Courses

CSDB specific

Advanced Bioinformatics: data mining and data integration for life sciences

Period: 8 April - 12 April 2019, see www.CSnD.nl/courses

Faculty
Joep de Ligt, Biomedical genetics/Genetics,
Pjotr Prins, Biomedical genetics/Genetics,
Edwin Cuppen, Biomedical genetics/Genetics,
Berend Snel, Theoretical Biology and Bioinformatics,

Invited speakers (different each year), 2016 participants listed below:
Jayne Hehir-Kwa, Radboud UMC,
Ruben van Boxtel, UMC Utrecht,
Victor Guryev, Groningen University/UMC,
Mark Wilkinson, Center for Biotechnology, Madrid.Description of content
Effective mining of data and integrating data is one of the major challenges in biomedical research. Decennia of research have led to an accumulation of databases world-wide, including important resources, such as NCBI, KEGG, ENCODE, SWISS-PROT etc. Lately, new data acquisition technologies, especially next generation sequencing (NGS), are rapidly increasing the amount of information available online, from data published with papers all the way to large scale collaborations, such as The Genome Cancer Atlas (TCGA) involving a wide range of hospitals and research groups offering information on patients, diagnostics, treatments together with data on sequenced tumors, gene expression, methylation, etc. For an inspiring example see
http://www.cbioportal.org/public-portal/tumormap.do?case_id=TCGA-A2-A0CX&cancer_study_id=brca_tcga_pub.

The challenge is to effectively mine resources, such as the TCGA, after performing an experiment or getting clinical results. For example, if you are sequencing cancer tumors of patients, the question is: how to mine this public data and compare the results against your own data and results. TCGA alone numbers over 50,000 files, there is no way to mine this data by hand. Likewise we have access to 1,000 public genomes and the genome of the Netherlands (GoNL). What are feasible strategies for using this data?

In this course the morning is started with a lecture by a leading biomedical scientist. The topic can be in cancer research, for example, diagnostics or personalised medicine. The presenter will tell us about his/her research and the short term data mining and data integration issues he or she is facing. The lecture is followed by a discussion on possible approaches in solving one or more of these issues. Topics covered will include parsing tabular data, SQL databases, web services and the semantic web. The rest of the day the students will be tasked with finding a solution to a particular problem. Solving such problems can only be done through writing (small) computer programs. This course is suitable for students who take an interest in informatics and biomedical application of informatics. The course builds on the skills acquired in introductionary programming courses; having completed one of these is a hard prerequisite. The introduction to bioinformatics course is not a prerequisite but is highly recommended.

The goal of this course is to outline current data integration challenges in biology and biomedical research and discuss state-of-the-art approaches for tackling these challenges. Students from other disciplines and other universities are invited to attend this course. The topic is suitable for all students in the life sciences dealing with NGS data.

Literature/study material used:
Lectures, Scientific articles, Course laptop (students can bring their own), Online resources and documentation, Online tutorials, Unix operating system, Online discussion and Q&A platform.

Registration:
Please register online on the CS&D website: www.CSnD.nl/courses. CS&D students have priority in registration until 3 weeks before the start of the course. Thereafter, registration is on 'first-come-first-serve' basis until the maximum number of 30 participants is reached.

Mandatory for students in own Master’s programme
No.

Optional for students in other GSLS Master’s programme:
Yes.

Prerequisite knowledge:
Basic programming knowledge

Advanced Omics for Life Sciences

Period: 15 June 2020 - 19 June 2020

Lecturers:
Joep de Ligt, Biomedical genetics/Genetics, 100%
Jeroen de Ridder, Biomedical genetics/Genetics, 10%
Edwin Cuppen, Biomedical genetics/Genetics, 10%
Berend Snel, Theoretical Biology and Bioinformatics, 10%

Invited speakers (differs between years), scheduled speakers listed below:
(Cuppen) Francis Blokzijl, UMC Utrecht, 10% (DNA)
(Veldink) Wouter van Rheenen, UMCU / Rudolf Magnus, 10% (RNA)
(Heck) Maarten Altelaar, Utrecht University, 10% (Protein)
(Verhoeven-Duif) Judith Jans, UMC Utrecht, 10% (Metabolic)
 
