Software
To carry out our research projects, our group develop a myriad of software, using different programming languages and techniques. We list below some of them, including reference for the project they are related and a link for the source code repository (importantly, our programs are always available as open and free software, since we believe that is a good practice in Science). As in the case of the research projects, you can contact us if you are interested to contribute to the further development of any of those software and/or the tailoring of them to your problem.featsel
featsel is a framework especially designed for the benchmarking of feature selection algorithms and cost functions. Through a clean object-oriented structure and coded in C++, this framework allows the user to easily include new algorithms and/or cost functions and to carry out fast computational experiments. Moreover, featsel allows the user to take advantage of the fact that the search space of a feature selection procedure can be organized into a Boolean lattice; to this end, several methods are included in this framework especially for Boolean manipulation of feature subsets. featsel is also accompanied by several scripts to assist the user in the inclusion and removal of algorithms and cost functions, to carry out benchmarking experiments and to create tables and graphs with the obtained results.
The featsel framework architecture was firstly presented by Reis, Estrela et al. (2017), and was used to generate results of the computational experiments presented in Reis et al. (2019). Currently, it is being used in the project "Development of ABC-based approaches to tackle the lack of isolation problem in signaling pathway".
Source code license: GNU GPL-3.0.
Source code availability: github.com/msreis/featsel.
ReDyMo
The Replication Dynamic Model (ReDyMo) is a stochastic dynamic model simulator that reproduces the DNA replication process of trypanosomatids. Initially, we focused on Trypanosoma brucei strain TREU927. This simulator is capable of:
- Calculation of various relevant properties about the replication process, including S-phase duration, mean inter-origin distance between replication origin sites, and the achieved replication percentage given a time limit;
- Storage of information about each step of the simulation, such as the replication stage at each model simulation iteration and whether any collisions happened during a given iteration;
- Storage of information regarding the replication timing program, that is, for each base pair it is recorded at which simulation iteration it was replicated;
- Simulation of replication-transcription conflicts with a variety of input parameters like replication machinery speed and transcription frequency;
- Simulation of dormant origins firing.
Source code license: GNU GPL-3.0.
Source code availability:
github.com/msreis/ReDyMo (Python version)
github.com/msreis/ReDyMo-CPP (C++ version)
MITE
The Matrix of Intensity by Time of Elution (MITE) is a collection of programs for the designing of phyloproteomic cladograms (trees) based on mass spectrometry-based proteomics data (either identified peptides or raw data) and using the Markov Chain Monte Carlo (MCMC) procedure implemented in the MrBayes software. Those programs were coded in Python and include procedures to prepare the NEXUS files necessary for the MCMC method and also the CADM statistical test for comparison of the yielded cladograms.
Details about the programs that compose MITE can be found at Victor Raposo's term paper and also at Gustavo Maciel's term paper. This software is being developed in the project "Unsupervised learning of snake venom proteomes yielded by mass spectrometry-based assays".
Source code license: GNU GPL-3.0.
Source code availability: github.com/msreis/MITE.
Scientiometer
Scientiometer is a platform for scientometric analyses of research institutions. Although Scientiometer was originally designed for evaluation of researchers and scientific production at Butantan Institute, this software may be employed for evaluation of any other institution. Scientiometer is being implemented using Ruby on Rails and also the Vue.js web framework.
The architecture of Scientiometer initial components (e.g., relational database and report submission system) is described in Bruno Scholl's term paper (in Portuguese). This software is used in the project "Development of an information system for the gathering and analysis of scientific production reports".
Source code license: GNU GPL-3.0.
Source code availability: github.com/msreis/Scientiometer.