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Bioinformatics

“BioInformatica is niet meer weg te denken uit de hedendaagse Biologie. Het werkveld van de biologie en biotechnologie vraagt expliciet om studenten/werknemers met BioInformatica-ervaring voor stages en banen.”

Bioinfomatics is a combination of life science and informatics. It always involves programming and data handling, knowledge of Linux beside Windows, numbers of applications and software packages to handle and visualize data, and, maybe most important, a lot of communication between biologists and scientific programmers. In this field you can work with DNA sequences in comparative genomics and Phylogenetics, RNA expression in transcriptomics research, amino acid sequences in 3D proteomics and structural or functional genomics, or even in systems biology or epi-genomics.

In this minor you will learn how to process and visualize biological data. You can divide the minor into roughly three parts:

  • Informatics (programming, SQL data management, Linux, cloud computing)
  • Biological problem solving (computational biology, Data & Database analysis, Next Generation Sequencing, and Transcriptomics)
  • Protein 3D modelling and visualization

In the setup of the courses and training, diverse aspects of bioinformatics are highlighted. Within the projects, it is possible to gain in-depth knowledge of various aspects of bioinformatics.  For example, research on the DNA/RNA (NGS, Phylogenetic, transcriptomics) level, on the protein level (3D protein modelling) or on visualization level by using the R environment. These three aspects will all be covered in the courses and trainings of this minor. Linux based exercises will be performed using the LISA computer cluster provided by SURFsara (Stichting Academisch Rekencentrum Amsterdam). In this way you will be equipped with the skills of cloud computing.

In order to stay up to date, the presented projects have been developed in collaboration with experts from the working field. These researchers will also be involved in the projects as your external supervisors.

Students of the Major Biomedical Research, Molecular Research and the Biotechnology are welcome to this minor. Other students will be admitted accordingly upon intake results. Students via KOM (https://www.kiesopmaat.nl/) or from abroad are welcome according to national/international agreements.

 

This minor will be given exclusively in English.

Leerdoelen

The weight of this minor is 30 ECs. Of which, 10 ECs is filled with courses and trainings, and 2 EC for CAA (extra curriculum activities).
  • Programming: Python scripting for biologists
  • Computational Biology
  • NGS data analysis
  • 3D modeling
  • Data management
  • Transcriptomic analysis

You will work within the AVANS Bioinformatics Centrum (ABC) on one of the work field related projects (or your own initiative) in the field of bioinformatics. You work on an assignment in groups of 2 persons or otherwise individually. The projects are divided into several categories. The assignments will be clarified during the kickoff meeting of the minor and will be further elaborated on by the person responsible for the minor. A balanced division of projects for the three categories is strived for in the minor.

The students are expect to be independent during these studies. He/she must study the course material individually. Through work discussions and development meetings with the lecturer(s) and fellow students, the material already mastered and yet to be learned will be dealt with. 18 ECs is reserved for the research project, in which you will work in groups of 2, setting up and implementing a research plan.

Possible topics of projects:

  • Genetics & (whole) genome sequence analysis
  • Systems Biology
  • Next Generation Sequencing / Data Pipe line construction (NGS)
  • 3D protein structure analysis
  • Cancer diagnosis marker gene selection
  • Multi-omics microbial drug-resistance analysis

Aanvullende informatie

The Avans training linked to this minor module is:

Biologie en Medisch Laboratoriumonderzoek Breda (BML-B)(You will need this information for registration in Studielink.)

Ingangseisen

  • Pass your Propaedeutic year evaluation (contact the minor coordinator is you haven’t passed yet)
  • At least 2 years full time education in the area of Biomedicine, Biology and/or Biotechnology
  • Get the allowance from your own academy to start a minor study
  • Have completed courses in (or similar subjects):
  • Mathematics
  • Basic statistics
  • 2 out of these 3:
    • Biological databases (Introduction of Bioinformatics)
    • DNA modification
    • DNA detection
  • 4 out of these 5:
    • Cell Biology
    • DNA and Evolution
    • Biotechnology and health
    • DNA technology and Ethics
    • Microbiology
  • Students who have completed the ATGM AVANS MOOC “Advanced in-silico Biology" have priority of admission
  • B2 level English speaking, writing and listening skills

If the course contents in your school are different comparing to the ones at ATGM Avans, please contact the minor coordinator for a discussion.

Toetsing

Courses and trainings should be completed successfully to gain 30 EC in this minor. The final mark for the professional task can be determined when all the parts have been assessed as sufficient or marks are ≥ 5.5 as indicated in the table below. 

The final mark will be determined using the following measures: 

  • Execution & Attitude of the project (individual) (40%) 
  • Project plan (in English)(10%) 
  • Presentation (subgroup; Choice: Dutch or English) (10%)
  • Article (in English)(20%)
  • Oral assessment (individual)(20%)

Literatuur

This minor is given in the fashion of “blended learning”. Several online learning platforms will be used. All literature and learning materials will be made available during the minor via BlackBoard.

Rooster

Training and project management are scheduled every week. You also work independently, for some software you have to register on a computer.