Course description:
The correct analysis and integration of omics data has become a major component of biomedical research. The advances in technology have allowed for more sophisticated and unbiased approaches to assess the different omics data types. Large collaborative projects combined with databasing efforts have led to invaluable resources like ENCODE [https://www.encodeproject.org/], Expression Atlas [https://www.ebi.ac.uk/gxa/home], the Human Protein Atlas [http://www.proteinatlas.org/] and KEGG [http://www.genome.jp/kegg/]. These resources can provide valuable insights into your omics data and serve as a validation or quality control set when used appropriately. The challenge is to effectively analyze omics data and these large online resources after performing an experiment or getting clinical results.
For example, when analyzing tumors derived from a set of patients, the question is: how to correctly analyze your OMICs data and leverage public data by comparing these against your own data. The Cancer Genome Atlas alone numbers over 50,000 files from 3 different OMICs types. What are the correct and feasible strategies to utilize these data?
In this course a scientist (active within the respective OMICs field) starts the morning with a lecture, the accompanying scientific article will be available for prior reading. The presenter will introduce a recent study performed within their group and outline the data mining and data integration opportunities and issues they encountered. The lecture is followed by a discussion on how to conduct this research and possible approaches to expand on the current work or solve one of the encountered issues. Topics covered will include mutation analysis, expression profiling, protein abundance and metabolic pathways. In the afternoon students will be tasked with finding a solution to a challenge set by the presenter. Solving such problems can only be done through writing (small) computer programs and integrating relevant data sources.
This course is suitable for students who take an interest in informatics and biomedical application of informatics. The course builds on the skills acquired in introduction programming courses; having completed one of these is a hard prerequisite. Following the "Introduction to Bioinformatics for Molecular Biologists" course is highly recommended.
The goal of this course is to outline current omics analyses methods and the challenges and value of integrating public data in life science research. We will discuss state-of-the-art approaches for tackling these challenges. Students from other disciplines and other universities are invited to attend this course. The topic is suitable for all students in the life sciences dealing with OMICs data.

Literature/study material used:
Lectures, Scientific articles, Course laptop (students can bring their own), Online resources and documentation, Online tutorials, Unix operating system, Online discussion and Q&A platform.

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum capacity is 20 participants.

Mandatory for students in own Master’s programme:
No.

Optional for students in other GSLS Master’s programme:
Yes.

Prerequisite knowledge:
Introduction to Python/R/ other programming language.

Advanced R for Life Sciences: in-depth techniques for analysis, visualization and publishing

Many researchers will need to apply statistical analysis in their work. Often, the R statistical language is chosen, since it is well established, free, and has many packages available for different tasks. If you want to be able to use the more powerful features of R, create visually attractive figures with ggplot, write concise and organized code that you can share with others, create automatically generated reports. This course gives you the knowledge to follow one of the subsequent courses of statistical analysis for omics technologies, and linear models with R.

Literature/study material used:
Provided during the course. Students are required to bring a laptop to work online via a web page.

Analytics and Algorithms for Omics Data

Period (from-till): 3 June 2019 - 7 June 2019

Lecturer(s):
Name, faculty/department, participation (%) in course
Dr. Jeroen de Ridder, UMC University, 60%
Dr. Alexander Schoenhuth, Utrecht University, 40%

Extended course description (for Osiris):
Bioinformatics is at the heart of many modern genomics research, and encompasses the application of statistics and computer science to (large-scale) biomolecular datasets. In essence, bioinformatics is about smart ways of extracting knowledge from the enormous amounts of data that can be generated using modern measurement techniques. For instance, it plays an important role in finding the genetic origins of various diseases, such as cancer, diabetes or alzheimer.

In this course we will study some key examples of bioinformatics analyses, i.e. data analytics and computational algorithms, by reading a set of selected papers that present some significant biological conclusions. Instead of the teachers giving lectures about the methodologies, the students are stimulated to read, study and comprehend the available course material. Some lectures will be provided to ensure the basic concepts are clear.

