MSc Bioinformatics 2020/2021

Joan Wellink

This presenation about the Bioinformatics Master program is made by Joan Wellink study advisor of the program. Several slides are provided by Sandra Smit, assistantprofessor Bioinformatics.

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What is Bioinformatics?

Bioinformatics

Biology

-omics

biological data science

MBF is basically Biological data science. It combines knowledge from computer science such as programming, data management and visualization, with statistics, mathematics, in order to analyseand understand biological data, especially –omics data, such as genomics, transcriptomics, proteomics and metabolomics.

Bioinformatics

Thesis oriented program with two tracks

Course and Thesis topics:

Data analysis

Data mining

Tool development

Algorithm development

Modelling

Systems biology

Biosynthe1cpathwaydiscovery

MarnixMedema

Connec0nggenestomolecules

Sequencesimilaritynetworks

Coexpressionanalysis

Tracks:

• Bioinformatic tools

• Systems Biology

The Bioinformatics program is thesis oriented, so the idea is that you choose courses that you are interested in and will help you to carry out a nice thesis project. The program offers two tracks, one with a focus on courses in informatic tools, algorithms, the other with a focus on courses in systems biology and mathematicalmodels.

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▪Admission Committee

●Relevant Bachelor degree (life sciencesor informatics)

●GPA >7.0

●English certificate (eg Toefl internet based >80 or OOPT 60)

HAVO 7 or VWO 6

▪Direct admission (only some WU bachelors)

▪Deadline July 1 (May 1 Non EU)

Enrolment studielink

Enrolment is possible with BSc degree in Bioinformatics, Life Science or Computer Science. An admission committee will judge applications on an individual basis.

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Academic calendar WU

▪ period 1,2,5 : 1 course in the morning, one in the afternoon

▪ period 3,4,6 : also whole day courses

▪ every student takes 9 - 10 courses/year = 60 ECTS (credits)

▪ holiday: Christmas 2 weeks; July / August

▪ re-exams: 2 weeks July (August) and February

Period 2Period 1 Period 4 Period 5 Period 6Period 3

Nov+DecSep+Oct Feb Mar+Apr May+JuneJan

8 weeks8 weeks 4 weeks 8 weeks 8 weeks4 weeks

Christmas

break

2 re-exam weeks

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CoursesSee study hand book for details

https://ssc.wur.nl/Handbook/Programme/MBF

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MSc Bioinformatics programme

(Research) thesis

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ear

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am

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1st year

Internship(or 2nd thesis)

Academic Master Cluster

Period 5 Period 6Period 1 Period 2 Period 3

Restricted optionals or free

optionals

Period 4

Co

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ory

Res

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free

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The first year consist of courses, the second year you do a thesis of 6 months and an internship of 4 months. Exact program will depend on background and interests of the student, and for example the Academic Master Cluster can also be scheduled for the second year.

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Entry courses

RO0

RO1 Statistics

2 “Tracks”

RO2 or 3

RO4 Biology

Academic

master

cluster

Screen shot from the study handbook, for detailed explanation see the next slides.

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Entry courses

See study handbook for description courses:https://ssc.wur.nl/Handbook/Programme/MBF

RO0 Entry courses: depends on background0-2 courses biology/programming (~ 80h)

RO-0: Choose in consultation with your study adviser in dependence of pre-education; students with limited life science background have to choose GEN-21306; students without programming skills (< 80h of experience with programming) have to choose INF-22306; students who did not follow SSB-20306 in their pre-education have to include SSB-20306.

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(Bio-) Informatics TrackRO-2: Developing pipelines and software tools for data analysisChoose at least 2 courses

Choose at least 12 credits from either RO-2 / 2A or RO-3 / 3A. If you did not choose from RO2A or RO3A include at least additional 6 credits from either RO-2A or RO-3A.

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Systems Biology Track

RO-3: Systems Biology is the field in which an integrated, quantitative analysis is performed (using mathematical and statistical methods and computer simulations) to study the mechanisms by which cellular components, cells, organisms and communities interact in space and time. Choose at least 2 courses

Choose at least 12 credits from either RO-2 / 2A or RO-3 / 3A. If you did not choose from RO2A or RO3A include at least additional 6 credits from either RO-2A or RO-3A.

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Compulsory course:

RO1 statistics

RO4 Biology

advanced

One compulsory course in period 3. Choose at least one statistics course, two are basic the others more advanced. Choose one advanced Biology course.

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RO6: Academic master cluster, 3 different flavours

(end of first year or after the thesis)

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Choices MSc Bioinformatics

1. Compulsory for all

• 0-2 entry courses (biology/programming)

• 6 ECTS molecular systems biology (3rd period)

• 6 ECTS statistics (different options all over the year)

• 12 ECTS academic master cluster (different options)

2. Track

• 12 ECTS from either informatics or systems biology

3. Restricted optional Biology course

• 6/12 ECTS from list(s)

4. Free optionals

• 18 ECTS (also from other MSc programmes of WU)

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CoursesSee study hand book for details

https://ssc.wur.nl/Handbook/Programme/MBF

Projects

assignments

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Thesis and Academic Internship

• Start thesis at the end of the first or start of the 2nd

year

➢ topics at website of chair groups

• Internship at company/university/institute: last part 2nd year

➢ placement with help of chair group

thesis is 6 months and an internship is 4 months

Understand living cells

Understand evolution

Cure/prevent diseases

Improve crops

Improve food quality

Improve cell factories

Humans/animals/plants/micro-organisms

WUR Research themes that involve

Bioinformatics

Research in Wageningen is done in all of these domains. Doing many experiments, producing data. Bioinformatics is necessary to analyse all these data and help answer the questions.

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Thesis and internship examples

• Connecting metabolome data to biosynthetic gene clusters using quantitative trait loci analysis

• Haplotyping using 10X Genomics synthetic long reads

• Genome-Wide Variant Annotation using Convolutional Neural Networks

• Circuit design in bottom-up synthetic biology

• Comparative genomics in the fungal genus Botrytis

• Metabolic modelling of actinobacteria

• Trait-based Comparative Transcriptomics

• Greengenes: bioinformatics and modeling approaches for researching algal-bacterial symbiosis

• Finding genes related to regeneration from RNA-seqdata

Examples of titles of thesis and internship projects

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The Hyve open source medical data analysis Utrecht

Examples of internship options at companies and institutes

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A career in Bioinformatics

Biotech

Agendia AstraZeneca NovartisCrucell

PamgeneKeygeneGeneTwister

Isotis

HeinekenDSMFrieslandCampina

Medical and pharma

Health

FundamentalScience

Food

T2O'sBreeding companies

Universities

Unilever

Philips

Medical centersResearch institutes

There is a need for bioinformaticians at universities, institutes andindustry/companies, in variuos areas of research. About 50% find a job in companies 50%, about continue with a PhD.

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Varia

▪ Students MBF 16 nationalities

▪ Options for Internship abroad

▪ Student association MBF

▪ 30-40 students start each year

▪ MSc degree within 3 years: 75-85 %

▪ Companies 50%, PhD 50%

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study advisor

▪ Anything study related

▪ Planning individual programme

● June-August

https://ssc.wur.nl/Handbook

Program director

Role study advisor is to discuss the entry courses and help with choosing other courses and making an individual study program. This is usually done during an ‘intake’ session before the start of the program in September, and also later at moments when advise is needed.

Questions.... Ask via the chat or phone

(0317 483266) or use the contact form

on the MBF website

mbt.msc@wur.nlstudentcoachmbt@wur.nl

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