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News
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 comparability 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.LiSA Web
LiSA is the Library of Structural Analysis algorithms. It is an open source C++ software library providing sophisticated algorithms and data structures for comparing, analysing, and aligning structural information in the life sciences. The applications range from RNA and protein secondary structure alignment via a collection of threading algorithms to the comparison of complex networks. Many users will be interested only in special LiSA functionality and do not want to download the whole library and compile it. Therefore, we offer binary versions of so-called LiSA tools for download. More precisely, LiSA currently contains| charles | hierarchical disease classification based on noisy data (optimal comparability editing) |
| heinz | identification of heavy induced subnetworks (maximum-weight connected subgraphs) |
| lara | multiple sequence-structure alignment of RNA sequences by means of Lagrangian relaxation based on all pairwise sequence-structure alignments |
| natalie | network alignment tool |
| paul | protein distance matrix alignment based on Lagrangian relaxation |
| peggi | permutation equivalence based on generalized subgraph isomorphism |
| plara | progressive multiple sequence-structure alignment of RNA sequences by means of Lagrangian relaxation |
| scp | exact side-chain placement using a Lagrangian branch-and-bound approach |
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Topic revision: r29 - 04 Mar 2011, GunnarKlau