Schedule: The course runs for five days from 9.00 till approximately 17.00. Each day will start with a lecture followed by two rounds of paper discussions that goes into depth with regards to the computational approaches taken.

Content:

  • Unsupervised learning, Hierarchical and k-means clustering, spectral clustering
  • Supervised learning, cross-validation, overtraining, Bayes classifier, Random Forest classifier
  • Dimension reduction, PCA, NMF, tSNE
  • Hidden Markov Models, Forward Backward algorithm, Viterbi
  • Sequence alignment, Dynamic programming
  • Read mapping techniques
  • Sequence data indexes, such as Burrows-Wheeler Transform
  • Genome assembly basics, de Bruijn graphs, overlap graphs
  • Hash-based techniques, for example for overlap detection

Literature/study material used:
Provided course materials (slides) will be made available through our online learning platform: elearning.ubc.uu.nl

Registration:
Please register online on the CS&D website: www.CSnD.nl/courses.
Bioinformatics Profile students will have priority when this course is followed as a part of their profile.
Thereafter, registration is on 'first-come-first-serve' basis until the maximum number of 20 participants is reached.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Basic knowledge of Linear Algebra and Statistics.

Cell Organisation in Health and Disease

Period (from – till): 16 March 2020 - 20 March 2020.
Faculty
dr. Madelon Maurice
Prof. Dr. Judith Klumperman
dr. Peter vd Sluijs
dr. Catherine Rabouille
Prof.dr. Willem Stoorvogel
Invited speaker (international)
Description of content
The purpose of this Master Class has two aspects:
-Acquire basic and advanced knowledge on membrane traffic and its relationship to disease and development.
-Use this knowledge to read a series of articles on a given subject and produce an integrated view of how the studied membrane traffic defect (due to a given mutation) explains the etiology of the disease or the developmental defect.

Course organization:
- 20 students (max) will receive training in reading and interpreting scientific literature dealing with membrane traffic in disease and development.

- First, the students get 5 introductory lectures on the relationship between different aspects of membrane traffic with diseases and development by Judith Klumperman, Peter van der Sluijs, Catherine Rabouille, Willem Stoorvogel and Madelon Maurice.
-The students are divided in 5 groups and assigned a given subject that they will prepare so at the end of this week, the students are expected to: 1) provide a concise and coherent oral presentation of research papers in a format of a journal club 20 min, including 10 min discussion combining several papers (see guidelines) given by the teachers. The presentation will have to integrate the data of these papers to make a single and cohesive story while presenting primary data (see guidelines). This is an important research exercise, so you learn to read, integrate information and write an introduction, a review, a thesis, etc.
2) After the final presentation on Friday, there will be an exam: students will be asked to answer questions about all subjects (5 in total) for 1 hour. Thus it is important that the students gather sufficient information during the presentation of fellow students. The exam also drives all participants into presenting the best you can so that others can understand.

Further remarks: The week is meant to be dedicated to this course. The students have to be together all the time, either as a small or large group. The preparation of the presentation and the research proposal has to be made together as a small group to start with. Thursday, however, is dedicated to rehearse the presentation and improve it with all fellow students of the course who do not deal with the same subject but who will critically evaluate and ask questions to improve the talks.
Grades: The grade will be based on performance during the week (interest, participation 20%), the presentation itself (with individual marks of students for presentation and discussion 40%), and the exam at the end (40%)

Literature/study material used:
varies according to assignments

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum of 20 students.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Bsc BMW / Biology

Chromosome Segregation, Aneuploidy and Cancer I

Period: 20 January 2020 - 24 January 2020

Faculty
Prof. Dr. Susanne Lens
Prof. Dr. Geert Kops
Invited guest speakers

Course description
This course will address the molecular basis for correct chromosome segregation during cell division. Defects in this process give rise to aneuploidy and many contribute to carcinogenesis.

Topics will include:

  • Checkpoints that guard proper chromosome segregation and cell division
  • Chromosome mis-segregation and cancer
  • Mitotic spindle assembly
  • Cohesion of sister-chromatids
  • Meiosis in mammalian oocytes
  • Molecular organization and mechanical properties of the kinetochore

The course will consist of lectures and discussions by national and international experts in the field, combined with literature surveys, as well as work groups on the experimental aspects of mitosis research.

