Pedro T. Monteiro @ INESC-ID/IST

		Pedro T. Monteiro
		Affiliation:	INESC-ID / IST - Universidade de Lisboa
		Address:	INESC-ID Lisboa Rua Alves Redol 9 P-1000-029 Lisboa PORTUGAL
		Email:
		Telef:	Alameda campus - ext: 2320 / tel: +351 21 3100 320 TagusPark campus - ext: 5281

pyFunctionHood

URL: https://github.com/ptgm/pyfunctionhood
pyFunctionHood is a Python library that implements the set of rules described in arxiv:2407.01337 to compute the immediate neighbours of a given monotone non-degenerate Boolean function, without the need to generate the whole function space. This work corrects and extends our previous work available in https://github.com/ptgm/functionhood/.
Work done in collaboration with Patrícia Tenera Roxo, Vasco Manquinho, José E.R. Cury and Claudine Chaouiya, at Universidade Federal de Santa Catarina, Université de Marseille, Instituto Superior Técnico and INESC-ID.

CommunityYeastract

URL: https://gitlab.com/oliveira.jorge.88/web/
CommunityYeastract is a new tool for the systematic conversion of genomic sequences into organism focused databases that provide genome annotation at the gene and promoter levels. From a genome of interest from NCBI in the GenBank Flat File (.gbff) format, and with a minimum set of commands, the setup procedure enables to have all the information parsed, organized in a local database and provide a local web interface with similar tools to the ones available in the Yeastract database. This permits other communities to install the platform independently, without any constraints, thus benefiting from the experience gathered with the construction and continuous support of the YEASTRACT+ portal.
Work done in collaboration with Jorge Oliveira, Miguel Antunes, Cláudia Godinho, Miguel C. Teixeira and Isabel Sá-Correia, at Instituto Superior Técnico and INESC-ID.

ModRev

URL: https://filipegouveia.github.io/ModRev/
ModRev is a command line tool to revise Boolean logical models of biological regulatory networks. It is able to repair inconsistent Boolean models considering one two modes: a set of stable state observations; and a set of time-series observations. For the latter, it supports both synchronous and asynchronous update schemes.
Work in progress in collaboration with Filipe Gouveia and Inês Lynce, at INESC-ID.

FunctionHood

URL: https://github.com/ptgm/functionhood
FunctionHood is a Java library to locally compute the set of direct neighbours of any monotone Boolean Function. It considers the set of rules described in to avoid generating all possible monotone Boolean functions.
Work done in collaboration with José E.R. Cury and Claudine Chaouiya, at Universidade Federal de Santa Catarina, Instituto Gulbenkian de Ciência and INESC-ID.

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 currently provides information for the prevalent of pathogenic yeasts, C. albicans, C. glabrata, C. parapsilosis and C. tropicalis. Expansion to 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

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

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

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 writing 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.