SSB-20806 iBiosystems

This Study Handbook is published with reservation. It is not official yet.

Course

Credits 6.00

Teaching methodContact hours
Lecture12
Tutorial28
Practical50
Group work2
Course coordinator(s)dr. I Sanchez Andrea
MSc JJ Koehorst
Lecturer(s)dr. C Furlan
dr. I Sanchez Andrea
MSc JJ Koehorst
dr. PJ Schaap
prof. dr. D Weijers
prof. dr. SC de Vries
Examiner(s)dr. PJ Schaap

Language of instruction:

EN

Mandatory knowledge:

ZSS06100 Laboratory Safety


Assumed knowledge on:

BIC-10306 Practical Biological Chemistry; CBI-10306 Cell Biology; MIB-10306 Microbiology & Biochemistry; MIB-20306 Microbial Physiology

Continuation courses:

Bioinformation Technology, Molecular Systems Biology

Contents:

The course integrates wet lab experiments and dry lab computational techniques to inform the understanding of genotype-phenotype relationships.
i)    Wet lab: Application wet lab techniques for characterizing strains based on fundamental principles. (Group work)
ii)    Dry lab: For informing the understanding of the genomic information underlying physiological properties, lectures will be given on sequencing techniques and commonly used computational tools in the field of genomics. Students will learn and apply the principles of genome assembly, annotation, comparison, identification of metabolic processes and integration of large biological datasets.
iii)    Integration of wet and dry lab results and FAIR reporting: Student will learn how to keep track of wet and dry lab results in a Findable, Accessible, Interoperable, Reusable (i.e. FAIR) way. To keep track of the entire ‘Moist’ process digital lab journals will be maintained and graded to keep track of the entire ‘Moist’ process. In an interactive cycle, wet and dry lab results will be integrated. Results and conclusions will be presented in a draft and final scientific paper.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- analyze and design moist-lab experiments;
- document experimental procedures and store data and data provenance in a FAIR way;
- communicate research findings in a concise and effective way;
- evaluate the quality of research communications;
- apply concepts of genomics to genome processing and description;
- analyze predictions of commonly used computational tools in the field of genomics;
- apply concepts of physiology and pathways to interpret functions in the genomes.

Activities:

iBiosystems is a practical intensive course in which wet-lab as well as computational experiments (dry-lab) are performed in an integrative manner. The students will perform experiments in the laboratory with given microorganisms. They will characterize physiologically the microorganisms as well as sequence their genome. Afterwards, they process the genome information from sequence to function. During the course students will work in pairs and present their digital lab journal following the FAIR principles. Students then will write a first draft of a scientific paper integrating both wet and dry results . Peer-feedback will be provided on the draft and can be used to finalise the scientific article.

Examination:

The final mark is based on; a written exam (40%), a concise digital lab journal (10%), a scientific paper (40%) and the quality of the peer-review (10%). To pass the course, the mark for each part should be at least 5.5.

Literature:

Book: Introduction to Bioinformatics, Arthur Lesk, Fifth edition ISBN: 9780198794141; Brock Biology of Microorganisms 14th Edition & Practical Bioinformatics.

Guidelines and protocols will be supplied in Brightspace.

ProgrammePhaseSpecializationPeriod
Restricted Optional for: BBTBiotechnologyBSc2MO
MinorPeriod
Restricted Optional for: WUSYBBSc Minor Systems Biology2MO