Literature/study material used
Research and review papers proposed by the guest lecturers

RegistrationYou can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum capacity is 25.

Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Bsc BMS / Biology

Chromosome Segregation, Aneuploidy and Cancer I

Period: 20 January 2020 - 24 January 2020

Faculty
Prof. Dr. Susanne Lens
Prof. Dr. Geert Kops
Invited guest speakers

Course description
This course will address the molecular basis for correct chromosome segregation during cell division. Defects in this process give rise to aneuploidy and many contribute to carcinogenesis.

Topics will include:

  • Checkpoints that guard proper chromosome segregation and cell division
  • Chromosome mis-segregation and cancer
  • Mitotic spindle assembly
  • Cohesion of sister-chromatids
  • Meiosis in mammalian oocytes
  • Molecular organization and mechanical properties of the kinetochore

The course will consist of lectures and discussions by national and international experts in the field, combined with literature surveys, as well as work groups on the experimental aspects of mitosis research.

Literature/study material used
Research and review papers proposed by the guest lecturers

RegistrationYou can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum capacity is 25.

Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Bsc BMS / Biology

Concepts in Cancer Biology

Period (from – till): 4 November 2019 - 8 November 2019

Faculty
Prof. Dr. B. Burgering, Molecular Cancer Research, UMC Utrecht
Dr. T. Dansen, Molecular Cancer Research, UMC Utrecht
Guest lecturers

ContentThis (combined AIO - Master students) course features a number of seminars by renowned scientists in the field of Signal Tranduction in Cancer Biology. The Master students course is centered around the contributions of these speakers. In general, the programme of the course is set-up according to the scheme below:
Morning session:
Introduction to the Topic of the Day by a staff member.
Discussion of papers written by the 'speaker of the day' (the papers will be available for 'reading in advance' on each day of the course).
Small groups of students prepare their sets of questions they would like to have answered during the rest of the day's programme.
Afternoon session:
Seminar by the Speaker of the Day, followed by ample discussion of the work presented by the lecturer.
Students in their groups prepare a written report of the answers they have found to their original sets of questions for that day. The report is handed in at the end of the day.
Time permitting: reading in advance for the next day of the course.

The last two days of the course consist of the participation in a scientific meeting organised by CGC.nl (Cancer Genomics Consortium) held at the KIT (Royal Institute for the Tropics). This meeting has on average 10 foreign speakers many of them top class, but also of special interest to students as they are authors of their study books (e.g. Robert “BoB” Weinberg). See for the program: http://www.cancergenomics.nl/home/agenda/

Literature/study material used:
A general introduction with literature is provided, further portfolio is put together on the basis of the invited speakers, subject to be discussed is also dependent on the subject of study of the invited speakers

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Bachelor BMS / Biology

Digital Pictures: Data Integrity & Display

Period: This course is offered twice a year. First course 30 April and 1 May 2020 (BMS_P4_A), Second course 19 and 20 May 2020 (BMS_P4_B)

Lecturer
Dr. Tobias Dansen, Molecular Cancer Research, UMC Utrecht
Description of content
The output of scientific experiments often comes in the form of digital images e.g. scans of Western blots and microscopic images. This certainly has a lot of advantages, because digital images can contain spatial information and can be more telling than plain numerical data. A disadvantage of data in the form of digital images is that they can, often unintendedly, be manipulated using computer software in a way that is not in agreement with scientific standards.

In this course we will focus on what you can do and what you shouldn’t do to get the best representation of your digital image without altering the actual data. The course will be given in an interactive way, with time for practicing on assignments on laptops (provided).

The first day we will go into some theory behind digital images and practice with two different image processing software packages. The second day we will go more into presenting your images in publication quality figures and/or presentations using vector based software.

There will be a pre-course assignment to start getting a feeling for working with images. As a final assignment the students will hand in a publication quality figure made from images provided at the course.

Literature/study material used:
literature will be e-mailed to participants. Course handouts are available after the course

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Open for master students of other LS masters and PhD students

Prerequisite knowledge:
Master’s students should be in the second year of their programme.

