BIOSYSTEMS - Software Tools


MERLIN - MEtabolic models Reconstruction using genome-scaLe INformation

merlin, is a user-friendly program that performs functional genomic annotations of lists of genes. Merlin retrieves information of each homologue and automatically scores the results, allowing the user to change the score selection, and dynamically (re-)annotate the genome. Merlin expedites the transition from genome-scale data to SBML metabolic models, allowing the user to have a preliminary view of the biochemical network.

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JECoLi - Java Evolutionary Computation Library

This work proposes JECoLi-a novel Java-based library for the implementation of meta-heuristic optimization algorithms with a focus on Genetic and Evolutionary Computation based methods. The library was developed based on the principles of flexibility, usability, adaptability, modularity, extensibility, transparency, scalability, robustness and computational efficiency. The project is open-source, so JECoLi is made available under the GPL license, together with extensive documentation and examples, all included in a community Wiki-based web site ( JECoLi has been/is being used in several research projects that helped to shape its evolution, ranging application fields from Bioinformatics, to Data Mining and Computer Network optimization.

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OptFerm - Computational Platform for the Simulation and Optimization of Fermentation Processes

The aim of this project is to offer a platform-independent, user-friendly, open-source and extensible environment for Bioengineering process optimization that can be used to increase productivity. This tool is focused in optimizing a feeding trajectory to be fed into a fed-batch bioreactor and to calculate the best concentration of nutrients to initiate the fermentation.Also, contains a module for the estimation of kinetic and yield parameters, allowing the use of experimental data obtained from batch or fed-batch fermentations to reach the best possible model setup.

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@Note - A workbench for Biomedical Text Mining

Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. However, most efforts have addressed the benchmarking of new algorithms rather than user operational needs. Bridging the gap between BioTM researchers and biologists’ needs is crucial to solve real-world problems and promote further research. We present @Note, a platform for BioTM that aims at the effective translation of the advances between three distinct classes of users: biologists, text miners and software developers. Its main functional contributions are the ability to process abstracts and full-texts; an information retrieval module enabling PubMed search and journal crawling; a pre-processing module with PDF-to-text conversion, tokenisation and stop-word removal; a semantic annotation schema; a lexicon-based annotator; a user-friendly annotation view that allows to correct annotations and a Text Mining Module supporting dataset preparation and algorithm evaluation. @Note improves the interoperability, modularity and flexibility when integrating in-home and open- source third-party components. Its component-based architecture allows the rapid development of new applications, emphasizing the principles of transparency and simplicity of use. Although it is still on-going, it has already allowed the development of applications that are currently being used.

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OptFlux - computational platform for metabolic engineering

OptFlux is an open-source and modular software aimed at being the reference computational platform in the field of Metabolic Engineering. It is the first tool to incorporate strain optimization tasks using Evolutionary Algorithms/ Simulated Annealing metaheuristics. It also allows the use of stoichiometric metabolic models for phenotype simulation of both wild-type and mutant organisms, Metabolic Flux Analysis and pathway analysis through the calculation of Elementary Flux Modes. The software supports importing/ exporting to several flat file formats and it is compatible with the SBML standard. The OptFlux software is freely available, together with documentation and other resources. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities.

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FRAMED - python package for analysis and simulation of metabolic models

The main focus is to provide support for different modeling approaches. Modeling: Constraint-based models, Kinetic models, Bioprocess models; I/O: Import/Export from SBML and/or plain text formats; Solver support: Gurobi, CPLEX, GLPK; COBRA tools: Simulation: FBA, pFBA, loopless-FBA, MOMA, linearMOMA, ROOM; Analysis: FVA, gene essentiality, PhPP, flux envelope plots; Omics integration: GIMME, E-Flux; Strain design: brute force, hill climbing; Kinetic tools: Time-course and steady-state simulation, Parameter and flux sampling, Calibration from metabolomics data; Bioprocess modeling: Dynamic FBA (single and multi-species).

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optimModels - The Python framework for strain design of single and microbial community cultures.

It allows simulating different kinetic metabolic models considering different phenotypes and perform the optimization using evolutionary computation.

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JBiclustGE - Algorithms for Gene Expression Data Analysis

Java API with Unified Biclustering Algorithms for Gene Expression Data Analysis

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Specmine - A package for metabolomics data analysis

A R package providing a set of functions for metabolomics data analysis, including data loading in different formats, pre-processing, univariate and multivariate data analysis, machine learning and feature selection. The package supports the analysis of data from the main experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment, promoting the rapid development and sharing of data analysis pipelines

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