G_m:
     0 - Candidate list
     1 - BLAST (default)
     2 - Co-expression
     3 - LGF
  -k int
     Number of nondecreasing iterations after which
     to update mu (default: 20)
  -l int
     Number of increasing iterations after which
     to update mu (default: 10)
  -maxSwitches int
     Maximum number of switches
     (only used in conjunction with -s 3, default: 3)
  -n int
     Number of iterations to compute (default -1: no limit)
  -nd int
     Number of dual descent steps before switching method
     in the combined solver (default: 100)
  -no int
     Number of outputs to generate (default 1)
  -ns int
     Number of subgradient steps before switching method
     in the combined solver (default: -1; switch when subgradient
     method has converged)
  -o str
     Output file name
  -of str
     Specifies the output file format:
     0 - DOT format
     1 - GML format
     2 - LGF format
     3 - SIF format (default)
     4 - JSON format
     5 - NEATO format
     6 - CSV (matched) format
     7 - CSV (unmatched in G_1) format
     8 - CSV (unmatched in G_2) format
     9 - CSV (alignment) format
  -op int
     Specifies parts of the matching graph to output:
     0 - Nodes and matching edges present in the solution
     1 - Nodes, matching edges and original edges present
         in the solution (default)
     2 - Nodes and matching edges present in the solution
         as well as all original edges
  -phi num
     Parameter phi of dual descent procedure
  -s int
     Specifies the solver to use:
     0 - Subgradient optimization
     1 - Dual descent method
     2 - Enhanced dual descent method
     3 - Combined method (default)
  -sf int
     Specifies the score function to be used:
     0 - Average weights (default)
     1 - Coexpression-based
  -t int
     Time limit in seconds (default -1: no limit)
  -tau num
     Parameter tau of dual descent procedure
  -v|--verbosity int
     Specifies the verbosity level:
     0 - No output
     1 - Only necessary output
     2 - More verbose output (default)
     3 - Debug output
  -version
     Show version number
  -w
     Web server mode


Sample data

The protein-protein interaction networks used in [1] are available via this link; the corresponding candidate matching edges can be downloaded here.


References

[1] El-Kebir M, Heringa J, Klau G, Langrangian Relaxation Applied to Sparse Global Network Alignment. http://arxiv.org/pdf/1108.4358v1.

Download

version date platform link description
2.0, 368 Jan 27, 2012 64 bit linux natalie2-linux64-v368 latest version
2.0, 368 Jan 27, 2012 32 bit linux natalie2-linux32-v368 latest version
2.0, 368 Jan 27, 2012 64 bit windows natalie2-win64-v368 latest version
2.0, 368 Jan 27, 2012 32 bit windows natalie2-win32-v368 latest version
2.0, 368 Jan 27, 2012 64 bit mac natalie2-mac64-v368 latest version
2.0, 300 Aug 24, 2011 64 bit linux natalie2-linux64-v300 version used for PRIB2011 paper
2.0, 300 Aug 24, 2011 32 bit linux natalie2-linux32-v300 version used for PRIB2011 paper
2.0, 300 Aug 24, 2011 64 bit windows natalie2-win64-v300 version used for PRIB2011 paper
2.0, 300 Aug 24, 2011 32 bit windows natalie2-win32-v300 version used for PRIB2011 paper
2.0, 300 Aug 24, 2011 64 bit mac natalie2-mac64-v300 version used for PRIB2011 paper
0.9 Dec 08, 2009 64 bit linux natalie 0.9 version used for computations in the APBC paper (BMC Bioinformatics)
Topic revision: r9 - 08 Mar 2017, BodoRiedigerKlaus
 
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