PhD Position in Computer Sciences (Marie Curie)
Location: Ljubljana, Slovenia
PhD position in the field of computer and information sciences in a Marie Skłodowska Curie European Innovative Training Network- INEXTVIR project focusing on “Development and integration of decision making tools in data analysis procedures for NGS-based plant virus diagnostics”
We are looking for a PhD student with the background in computer and information sciences who would like to join BioSistemika with the aim to participate in a Marie Skłodowska Curie European Innovative Training Network project “INEXTVIR”.
This is a full-time position for 3 years, during which you will be employed at BioSistemika d.o.o.. You will be working on research project “Development and integration of decision making tools in data analysis procedures for NGS-based plant virus diagnostics” and will enrol in Doctoral Programme at Jožef Stefan International Postgraduate School (https://www.mps.si/en/). During the project you will undertake mobility (travel to other partner organisations in INEXTVIR project) in order to implement your individual Research Project, as well as to participate in complementary training activities.
Your responsibilities, specific areas of work and relevance for your career
You will be contributing to the bioinformatics and software development segments of the project. Your main areas of work will include:
1. Development of machine learning approach for decision support in detection and classification of plant viruses based on High throughput Sequencing (HTS) data.
2. Development of computational approach for evaluation of performance of bioinformatics pipelines for analysis of HTS data.
3. Simplification and automation of bioinformatics pipelines to be more user friendly and their integration with laboratory data management systems and workflow tools.
You will learn state of the art machine learning approaches for analysis of HTS sequencing data and integration of public datasets (data fusion). You will gain experience in transferring the developed pipelines into user friendly software interface, integration with laboratory data management systems and thus contribute to digitisation of laboratories. Through this you will gain experience with good software development practices and software development lifecycle management. In addition, you will get experience with working in an interdisciplinary team and working in a company setting.
Your menthors and supervisory team
Assist. Prof dr. Tomaž Curk will be the academic supervisor. His main focus is bioinformatics, where he uses data mining and machine learning for sequence analysis and data fusion of biological data. He is co-author of the Orange Data Mining tool (https://orange.biolab.si) and iCount (https://github.com/tomazc/iCount) for protein-RNA interaction analysis.
Dr. Matjaž Hren has experience in managing software development projects with emphasis on user interfaces, digitization of laboratories and bioinformatics.
Luka Murn is a senior software engineer and a team lead with experience in designing software architecture, developing integrations between software platforms and is generally involved in delivery of software solutions to the market.
Background about the INEXTVIR project
INEXTVIR – Innovative Network for Next Generation Training and Sequencing of Virome – is funded by the European Commission under the Horizon 2020 programme (https://ec.europa.eu/research/mariecurieactions/) and offers 15 fully funded PhD positions with an attractive stipend, complementary training activities and generous travel and laboratory and research budgets. The successful candidates will be hosted by a member of a European Consortium of universities, research institutions and companies in Belgium, France, Spain, Slovenia and the UK. Successful candidates will have natural or social-science based research interests and will participate in a transdisciplinary network of research and training aimed at accelerating the start of the applicants’ scientific career. We are specifically looking for a candidate with computer and information sciences background.
Plant viruses cause 50% of the emerging plant diseases globally and pose an important threat to many agricultural crops. Losses are estimated at €15 to 45 billion per year through lower yields and reduced product quality. The project seeks to generate a better understanding of viral communities and their role in agricultural ecosystems by using the latest advances in high throughput sequencing (HTS) technologies coupled with modern big data analytical approaches and socioeconomic analysis and communication based on societal requirements and concerns. The project provides a timely opportunity to change our approach to plant health and improve our ability to overcome global agricultural, food security and environmental challenges. The main objectives are:
- To define the virome present in selected agricultural crops across Europe using cutting-edge Highthroughput sequencing (HTS) technologies.
- To understand the biological impact virus communities, have on the biology and ecology of farming systems.
- To improve virus detection capabilities in plant health and certification settings thorough the development and validation of HTS methods including the use of novel sequencing technologies (e.g. Nanopore sequencing) and development of bioinformatics approaches based on AI and machine learning.
- To assess the agronomic and socio-economic impact of the virome and translate it into practical decision tools for different stakeholders including
Eligibility criteria for applications
Marie Skłodowska Curie European Innovative Training Network has the following eligibility criteria that you have to comply with:
1. Nationals from any country may apply.
2. Mobility criteria: at the time of the recruitment, the researcher must not have resided or carried out his/her main activity (work, studies, etc.), in Slovenia for more than 12 months in the 3 years immediately prior to the date of the recruitment.
3. At the time of the recruitment, you should have not yet been awarded a doctorate degree and are in the first 4 years (full-time equivalent) of your research career, including the research training period that would entitle them to a doctorate.
We’re looking for the following in you:
- Master or equivalent in computational sciences.
- Experience with Git version control
- Programming experience, e.g. with scripting languages (Python, R, etc.) and command line
- Good knowledge of English – you will be using it every day
- Used to work with good development practices such as code review and awareness of importance of QA/QC in software development
- Self-initiative and eagerness for learning new things and self-improvement
- Positive, make-it-happen, lead-by-example attitude
- Knack for automating things & seeking ways to improve the work process
- Experience with machine learning algorithms
- Experience with modern web languages such as Ruby on Rails, React.js, Angular.js, Vue.js,
Python, Golang, Scala, Elixir
- Experience with databases (relational, NoSQL, etc.)
We are a young, dynamic team that originated from a startup environment.
We offer a permanent full-time job position for 3 years (for the duration of the INEXTVIR project), located in Ljubljana, Slovenia.
You will be joining an interdisciplinary and international team of life-scientists, UX/UI designers, software developers and digitalization enthusiasts that develop custom software solutions for life scientists. In the scope of project you will also be closely collaborating with the rest of the ESR students.
Salary and financial benefits
Salary granted according to MSCA ITN rules. Generous stipend per month depends on the host country correction coefficient following the EC rules (for details see Table 2 of the MSCA Work Programme 2018-2020, http://ec.europa.eu/research/participants/data/ref/h2020/wp/2018-2020/main/h2020-wp1820-
msca_en.pdf, page 82), which means approximately 2815 EUR. Net salary results from deducting all compulsory (employer /employee) social security contributions as well as direct taxes (e.g. income tax) from the gross amounts.
In addition to the stipend, mobility allowance (600€ per month net) will be paid as part of the salary or as other benefits depending on the organization. Family allowance*(500€ per month) will be paid as part of salary where the researcher has a family by the time of recruitment.
PhD tuition fees will be covered by the host organisation.
How to apply
Please send the following documents to e-mail with subject Marie Curie INEXTVIR:
a) Curriculum Vitae (Europass format recommended; Please specify your residence/work place in the last 3 years).
b) University diploma and transcripts (grades)
c) A motivation letter addressing his/her research interests in relationship to the selected individual research project.
d) At least two recommendation letters