Bioinformatics

General information

Name of the programme: Bioinformatics
Type of programme: academic, 1st Bologna cycle
Degree awarded: "diplomirani bioinformatik (UN)" equiv. to B.Sc. in Bioinformatics
Duration: 3 years (6 semesters)
ECTS-credits: 180
Programme structure: 32 courses (4 electives) and final project paper (6 ECTS)
Mode of study: full-time
Language of study: Slovene, English (in English from 2018/19)

Programme coordinatortop

Assist. Prof. Matjaž Hladnik, PhD  

For information regarding application, enrolment and other administrative procedures please contact Student Services.

About the programmetop

At the beginning of the third millennium, modern technologies as applied to the natural sciences and quality of life present especially great challenges. The rapid growth of various biological data which is stored in databases and is suitable for computer management and analysis has created the need for experts who have mastered techniques in the areas of mathematics and computer and information sciences. In addition, boundaries between the various profiles of natural scientists (biologists, chemists and physicists) are becoming increasingly blurred, and therefore the various tools used in bioinformatics have become invaluable. A classically trained biologist is normally unfamiliar with statistics and is not skilled in computer science; however these skills will be increasingly demanded in this work environment. A classically trained mathematician or computer scientist, on the other hand, does not have the knowledge of biology and chemistry required for a career in bioinformatics.

Students of the undergraduate study programme Bioinformatics will acquire basic knowledge in the natural sciences (biochemistry, biology, genetics, chemistry, and physics), computer science and mathematics, and also specific bioinformatics-related knowledge.

Educational and professional goalstop

To produce experts who:

• have sufficient knowledge in the natural sciences (biochemistry, chemistry, biology, genetics, chemistry, physics), and who will also be skilled in mathematical techniques as well as in computer programming and computer-assisted analysis of biological data;
• are able to recognise connections between various mathematical theories, and natural and social sciences, in particular those connected with biology;
• have developed skills for analysing data and reaching new conclusions and findings;
• have developed cooperation skills in solving biomathematical problems;
• are trained to further their knowledge of bioinformatics through professional development;
• are trained in solving concrete problems of a biological nature, and developing and using appropriate mathematical skills and tools from computer and information sciences;
• have developed interdisciplinary thinking and the capacity to connect areas within natural and mathematical sciences;
• are trained in independent research, allowing them to stay current in terms of developments in science.

Course structuretop

During their studies, students must complete a total of 32 courses (28 compulsory and 4 electives) and prepare a final project.

All courses are awarded 3 or 6 ECTS-credits. One ECTS-credit encompasses 30 hours of student work. In addition to the student’s presence (at lectures, seminars, in-class and laboratory practical work), this also includes independent work (literature study, preparation for examinations, home assignments, seminar and project work, etc.). The courses require a minimum of 40 and a maximum of 90 hours of a student’s presence (contact hours).

The student may select 2 out of 4 elective courses from study programmes provided by other institutions of higher education in Slovenia and internationally. The courses selected may fall within the fields of Mathematics, Financial Mathematics, Computer Science, Biology, Chemistry, Physics, and Agriculture.

Short descriptions of courses are available HERE.

Year of study	Study obligation	Number	ECTS-credits (ECTS)
			ECTS	ECTS/Year of study
1.	Compulsory Course	10	60	60
2.	Compulsory Course	10	54	60
	Internal Elective Course	1	6
3.	Compulsory Course	8	36	60
	Internal Elective Course	1	6
	External Elective Course	2	12
	Seminar - Final Project Paper	1	6

No.	Course	ECTS	Form of contact hour
			L	T	SE	LW	Total
1.	Analysis I – Foundations of Analysis	6	45	30	-	-	75
2.	Analysis II – Infinitesimal Calculus	6	45	30	-	-	75
3.	Algebra I – Matrix Calculus	6	45	30	-	-	75
4.	Algebra II – Linear Algebra	6	45	30	-	-	75
5.	Computer Practicum	6	-	-	-	60	60
6.	Programming I	6	45	-	-	30	75
7.	Theoretical Computer Science I	6	45	30	-	-	75
8.	Data Programming	6	45	-	-	30	75
9.	Organic Chemistry and Biochemistry	6	30	-	-	45	75
10.	Genetics	6	30	-	15	30	75

