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Pedro T. Monteiro
  Tecnico
INESC-ID
Address: INESC-ID Lisboa, SAT group
Rua Alves Redol 9
P-1000-029 Lisboa
PORTUGAL
Email:
Tel: (+351) 21 3100 320

Index - Teaching - Research - Software

Software

PathoYeastract URL: http://pathoyeastract.org
PathoYeastract (Pathogenic Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of all known regulatory associations between transcription factors (TF) and target genes in pathogenic Candida species, based on hundreds of bibliographic references. It provides currently information for the first and second most prevalent of pathogenic yeasts, C. albicans and C. glabrata. Expansion to six additional pathogenic Candida species is underway.
Work in progress in collaboration with Pedro Pais, Catarina Costa, Sauvagya Manna, Isabel Sá-Correia and Miguel C. Teixeira, at Instituto Superior Técnico and INESC-ID.

bioLQM 0.4 URL: https://github.com/colomoto/bioLQM
bioLQM is a Java library which aims to improve interoperability between logical modeling tools, motivated by the CoLoMoTo discussion group. For this, it defines some core interfaces for the definition of Logical Models, as well as some tools for their manipulation.

EpiLog 0.4 URL: http://epilog-tool.org
EpiLog is a tool used for qualitative simulations of logical models of epithelial patterning. It defines an epithelium as a 2D grid of hexagonal cells, each containing a LRG regulating the internal proper components. Additionally, it integrates onto input components of each cell, the table environmental influences as well as varying signals from neighbouring cells. The software provides a graphical user interface representing the hexagonal grid of cells to facilitate the definition of initial conditions, definition of perturbations, and visualization of the simulation.
Work in progress in collaboration with Pedro L. Varela, Camila Veludo, Adrien Fauré and Claudine Chaouiya, at Instituto Gulbenkian de Ciência, Yamaguchi University, Instituto Superior Técnico and INESC-ID.

GINsim 2.9.4 URL: http://ginsim.org
GINsim (Gene Interaction Network simulation) is a computer tool for the modeling and simulation of models of genetic regulatory networks, based on the multilevel logical formalism. Networks are modeled in terms of logical regulatory graphs, where nodes represent regulatory components and edges represent regulatory associations. Then the evolution of each component is described by a logical rule encoded as a Multivalued Decision Diagram.
Work done in collaboration with Aurélien Naldi, Lionel Spinelli, Nuno Mendes, Denis Thieffry and Claudine Chaouiya, at Instituto Gulbenkian de Ciência, École Normale Supérieure, Université de Lausanne, Instituto Superior Técnico and INESC-ID.

BoolNetR2GINsim URL: https://github.com/ptgm/BoolNetR2GINsim
BoolNetR2GINsim is a small script for the generation of random boolean logical models, using the BoolNet R package, and write them into the GINML format. The models are generated by randomly selecting (uniform distribution) the parameters regulating each gene. The number of possible regulators for each gene (influencing the number of parameters) can be either: by considering a fixed number of regulators (same number) for all genes, or by drawing the number of regulators from a poisson distribution for each gene.
Work done at Instituto Gulbenkian de Ciência, Oeiras.

PHYLOVIZ plugins LoadMLSTDBs/PubMLST/DataStats/SynthData URL: http://www.phyloviz.net/wiki/
PHYLOViZ is platform independent JAVA software that allows the analysis of sequence-based typing methods that generate allelic profiles and their associated epidemiological data.
The PHYLOViZ LoadMLSTDBs endows PHYLOViZ with the capability of loading from MLST public repositories, typing and sequence data.
The PHYLOViZ PubMLST module endows PHYLOViZ with a webservice client for the loading of PubMLST typing and isolate data through a SOAP API.
The PHYLOViZ DataStats module provides the relative frequencies of the typing/isolate data.
The PHYLOViZ SynthData provides a plugin for PHYLOViZ with the capability to generate its own MLST synthetic data.
Work done in collaboration with Alexandre A. Francisco, Cátia Vaz, João A. Carriço and Mário Ramirez, at INESC-ID and Instituto de Medicina Molecular.