Gene Expression, Epigenetics and Disease

Period (from – till): 27 January - 7 Febuary 2020

Course coordinator:
Dr. Eric Kalkhoven
Faculty
Dr. Eric Kalkhoven, Center for Molecular Medicine UMCU
Prof. Dr. Wouter de Laat, Hubrecht Institute
7-10 guest lecturers
Description of content
Regulation of gene expression is pivotal for the understanding of developmental programs, cellular homeostasis and many disease states including cancer, immune diseases and metabolic disorders. The gene transcription process is critically linked to regulation of chromatin. Epigenetic mechanisms such as histone modifications can transmit active/inactive states of a gene through cellular divisions. The study of transcription and chromatin regulation has received a great impetus through the availability of whole genome sequences, which sparked novel applications of high-throughput sequencing technologies. Integration of biochemistry, molecular biology, genomics, proteomics and cell biology approaches can now provide unprecedented insight into transcription and chromatin regulation in health and disease.
This course will teach the crucial concepts of regulation of gene expression, with a focus on the process of transcription at the molecular level, but also including concepts derived from cellular, developmental and disease states. Epigenetics, chromatin and genome organization will be taught, as well as state-of-the-art strategies and techniques in the field of gene regulation and genome research, all with a reference to human disease.
The covered topics are: nuclear organization, genome/gene organization, the pol II transcription machinery, chromatin regulation, epigenetics, regulation through small and long non-coding RNAs. Many techniques will be explained, including classical assays used to investigate transcription, as well as high-throughput genomic approaches and systems biology analyses. When you are only superficially interested in mechanisms of gene expression/epigenetics, this course is not suitable for you.
The course consists of a combination of lectures, exercises, literature and discussions and closes with a written exam. A large part is taught by leading (inter)national scientists (9-11 different instructors in total). The course is ideal to become acquainted with top labs working in gene expression control. The course is intense and challenging and requires full attention throughout the full duration. Although many basic molecular principles will be reintroduced, the course is only suited for students with a basic molecular understanding of gene expression and chromatin through bachelor programs such as Biomolecular Sciences taught from textbooks like Molecular Biology of the Cell (“Alberts”) or Genes (“Lewin”). In previous years this course was rated very highly (8.2-8.7).

Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
The maximum number of participants is 40.

Literature/study material used
Research papers, handed out during the course

Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
Students must have a basic molecular understanding of gene expression and chromatin through bachelor programs such as Biomolecular Sciences taught from textbooks like Molecular Biology of the Cell (“Alberts”) or Genes (“Lewin”).

Human Disease Genetics

Period (from – till): 25 May 2020 - 29 May 2020
Faculty
Koeleman B.P.C.
Bakker de, P.I.W.
Haaften van, G;
Kloosterman, W.

all from UMCU, Afdeling medische Genetica

Description of content
Most human diseases have, in part, a genetic basis. For monogenic diseases, a single DNA mutation is sufficient to cause disease, whereas a large number of DNA variants are likely to play a role for increasing one’s susceptibility to multifactorial diseases. The search for genetic variants causing monogenic diseases, such as cystic fibrosis, forms of deafness and blindness, Huntington’s disease etc., has been going on for decades, but pinpointing the genetic basis for multifactorial diseases has been unsuccessful until recently. Multifactorial diseases, such as diabetes, rheumatoid arthritis, coronary artery disease and many more, affect millions of people around the globe, and have attracted increasing scientific attention over the past ten years or so. New technological developments have made it possible to interrogate large numbers of individuals and to detect genetic risk factors with modest effect sizes that are predicted to underlie these complex diseases. These new approaches (specifically, next-generation sequencing) are now also routinely applied for research in the context of monogenic diseases (where the root causes have not yet been identified) and for diagnostics and patient care.

In this course, we will introduce the approaches taken to discover genetic variants related to disease with an emphasis on the genetic architectures for monogenic and multifactorial diseases. We will present an overview of the various technologies currently available. We will discuss the (population genetic) theory behind genetic disease studies and illustrate results for specific diseases. Exercises will give the student hands-on experience in the design and analysis of genetic disease studies.
Literature/study material used
Various papers, to be handed out.
Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum capacity is 30.

Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge
Bsc BMW / Biology

Introducing Cancer, Stem Cells & Developmental Biology

Period: 9 - 20 September 2019

Lecturer(s):
dr. Joost Koedam, Center for Molecular Medicine, DBG, UMCU
Prof. dr. Boudewijn Burgering, Center for Molecular Medicine, DBG, UMCU
>30 lecturers from UMCU, UU, Hubrecht Institute

Course descriptionThis course is a compulsory introduction to the fields of developmental biology, stem cells, cancer, genetics/genomics, and all of its associated techniques and model systems. Through lectures, literature studies and demonstrations, the new students of the CSDB Master’s program will become acquainted with many aspects of their program. The topics will be introduced by experts in the field, most of which also coordinate or participate in the elective Theoretical Courses that are offered later in the year. This will lay a good theoretical foundation, while also model systems such as C.elegans, Zebrafish and organoids will be covered. These lectures will help students in their future choices for these in-depth courses. Moreover, students will get a good impression of the research that is going on, and will start building their network and community.

The topics of the first week will include basics in developmental biology, stem cells, cancer and genetics. Recent key research papers will be handed out, which will serve as background for presentations by the students on the final day of the course. Ample time will be devoted to the ethical and societal aspects of performing research in these areas. Students will write an opinion article (essay) about an ethical issue of their choice. The second week will have self-study time scheduled to prepare these assignments.

The final day of the first week, and several days of the second week will be devoted to proteomics, metabolomics, genomics, microscopy techniques and bioinformatics. Tours and demonstrations, as well as do-it-yourself bioinformatics exercises (BYOD, bring your own device!) will be part of this.

Literature/study material used:
handouts of lectures
research papers

Registration:
Automatically upon entering the CSDB programme.

Mandatory for students in own Master’s programme:
Yes

Optional for students in other GSLS Master’s programme:
No

Prerequisite knowledge:
Same as for admission to the CSDB Master’s programme

Introduction to bioinformatics for Life Sciences

Description: “Introduction to Bioinformatics for Molecular Biologists” is a joint course for the various life science Masters programs at the Utrecht University. This introductory course provides an overview of the importance of bioinformatics in various biological disciplines. While a biological background is required, no programming skills are needed. The course can be considered a general introduction to bioinformatics, with a focus on the research that is performed at Utrecht University. The theory and tools for bioinformatics provided are very useful for any life science researcher. The course will be partially theoretical with lectures taking up to 30% of the day while the major focus will be on working with various tools and datasets. These computer tasks are performed in groups of 2 students. The maximum number of participants for this course is 40 students. The course will be concluded on the last day with an exam that consists of normal pen-and-paper questions but also of tasks that should be completed on the computer. Active participation during the course provides sufficient preparation to complete the exam. Furthermore, follow-up courses are organized later in the year that will allow you to specialize in specific directions. Students are expected to be familiar with the subjects from this introductory course when participating in any of the follow-up courses.

Registration: via the webpage of the CGDB: http://www.cgdb.nl/courses/

Mandatory for students in Master’s programme: No

Optional for students in other Master’s programmes GS-LS: Neuroscience and Cognition, especially the tracks Cognitive Neuroscience and Behavioural Neuroscience; Environmental Biology, especially the specialization programme Behavioural Ecology; and any other master programme with relevant basal courses.

Introduction to Python for Life Sciences

Period: This course is offered twice a year. First course 1 October – 5 October 2018, Second course: 11 February – 15 February 2019, see website www.csnd.nl/courses/
Course coordinator
Aridaman Pandit of the Laboratory of Translational Immunology. E-mail: a.pandit@umcutrecht.nl

Course description
Schedule: The course runs for five days from 9.15 till approximately 16.00. Each day will start with a lecture followed by an interactive hands-on computer practical to teach students the basics of programming in Python. Attendance is obligatory at all times. An assignment handed out on Wednesday is used for grading the course.

