Titulo Estágio
YLAB - Project and Research Facility Management Software for a Unit of Biological Drug Production in Eggs
Áreas de especialidade
Engenharia de Software
Engenharia de Software
Local do Estágio
DEI Polo II, UC, Coimbra ; CNC-UC-Biotech, Cantanhede
Enquadramento
Chicken and quail eggs are the source of high value natural proteins called the antibodies. These are found in the yolk of the egg and can be recovered without invasive methods to the animal (e.g. blood collection) and at low cost, to produce a vast range of biological drugs and research and diagnostic reagents. At the Center for Neuroscience and Cell Biology of University of Coimbra, our group [1] established an Avian Antibody Research Facility [2], unique in Portugal (and Europe) and developed proprietary housing systems to further explore Quails as model birds for antibody development and customization. These are fast experimental turn-over birds that can be accommodated in smaller housing setups than chickens and thus are very promising for biopharmaceutical R&D.
Our Avian Facility houses 80-120 birds in experimental conditions. Typically, birds and grouped (2, 3 birds) per cage and each cage is allocated to the development of a specific antibody (final product); we have 40 cages available. For that birds, need to be individually catalogued and continuously monitored for periods of 2-12 months, after being stimulated to produce the antibody of interest by immunization (vaccination). The main activity in the unit is indeed egg laying monitoring and egg collection and processing. Each bird will lay on average one egg per day, meaning that (at full speed) one needs to deal with 26,000 eggs per year. For reference, some of these eggs have a market value ranging from 5.00€ - 300.00€ (per egg!).
Each protocol for a new antibody development needs to cope with a good amount of information, including all IDs for protocol, birds, cage, cage location, bird welfare status, egg laying capacity, egg processing and storage vaccine composition, preparation and administration, vaccination calendar, immune response outcome.
[1] http://www2.biocant.pt/structuralbiotechnology/
[2]http://www2.biocant.pt/structuralbiotechnology/index.php/resources/
Objetivo
YLAB - Project and Research Facility Management Software intends to be a software application to control and optimize the management of our Avian Antibody Facility activities. It should be designed in a versatile way that allows long term integration of multiple wet-lab, office and client/service inputs, that converge to speed up the research and development of a new antibody product.
In a first stage the software should cope with the most important data input derived from daily egg collection, counting and monitoring, since this represents the core value of our unit. It is important that the software will allow a comprehensive and easy to use user interface, that can facilitate immediate egg counting of each protocol and the data will build up a daily trend for egg laying capacity (and respective plot), meaning the daily average of eggs per day (of the last week and month) should be easily accessed, ideally with metrics and color code for intuitive interpretation. This is critical for monitoring bird welfare and regular adjustments of the experimental setup and procedures in accordance.
Mid-term or long term functionalities of the software, include automatic experimental cage selection upon the request for a new internal protocol or external client demand for a new antibody product. This will result from integrating service and clients portfolio with routine core procedures and monitoring. Also refined features, such as automatic egg harvesting and counting per cage (without human intervention) can be considered in the future, since our proprietary systems do allow such technical implementation.
Plano de Trabalhos - Semestre 1
In the first semester the student will focused on the following tasks:
- Understanding and studying the business case behind the core production process to which the Management Software application should be designed for;
- Analysis of the current production process set up and characterization/identification of the technical features, its advantages, limitations and inherent problems;
- Analysis of the advanced technical features of the animal housing system installed in facility and the different production steps enabled by the system.
- Analysis and specification of the different requirements intended to be implemented within the Management Software application;
- Selection of the most adequate set of technologies for proper implementation of the Software application.
Plano de Trabalhos - Semestre 2
In the second semester, the student will continue the work with the following tasks:
- Development of the detailed architecture and design of the software, according to the requirements previously studied and identified;
- Build on such developed architecture and refine it towards an implementation specification project;
- Implementation, working tests and validation of a preliminary version of the Software application;
- The test results will be used to prepare conference poster communication and a thesis chapter;
- Preparation of the final thesis written document.
Condições
The student will have the opportunity to integrate a multidisciplinary and international research team, with research lines where biotechnology cross-talks with information technology and data management. The student will also be encouraged to participate into national or international conferences, with expenses paid by partnership agreements currently in place with industry partners.
Observações
Proposta de Dissertação/Estágio MEI 2018/2019, no âmbito de projecto de colaboração entre DEI/UC e Centro de Neurociências e Biologia Celular, UC.
Orientador Principal proposto (DEI): Professor Paulo Rupino da Cunha
Curriculum_Vitae
https://www.cisuc.uc.pt/people/show/2040
Co-orientador (CNC): Doutor Ricardo Simão Vieira-Pires
Função: Investigador Auxiliar
Curriculum_Vitae
1526924464_RicardoVieira-Pires_FCTSIG_Curriculum_Vitae.pdf
Nota: O ficheiro PDF Curriculum Vitae anexado é relativo ao co-orientador aqui proposto. O CV do Orientador principal não é anexado em PDF dado se tratar de um orientador interno do DEI.
Orientador
Paulo Rupino da Cunha
rupino@dei.uc.pt 📩