YEASTRACT-SERVICES URL: http://yeastract.com/services/
WEBSERVICES is a set of resources for accessing the curated biological data, provided by YEASTRACT, through RESTful web services. It provides the user with the power to develop their own views of the data, by retrieving and exploiting them according to their needs. WEBSERVICES provides the output for the implemented resources through a RESTful JSON API.
Work done in collaboration with Dário Abdulrehman, Miguel C. Teixeira, Nuno P. Mira, Artur B. Lourenço, Sandra C. dos Santos, Tânia R. Cabrito, Alexandre P. Francisco, Sara C. Madeira, Ricardo S. Aires, Arlindo L. Oliveira, Isabel Sá-Correia and Ana T. Freitas, at INESC-ID and IST.

PROCRUSTES: Pattern-based property editor URL: http://ibis.inrialpes.fr/article938.html
Models of the dynamics of cellular interaction networks have become increasingly large in recent years. The study of these models by analysis and simulation tools generates a large number of predictions of the possible dynamical behaviors of the system. When representing the system dynamics by means of discrete state transition graphs (e.g., Kripke structures), it becomes possible to use formal verification techniques for the verification of certain properties of interest. However, this requires the formulation of the properties in temporal logic, which is not evident for the non-expert user.
In order to deal with this problem, a set of patterns (high-level query templates) were defined to capture recurring biological questions posed by modelers. The patterns consist of structured natural language phrases which can be translated into temporal logic formulas.
Procrustes is a pattern-based property editor that enables the translation of each pattern into a temporal logic formula (currently CTL, CTRL and mu-calculus are supported).
Work done in collaboration with Ana T. Freitas, Radu Mateescu and Hidde de Jong, at INRIA Grenoble - Rhône-Alpes.

Genetic Network Analyzer 7.0 URL: http://ibis.inrialpes.fr/article122.html
Genetic Network Analyzer (GNA) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data.
Work done in collaboration with Bruno Besson, Estelle Dumas, Grégory Batt, Michel Page and Hidde de Jong, at INRIA Grenoble - Rhône-Alpes.

YEASTRACT-DISCOVERER URL: http://yeastract.com/discoverer/
DISCOVERER provides a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA and RISO algorithms. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database.
Work done in collaboration with Nuno Mendes, Miguel C. Teixeira, Alexandre Francisco, Sofia d'Orey, Sandra Tenreiro, Nuno P. Mira, Hélio Pais, Alexandra Carvalho, Artur Lourenço, Isabel Sá-Correia, Arlindo L. Oliveira and Ana T. Freitas, at INESC-ID and IST.

YEASTRACT URL: http://yeastract.com
(Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of regulatory associations between transcription factors and target genes in Saccharomyces cerevisiae, based on more than 1000 bibliographic references. It allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature, as well as a useful mechanism for grouping a list of genes based on their regulatory associations with known transcription factors.
Work done in collaboration with Miguel C. Teixeira, Pooja Jain, Sandra Tenreiro, Alexandra R. Fernandes, Nuno P. Mira, Marta Alenquer, Ana T. Freitas, Arlindo L. Oliveira and Isabel Sá-Correia, at INESC-ID and IST.

DECIDE URL: http://decide.inesc-id.pt (discontinued)
DECIDE was an interactive tool for the automatic evaluation of gene finding programs. This tool provided a standard environment, allowing new gene finding programs to be compared with existing ones. It could also be used to help the user in the choice of the most appropriate program and parameter setting to perform gene finding in a particular organism or dataset. To simplify the evaluation and the incorporation of new programs, a publicly available Web interface was developed. Several well known gene finding programs and datasets were integrated and were accessible through an unified interface. The accuracy of the programs was reported as a function of several accuracy measures at different levels, that included: nucleotide level, exon level, exon length, signal type and G+C content.
Work done in collaboration with Ana P. Ramalho, Ana T. Freitas and Arlindo L. Oliveira, at INESC-ID and IST.