 Legend:
 L = lecture, T = tutorial, SE = seminar, LW = laboratory work
 ECTS = ECTS-credits
  

No.	Course	ECTS	Form of contact hour
			L	T	SE	LW	Total
1.	Data Structures and Algorithms	6	45	-	-	30	75
2.	Introduction to Bioinformatics	6	30	-	-	45	75
3.	Introduction to Database Systems	6	45	-	-	30	75
4.	Foundations of Physics with Biophysics	6	30	-	-	30	60
5.	Analysis III – Functions of Many Variables	6	45	30	-	-	75
6.	Statistics	6	30	30	-	15	75
7.	Algorithms in Bioinformatics	3	20	-	-	20	40
8.	Introduction to Machine Learning and Data Mining	6	45	-	-	30	75
9.	Programming II – Concepts of Programming Languages	6	45	-	-	30	75
10.	Nucleotide Sequence Analysis	3	15	-	-	25	40
11.	Internal Elective Course I	6

No.	Course	ECTS	Form of contact hour
			L	T	SE	LW	Total
1.	Structure of Biological Molecules	3	15	15	-	-	30
2.	Biotechnology	3	20	-	5	15	40
3.	Evolutionary and Population Genetics	6	30	30	15	-	75
4.	Systems III – Information Systems	6	45	-	-	30	75
5.	Evolutionary Biology	6	30	30	15	-	75
6.	Physical Chemistry with Cheminformatics	6	30	-	-	30	60
7.	Functional Genomics	3	15	-	3	20	38
8.	Mathematical Modelling in Bioinformatics	3	22	15	-	-	37
9.	Internal Elective Course II	6
10.	External Elective Course I	6
11.	External Elective Course II	6
12.	Seminar - Final Project Paper	6	-	-	15	-	15

Internal Elective Courses (BF-19)

The list shows all internal elective courses of the study programme. Every academic year, the Faculty offers a different (shorter) selection of elective courses.

Internal elective courses of the study programme Bioinformatics:

• Biomolecular Modeling: 6 ECTS, 30 hours of lectures and 30 hours of tutorials;
• Mathematical Chemistry: 6 ECTS, 30 hours of lectures and 30 hours of tutorials;
• Systems Biology Approach in Human Disease Study: 6 ECTS, 30 hours of lectures and 30 hours of seminars
• Introduction to Environmental, Conservation and Animal Ethics: 6 ECTS, 15 hours of lectures, 15 hours of seminar and 15 hours of tutorials.

The student may also select elective courses (internal elective course) from other undergraduate study programmes (number of contact hours and short description of courses are available in the study programme, section Course structure):

• Mathematics: Introduction to Numerical Calculations; Algebra III – Abstract Algebra; Game Theory; Probability; Stochastic Processes I;
• Mathematics in Economics and Finance: Stochastic Processes II;
• Computer Science: Theoretical Computer Science II – Formal Languages and Computability; Theoretical Computer Science III – Information Theory; Systems I – Hardware; Systems II – Operating Systems and Computer Networks; Programming III – Concurrent Programming; Computer Networks;
• Conservation Biology: Conservation Biology; Systematic Botany and Geobotany; Environmental Monitoring; Geographical Information Science and Systems; Marine Biodiversity; Protected Areas and Sustainable Use; Biogeography; Ecotoxicology; Biodiversity and Ecology of the Mediterranean; Biological Topics in English; Ecology;
• Mediterranean Agriculture (VS): Plant Biotechnology; Plant Molecular Diagnostic; Plant Breeding and Propagation.

In their third year of studies, students can select a TRAINEESHIP IN A WORKING ENVIRONMENT as their elective course. The aim is to enable students to gain professional and practical experience in the field of bioinformatics. Traineeships last three weeks and students are awarded with six (6) ETCS credits. Traineeship is supervised by a qualified mentor in the field of bioinformatics.

Students that choose traineeship in a working environment, must first contact the study programme coordinator, and then mark their decision on the enrollment paper for the 3rd year.

