LUAR is a laboratory with ten main research interests described in the projects bellow. Its diverse nature contributes to a rich and multidisciplinary enviroment, that fosters interaction and intelectual growing among its members.
PRODIS: PRODIS (Proteomics Database Integrated System), a system for proteomic experimental data management. The proposed system enables an efficient management of the proteomic experimentation workflow, simplifies controlling experiments and associated data and establishes links between similar experiments through the experiment tracking function. PRODIS is fully web based which simplifies data upload and gives the system the flexibility necessary for use in complex projects. Data from Liquid Chromatography, 2D-PAGE and Mass Spectrometry experiments can be stored in the system. The system allows the upload, parsing of files, storage and display of experiment results and images in the main formats used in proteomics laboratories: for chromatographies the chromatograms and lists of peaks resulting from separation are stored; For 2D-PAGE images of gels and the files resulting from the analysis are stored, containing information on positions of spots as well as its values of intensity, volume, etc; For Mass Spectrometry, PRODIS presents a function for completion of the mapping plate that allows the user to correlate the positions in plates to the samples separated by 2D-PAGE. Furthermore PRODIS allows the tracking of experiments from the first stage until the final step of identification, enabling an efficient management of the complete experimental process.
Conclusions: The construction of data management systems for Proteomics data importing and storing is a relevant subject. PRODIS is a system complementary to other proteomics tools that combines a powerful storage engine (the relational database) and a friendly access interface, aiming to assist Proteomics research directly at data handling and storage.
SIGLa: The SIGLa project addresses the construction of a LIMS for Biology developed using Proteomics data as a model. SIGLa utilizes at its core a workflow system, allowing the users to specify protocols, parameters and instruments used as well as results produced and associated publications. The system has been developed using a web interface and uses Shark as the primary workflow management tool. Later the functionalities of the system will be extended to include other types of Biological experimentation besides Proteomics.
Project MODEL CHECKING
Formal verification is a methodology to model and analyze computer systems to determine if properties are true or not in the given model. The verification algorithms explore the state space of the system exhaustively and determine with certainty the validity of properties for the models. Efficient representations include BDDs and SAT solvers, and are able to analyze successfully a number of complex real systems. In this project we are studying new representations for the model and new ways of modelling systems to increase the efficiency of the verification.
Project SYSTEMS BIOLOGY
SYSTEMS BIOLOGY: In this project we use probabilistic model checking tools to model and analyze biological systems and understand better their behavior. The use of formal methods enable us to create predictive models that can uncover rare but important events that would otherwise go unnoticed. Currently we are studying cell membrane ion transport systems, namely ion pumps and channels, and how they react to the presence of toxins. These systems are important cell structures that would endanger an individual if its regular behavior was compromised. Some toxins such as palytoxin can disrupt regular ion pump behavior, essentially turning it into an ion channel.
P2PTV: Live streaming on the Internet has become a reality, with the number of streams being transmitted growing each day. Nevertheless, current tools are limited in their efficiency and in robustness. We have developed TVPP, a live streaming system that uses P2P technology to increase its efficiency and reduce server bandwidth requirements. We are currently exploring new algorithms to increase TVPP efficiency through a better choice of partners, video chunks and other paramenters during execution.
ELISA: An automated equipment for clinical diagnoses based on ELISA and Biochemistry
Projeto ELISA: This project aims to develop a fully automated equipment, small to medium sized, to be used by clinical analysis laboratories to perform diagnostic tests, based on biochemical and ELISA methodology. The project includes the development of a software for equipment control and data management to enable automatic operation and analysis of data generated in an integrated manner. This system will allow not only the operation of the equipment, but its configuration and programming as well as management of data generated by it in a broad and integrated way. The data generated for analysis will be processed by the system, stored in a database and made available via the web for both the laboratory and the client in a safe and simplified way. The main goal of this project is an integrated solution for automation of clinical laboratories to simplify the laboratorial routine and a laboratory data management making the process of request for examination and delivery the result faster, more secure and transparent.
Flux-MED: A LIMS for management of medical research and data
Flux-MED: The amount of data generated by hospitals and research centers health related is significant and growing constantly. these data consist of information on patients and researchs performed at these facilities include medical charts, documents, approvals, consents among others and can be large and difficult to obtain. The use of computational tools to assist in this management is common in some institutions. This project proposes the development of a tool for this purpose using as the basis of a LIMS or Laboratory Information Management System to manage the research activities of Centro de Pesquisas Clínicas (CPC) of the Hospital das Clínicas da UFMG and data from patients of diseases that receive care at the same institution. The LIMS systems are data management laboratory systems that adapt easily to the specific clinical research. In particular we propose the use of a flexible LIMS oriented workflows, which has great flexibility, allowing the establishment of new research and protocols quickly and efficiently. The system dubbed Flux-MED has the following branches: Flux-CPC for management of researchers and studies at CPC; FluxNMO-DBr: a system for management and analysis of data from neuromyelitis optica patients; FluxPCM: a system for management of data from paracoccidioidomycosis patients.
FluxTransgenics: A Management System for Production of Transgenic Plants
FluxTransgenics: The production and commercial release of Genetically Modified Organisms (GMOs) are currently the focus of important discussions. In order to guarantee the quality and reliability of their trials, companies and institutions working on this subject must adopt new approaches on management, organization and recording of laboratory conditions where field studies are performed. FluxTransgenics presents a solution for the management of the data produced by a laboratory of genetically modified plants that is efficient and supports different kinds of information. Its adoption will contribute to guarantee the quality of activities and products in the process of transgenic production and enforce the use of Good Laboratory Practices (GLP). Its current version is being used by EMBRAPA Maize and Sorghum at Sete Lagoas – MG – Brazil.
Flux-OJB: A system for management of data from the Brazilian Justice Observatory (OJB)
Flux-OJB: The Brazilian Justice Observatory has as its initial goal to collect a set of empirical data, in six states of the country, referring to the organization and the users of the formal justice system in a way that these data can subsequently help to reflect on the whole dynamics for the very concept of justice system The goal of the Flux-OJB system is to use a workflow-based management and data analysis tool for storage, management and analysis of the data collected by OJB to allow the discovery of patterns and correlations between variables that allow to obtain a picture of justice in Brazil.
This project aims to develop a system for data management that supports adherence of laboratories to the Good Laboratory Practices (GLP) and has among its features the hability to alllow traceability of test substances, with emphasis on the chain of custody and control of permissions of users; flexibility to suit different types of laboratory data, tools for identification of experimental features that best suit GLP; tools to provide a way for production of automatic or semi-automatic management reports that allow to monitor the implementation of this system of quality management.