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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.

planet LiSA

The Project has moved again.
On Interest Contact Prof. Gunnar Klau, Heinrich Heine University Düsseldorf

Part of the planet LiSA library is hosted in "Amsterdam"

LiSA used to be a Library of Structural Analysis algorithms and then grew into something more diverse. It is a collection of C++ software tools, loosely connected by a library. LiSA provides sophisticated algorithms and data structures for analysing structural information in the life sciences. The applications range from RNA and protein secondary structure alignment over finding clusters and modules in biological networks to network alignment.

The following old binary versions of LiSA tools are available for download.

Some of these MOVED To https://github.com/ls-cwi/
yoshiko transitivity and cluster editing
heinz heavy induced subnetworks (maximum-weight connected subgraphs)
lara (multiple) sequence-structure RNA alignment
natalie network alignment
paul protein distance matrix alignment
peggi permutation equivalence based on generalized subgraph isomorphism
plara progressive multiple sequence-structure RNA alignment
scp side-chain placement

Until September 2008, the LiSA project was based at the Mathematics in Life Sciences group at the Freie Universität Berlin. Now the project is carried out at the Centre for Mathematics and Computer Science (CWI) in Amsterdam, The Netherlands. It was partly supported by the DFG fund KL1390/2-1.
Topic revision: r34 - 08 Mar 2017, BodoRiedigerKlaus
 
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