Course structure and programme information for students enrolled 2017/18 - 2018/19

In the past year changes occurred in the course plan. In the beginning of this section you can find the course plan for students enrolled from the academic year 2019/20.

Here you can find information regarding course structure, compulsory and elective courses, and also short description of courses for students enrolled for the first time in the academic years 2017/18 - 2018/19 (BF-17):

• course structure, short description of courses.

Traineeship in a working environmenttop

If the student selected with the study programme coordinator a TRAINEESHIP IN A WORKING ENVIRONMENT as their elective course in the 3rd year of study, he/she should know all procedures defined in the INSTRUCTIONS FOR STUDENTS ABOUT THE PRACTICAL TRAINING (only in Slovene).

All procedures goes through ŠIS, also all form are available in ŠIS. The key steps in the procedure are listed below:

• student submits the application for the training; it is mandatory to attach the Statement of the institution for accepting the student for practical training;
• the coordinator of the practical training at the Faculty decides about the application;
• after the approval, the student prints 3 copies of the traineeship cooperation agreement and submits them at Student Services; he/she saves all other forms as he/she will need them during the training;
• student begins with the training only after the approval of the application and the agreement is signed;
• at the end of the training student submits a report; all mandatory forms that need to be attached are listed in the Instructions;
• the coordinator of the practical training at the Faculty decides about the report;
• after the approval of the report, the student is invited to complete a survey about the training.

If a student needs the Student traineeship cooperation agreement in English (due to the practical training abroad), he/she must inform the Student Services as soon as he/she is informed that his/her application for practical training has been approved by coordinator.

Field worktop

Within the individual courses of the study programme, part of the course is also carried out in the field (field work).

Field work is carried out as a complement to the study process and students are required to attend it. The field work provides students with practical knowledge that builds on the theoretical content covered in the lectures. Field work takes place over one or several days. In some courses, particularly in the second or third year, two- and three-day field work takes place in Slovenia or abroad (e.g. in Istria, Cres and Lošinj, Velebit). During the field work, students, assisted by professors and assistants and local guides, learn about local features and foreign research institutions, and carry out practical tasks in the natural environment. At the same time, it should not be forgotten that field work is one of the most enjoyable and popular study commitments, as it also allows students and teachers to socialise informally and get to know new places.

We recommend that students on fieldwork programmes be vaccinated against tick-borne meningitis because of the exposure and the possibility of infection during fieldwork. The vaccination is organised as part of the regular medical check-ups at the Koper Health Centre and will be free of charge for students on this study programme.

On the basis of the Regulation on Tuition Fees and Other Contributions in Higher Education (Official Journal of the Republic of Slovenia, No.40/94, 45/98) and in accordance with the Regulation on Contributions and Evaluation of Costs at the University of Primorska, the members of the University of Primorska charge students for the costs related to the implementation of the study programme in the field and the organisation of field trips at the actual cost per participant.

The management of UP FAMNIT decides, on the basis of an analysis of the costs of field work and an assessment of the financial capacity of the faculty in a particular academic year, to what extent it will be able to co-finance the costs (in recent years between 50% and 80% of the costs) of field work for a particular academic year.

The Faculty will continue to part-finance the costs of field work in the future, subject to the availability of financial resources, as in previous academic years.

Admission requirementstop

Admission to the first year of study shall be granted to applicants having:

• passed the matura examination; or            
• passed the vocational matura examination in a 4-year secondary-school programme and a final examination in a general matura subject; the selected subject cannot be the same as one of the subjects passed in the framework of the vocational matura;
• successfully completed any four-year secondary-school programme before 1 June 1995.

In the case of enrolment limitations, applicants shall be selected on the basis of overall matura, vocational matura or final examination results (70 %), and overall results in the 3rd and 4th year of secondary school (30 %).

Admission may also be gained by an applicant having completed a comparable study abroad. Prior to enrolment the applicant must apply for the recognition of completed education.

Continuation of studies according to the transfer criteriatop

Transfers between study programmes are possible on the basis of the Higher Education Act, Criteria for Transferring between Study Programmes and in accordance with other regulations of this field.

The transition between study programmes is the enrolment in the higher year of the study programme, in case of leaving the education at the initial study programme and continuing the study process at another study program of the same degree. The transition takes into account the comparability of the study programmes and the completed study obligations of the candidate in the initial study program.

