Software of SCD BioIBioMedSMC
BIOI: Bioinformatics
ModuleMiner, 2008	ModuleMiner is a tool to detect similar cis-regulatory modules (CRMs) in a set of co-regulated or co-expressed genes. The algorithm takes as input a set of genes thought to have similar regulatory elements in their upstream regions (under the form of Ensembl gene IDs), and detects these similar CRMs. Apart from the CRMs near the given genes, the algorithm also creates a model of these similar CRMs and uses this model to find new target genes in the whole genome. The algorithm is available as an online tool that emails the results when ready.
LOOP, 2007	LOOP is a tool to analyze arrayCGH loop designs in which three patients are placed in a loop design, which is advantageous over the classical dye-swap approach. ArrayCGH is a microarray technology that can be used to detect aberrations in the ploidy of DNA segments in the genome of patients with congenital anomalies.
aBandApart, 2007	Biomedical literature provides a rich but unstructured source of associations between chromosomal regions and biomedical concepts. By mining MEDLINE abstracts, we annotate the human genome at the level of cytogenetic bands. Our method creates a set of chromosomal aberration maps that associate cytogenetic bands to biomedical concepts from a variety of controlled vocabularies, including disease, dysmorphology, anatomy, development, and Gene Ontology branches. The association between a band (e.g., 4p16.3) and a concept (e.g., microcephaly) is assessed by the statistical overrepresentation of this concept in the abstracts relating to this band. Our method is validated using existing genome annotation resources and known chromosomal aberration maps, and is further illustrated through a case study on heart disease. Our chromosomal aberration maps provide diagnostics support to clinical geneticists, aid cytogeneticists to interpret and report cytogenetic findings, and support researchers interested in human gene function
Bioconductor package "CALIB", 2007	“CALIB” is a new Bioconductor package which is for normalization of two-color microarray data. This approach is based on the measurements of external controls and estimates an absolute target level for each gene and condition pair, as opposed to working with log-ratios as a relative measure of expression. Moreover, this method makes no assumptions regarding the distribution of gene expression divergence.
CGHGate, 2007	As Microarray-CGH is introduced into the clinical practice for the identification of submicroscopic genomic aberrations, tools to handle related data become essential for clinical geneticists. CGHGate is a web application that combines a constitutional cytogenetics database and tools for search, visualisation, genome annotation and data mining. CGHGate is a database tool for storage, reporting and mining Array CGH Case reports in a clinical setting. It features a constitutional cytogenetics patient database, allows genome annotation, data mining, literature search, it identifies candidate genes for patient phenotypes in deletion and duplication regions, it generates clinical reports, ...
SynTReN, 2006	A Generator of synthetic gene expression data for design and analysis of structure learning algorithms. The software is provided as an executable jar file.
ReMoDiscovery, 2006	ReMoDiscovery is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles.
M@cBETH, 2005	The M@CBETH (a MicroArray Classification BEnchmarking Tool on a Host server) web service offers the microarray community a simple tool for making optimal two-class predictions. M@CBETH aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.
biomaRt, 2005	The package provides and API in R to query BioMart databases such as Ensembl, a software system which produces and maintains automatic annotation on metazoan genomes.
Endeavour, 2005	ENDEAVOUR is a software application for the computational prioritisation of `test genes', based on a set of `training genes'. The ranking of a test gene is based on its similarity with the training genes, using different information sources such as MEDLINE abstracts and LocusLink textual descriptions, Gene Ontology annotation, BIND protein interactions, BIND protein interactions, Transcription factor binding sites (TFBS) and other.
BlockAligner, 2005	The BlockAligner uses a local ungapped alignment strategy based on dynamic programming to mutually compare conserved promoter regions (i.e. blocks) represented by their respective motif models.
BlockSampler, 2005	The BlockSampler is used to find conserved blocks in the upstream region of sets of orthologous genes.
TOUCAN2, 2004	TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes: comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes. It is a platform independent, standalone Java application that is tightly linked with Ensembl, and was built using the BioJava package. SOAP web services are used to remotely access multiple algorithms for comparative genomics, motif detection, and module detection.
TXTGate, 2004	TXTGate is a literature index database and is part of an experimental platform to evaluate (combinations of) information extraction and indexing from a variety of biological annotation databases. It is designed towards the summarization and analysis of groups of genes based on text.
