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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

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.


The planet LiSA library is now hosted in "Amsterdam"

ALERT! This entry is very much work in progress.

sally is a tool that solves the following combinatorial selection problem using Lagrangian relaxation.

Given k sets with n_i weighted elements per set (i = 1, ..., k) and a weighted k-partite graph G whose node set consists of the elements and whose edges links elements from different sets, choose exactly one element per set such that the induced k-partite graph has minimum weight.

This problem appears in many different areas, including protein side chain placement, frequency assignment, and RNA structure determination by exploiting homological relations.

Quick Start

Try running

sally -o ./sally.params

In sally.params you will find some options you can change, in particular the location and format of the data file.

More: to be done

Running sally

Manual goes here...



version date link description comments
1.0 18 Oct 07 sally 1.0 current release Linux, 32 bit
Topic revision: r3 - 28 Apr 2015, UnknownUser
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