Content: Nowadays almost all disciplines in medical and biological sciences have to deal with an increasing amount of data. Frequently Microsoft Excel was used to load and process such datasets, however there are many examples where datasets get simply to large or structurally to complicated that another approach, using a programming language) is not only very much preferred but basically essential.
The aim of this course is to provide students with a basis in programming using the programming language Python.
Students will learn how to use basic functions of Python via the command line and at the end of the week processes files and request data from the Ensembl database using self made scripts. Topics include: Linux basics, variables, lists, loops, functions, modules, regular expressions, file handling and obtaining data from Ensembl.

Literature/study material used:
Provided course materials (slides); Python (will be available via individual Amazon cloud computers, https://www.python.org/)

Registration:
Please register online on the CS&D website: www.CSnD.nl/courses. CS&D and MCLS students have priority in registration until 3 weeks before the start of the course. Thereafter, registration is on 'first-come-first-serve' basis until the maximum number of 25 participants is reached.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Prerequisite knowledge:
BSc BMW / Biology; Basic computer skills.

Introduction to R for Life Sciences

Period: 8 October - 12 October 2018 and 18 February - 22 Februari 2019.
Course descriptionSchedule:
The course runs for five days from approximately 9.00 till 16.00. Each day consists of a morning and afternoon session that will start with a short lecture followed by an interactive hands-on computer practical to familiarize students with R. Attendance is required at all times. A programming assignment in R is used for grading the course.

Content:
Due to technological advances in molecular biology (genomics, large-scale systems biology) research in the life sciences is becoming increasingly data rich. Currently, appropriate analyses of large-scale datasets (proteomics, genomes, Htseq, RNAseq, ChIPseq, etc) are a limiting factor. The aim of this course is to give a basic training in R for molecular biologists.
R is a widely used software environment for statistical computing and provides a wide variety of libraries for data manipulation, modeling and visualization. The course will give an introduction to R and Rstudio, an integrated development environment for R. Throughout the course you will use a single data set to take you through the basic functionality of R and Rstudio in an interactive fashion. Supplemented with several commonly used libraries, plotting and analyses routines and supporting data sets this will familiarize students with R and at the same time show the value of using R for analyzing and visualizing large amounts of data. At the beginning of the course you will be given a programming assignment that has to be handed in at the end of the course, based upon which a grade will be given.

Prerequisites knowledge

  • A good understanding of molecular biology
  • Affinity with data-driven life science research
  • Previous experience with computer programming is not required

Course material:

  • R (will be available on the provided course laptops, www.r-project.org)
  • Rstudio (will be available on the provided course laptops, www.rstudio.com)
  • Lectures, exercises and corrections handouts will be provided during the course.

RegistrationPlease register online on the CS&D website: www.CSnD.nl/courses. CS&D students have priority in registration until 3 weeks before the start of the course. Thereafter, registration is on 'first-come-first-serve' basis until the maximum number of 30 participants is reached.

Mandatory for students in Master’s programme:
No, except for students with a Bioinformatics Profile

Optional for students in other GSLS Master’s programme:
Yes

Introduction to Research Data Management for Life Sciences

The course Introduction to Research Data Management gives practical insights on Data Management for scientists. Basic knowledge of relational databases, entity-relationships models, relational models and SQL with MySQL is provided during the course. The programming language used to process data from and to the database is Python.

Proper management of research data is a requirement by funding agencies, publishers or academic institutions. This course provides the technical keys to understand how to model, structure and query data. Benefits of having these skills are numerous: a better insight on how to manage research data and comply with research data management policies, more efficiently store and reuse important data for computational experiments and awareness of the current techniques available to make these tasks easier. The modeling part of the course is focused on communicating the important aspects of datasets to colleagues or an audience via simple models that can be included in posters or other types of publications.

The course is divided into six modules:

  1. Research Data Management and Databases
  2. Data and Models
  3. Starting with MySQL and Workbench
  4. Structuring and Querying Data
  5. Storing and Processing Data with Python
  6. Working with data repositories

Next, more practical insights are given, mainly about:

  • Data modeling with E-R and relational schemas
  • SQL (mainly DML)
  • Working with MySQL and Workbench (modeling)
  • Working with publicly available data by modeling, importing and integrating data into relational databases.
  • Working with data schemas and public repositories

The final grade consists of:

  • Online quizzes (10%), three attempts per quiz. Min. score is 6 per quiz.
  • Two minor assignments (20%), No minimum score. There is one opportunity to resubmit one of the two minor assignments to improve its grade.
  • A final assignment (70%), Min. score is 5. There is one opportunity to resubmit the final assignment is the grade is less than 6.