INCLUSive, 2003	INCLUSive is a suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements. The tools allow for normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval and detection of known and unknown regulatory elements. All tools are available via different web pages and as web services.
Adaptive Quality-based Clustering (AQBC), 2002	AQBC is a heuristic, iterative two-step algorithm to cluster gene expression data. First, we find in the high-dimensional representation of the data a sphere where the ‘density’ of expression profiles is locally maximal. In a second step, we derive an optimal radius of the cluster (adaptive approach) so that only the significantly coexpressed genes are included in the cluster. By inferring the radius from the data itself, the biologist is freed from finding an optimal value for this radius by trial-and-error.
MotifSampler, 2001	MotifSampler tries to find over-represented motifs in the upstream region of a set of co-regulated genes. This motif finding algorithm uses an extended version of Gibbs sampling to find the position probability matrix that represents the motif. The main extension are the use of higher-order background models to improve the robustness of the motif finding and a probabilistic framework to estimate the number of motif occurrences in a sequences. Both a web interface and a standalone version are available.
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BIOMED: Biomedical Data Processing
SPID, 2008	SPID is to provide the user with tools capable to *simulate*, *preprocess*,* process* and *classify* in vivo and ex vivo MRS signals. These tools are embedded in a matlab graphical user interface (*GUI*). for more information...
EEG Signal Processing, 2006	A semi-automatic tool is available for muscle artifact removal from the EEG for academic use.
AQSES, 2005	The aqsesGUI is a software package for processing magnetic Resonance Spectroscopy signals. The package contains methods to load, preprocess and process MRS data. It uses a plugin system to load all the functionalities.
Structured matrices, 2004	The package contains ANSI C software with Matlab mex interface for structured total least squares estimation problems. The allowed structures in the data matrix are block-Toeplitz, block-Hankel, unstructured, and noise free.
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SMC: Systems, Models and Control
The GLYCENSIT Procedure, 2006	The GLYCENSIT procedure is a method to validate (both discrete and near-continuous) glucose sensor devices (test sensor) with regards to a reference glycemia sensor. Possible consistent measurement behavior as a function of the glycemic range (phase 1) and the number of measurement errors with respect to a standard criterion for binary assessment of glucose sensors (phase 2) are successively analysed. In the third phase tolerance intervals that indicate possible sensor deviations for new observations (with the test sensor) are computed.
Deterministic Linear System Identification, 2005	A Matlab toolbox for exact linear time-invariant system identification is presented. The emphasis is on the variety of possible ways to implement the mappings from data to parameters of the data generating system. The considered system representations are input/state/output, difference equation, and left matrix fraction.
Approximate Linear System Identification, 2004	A Matlab function for approximate identification based on misfit minimization. Although the problem formulation is representation independent, we use input/state/output representations of the system in order to allow maximum compatibility with other software packages for system identification, analysis, and design.
LS-SVMlab, 2002	The Matlab/C toolbox LS-SVMlab1.5 contains a variety of techniques and algorithms for Least-Squares Support Vector Machines (LS-SVM). It contains tools for nonlinear regression, function estimation and classification, as well as implementations for related kernel methods.
SLICOT, 2000	The freeware subroutine library SLICOT provides Fortran 77 implementations of numerical algorithms for computations in systems and control theory. Based on numerical linear algebra routines from BLAS and LAPACK libraries, SLICOT provides methods for the design and analysis of control systems.
DAISY, 2000	The goal of this DAtabase for the Identification of SYstems to serve as a platform for the interchange of information and data in the field of System Identification. System Identification is the discipline of making mathematical models of systems, starting from experimental data, measurements, observations. Typically, a certain model structure is chosen by the user which contains unknown parameters (i.e. one puts forward a certain parameterisation). Having the model of a system is often very important for analysis, simulation, prediction, monitoring, diagnosis, control system design,...
Subspace Identification, 1996	This package contains Subspace algorithms described in the book "Subspace Identification for Linear Systems: Theory - Implementation - Applications" By Peter Van Overschee and Bart De Moor, Kluwer Academic Publishers, 1996. It also provides an electronic copy of the mentioned book.
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