Access to year 2 or year 3 of the study programme of Bioinformatics on the basis of the Criteria for Transferring between Study Programmes is granted to candidates of a related first-cycle study programme or a pre-Bologna reform undergraduate study programme, provided that the following conditions have been met:

• the candidate fulfils the requirements for admission to the study programme of Bioinformatics
• the completion of the initial study programme which the candidate is transferring from ensures the acquisition of comparable competencies as those envisaged by the study programme of Bioinformatics
• other conditions have also been met, in accordance with the Criteria for Transferring between Study Programmes (a comparable course structure, course requirements completed)

Individual applications for transfer shall be considered by the relevant UP FAMNIT committee. Apart from comparability between both fields of study, the committee shall also consider the comparability between the study programmes, in accordance with the Criteria for Transferring between Study Programmes.

Enrolment on the basis of the Criteria for Transferring between Study Programmes is also open to candidates of a related study programme abroad who have been, in the process of recognition of their studies abroad, legally granted the right to continue their educational training in the study programme of Bioinformatics.

Advancement requirementstop

For enrolment in the next study year it is necessary to collect at least 42 ECTS-credits from courses and exams in the current study year, and to fulfil all the study obligations (60 ECTS-credits) for the previous study year.

The Study Committee of the Faculty may permit a student who has not fulfilled all study obligations for the particular year to enrol in the next year. The student is obliged to submit a formal written request to the Study Committee. The progress may be approved if a student could not fulfil the obligations for justifiable reasons. Students may repeat a year only once during their study period.

Requirements for the Completion of Studies

Students shall be deemed to have completed their studies when they fulfil all the prescribed study requirements to a total of 180 ECTS-credits. Students must obtain a positive assessment for the Final Project Paper completed within the framework of the Seminar.

Graduate competenciestop

General competencies

• The ability to analyse, synthesise and predict solutions and consequences of various factors in biochemistry.
• The ability to critically assess developments in science, in particular in biology, biochemistry and molecular genetics.
• The ability to use mathematics and computer science and informatics in the natural sciences, in particular in biology, biochemistry and molecular genetics.
• Social, communication and teamwork skills in project work and team work.
• The ability to independently glean new knowledge and integrate it with existing knowledge.
• The ability to glean new information, to clarify it and place it into the context of bioinformatics.
• A cohesive overview of the development of bioinformatics as a new discipline.
• A sound education in the natural sciences.
• The ability to analyse certain situations, to critically verify the information and to predict solutions and potential consequences.
• The ability to apply theoretical and practical research methods, approaches and technologies.
• The ability to formulate strategies and creative solutions to problems arising in the use of biological information.
• Autonomy in professional work and a commitment to ethics.

Subject-specific competencies

• The ability to describe a biological phenomenon in the language of mathematics or computer science.
• The ability to explain one’s understanding of mathematical concepts and principles.
• The ability to solve problems with the use of modern information technology.
• The ability to use the algorithmic approach: to develop an algorithm to solve a given problem.
• The ability to analyse a given problem, numerically as well as graphically and algorithmically.
• To confidently tackle and solve a given problem in bioinformatics.
• The ability to solve problems with the use of numerical methods.
• The ability to bridge knowledge from different fields of natural sciences, e.g., biology, chemistry, genetics, biochemistry, mathematics, computer science and informatics.
• The ability to incorporate new research, and expert findings, information and interpretations into the context of bioinformatics.
• The ability to recognize the nature of biological information on the World Wide Web and to use it in practice.

Graduate employment opportunitiestop

Graduates will be employable in public administration (Ministry of the Environment and Spatial Planning, Environmental Agency, Ministry of Agriculture, Forestry and Food,) in health establishments and pharmaceutical companies, private and public laboratories, national and international non-governmental organisations (such as IUCN, WWF, and others), in the private sector, and in agricultural production and the food sector both nationally and internationally. Knowledge acquired in the areas of mathematics and computer and information sciences will also equip graduates for employment in teaching and research, establishments dealing with computer science, and establishments where knowledge of statistics is needed (such as Statistical Office, insurance companies, and banks).