Min. final grade to pass the course: 5.5

Literature/study material used:
Course content and material is hosted on https://elearning.ubc.uu.nl

A virtual machine (Ubuntu Linux) containing all the necessary software is available for students.
Alternatively, students may choose to install the required software on their own machine. In that case, they will need a computer environment with:

  • Minimum: Python 2.7.9 or Python 3.4.x/3.5.x
  • Jupyter (IPython) notebook
  • MySQL 5.7.X branch
  • MySQL Workbench CE 6.3.X
  • Python pandas (http://pandas.pydata.org/)
  • Windows users can install WinPython (http://winpython.github.io/) containing all the necessary modules by default

Introduction to Stem Cells

Period (from – till): 6 January 2020 - 17 January 2020

Faculty
Koen Braat, Cell Biology, UMC Utrecht, Course Director
Paul Coffer, Cell Biology, UMC Utrecht, Course Director
Niels Geijsen, Hubrecht Laboratory, Course Director
Geijsen, organizer theme day
Robin, organizer theme day
Van Rooij, organizer 0.5 theme day
Gawlitta, organizer 0.5 theme day
Middendorp, organizer theme day and “closing” seminar
Description of content
Stem cells have the remarkable potential to develop into many different cell types in the body during early life and growth. In addition, in many tissues they serve as a sort of internal repair system, dividing essentially without limit to replenish other cells as long as the person or animal is still alive. When a stem cell divides, each new cell has the potential either to remain a stem cell or become another type of cell with a more specialized function, such as a muscle cell, a red blood cell, or a brain cell.

Stem cells are distinguished from other cell types by two important characteristics. First, they are unspecialized cells capable of renewing themselves through cell division, sometimes after long periods of inactivity. Second, under certain physiologic or experimental conditions, they can be induced to become tissue- or organ-specific cells with special functions. In some organs, such as the gut and bone marrow, stem cells regularly divide to repair and replace worn out or damaged tissues. In other organs, however, such as the pancreas and the heart, stem cells only divide under special conditions. Given their unique regenerative abilities, stem cells offer new potentials for treating disease.

This 5-day course will address both fundamental mechanisms regulating stem cell function as well as considerations concerning the use of stem cell therapies in the clinic.

Literature/study material used:
Primary literature to be provided by course directors and guest speakers

Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Maximum number of participants is 50 students.

Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes. Registrations from Master and PhD students of the CSDB and RMT programs will be considered first
Prerequisite knowledge
Bsc BMW / Biology knowledge of molecular and cellular biology; interest in regenerative medicine and stem cell biology

Metabolic Pathways: From Cell to Disease

Period (from – till): 4 May 2020 - 15 May 2020

Lecturers
J. Koedam, PhD, UMCU, DBG, Afdeling MCR en Metabolic Diseases, lecturer, supervisor, coordinator
E. Kalkhoven, PhD, UMCU, DBG, Afdeling MCR en Metabolic Diseases, lecturer and supervisor
S. van Mil, PhD, UMCU, DBG, Afdeling MCR en Metabolic Diseases, lecturer and supervisor
Prof. B. Burgering, UMCU, Afdeling MCR en Metabolic Diseases, lecturer and supervisor
Dr. T. Dansen, UMCU, Afdeling MCR, lecturer
N. Verhoeven, PhD, UMCU, DBG, Afdeling Medische Genetica, Metabole Diagnostiek, lecturer and supervisor.

Course content
The course Metabolic Pathways approaches metabolism and endocrinology from several different angles. Lectures and tutorials in the first week discuss the molecular mechanisms involved in regulating glucose, fat and protein homeostasis. Transcriptional regulation of metabolism and oxygen metabolism will be discussed, as well as metabolic dysregulation in diseases like type 2 diabetes and cancer. Finally, the course will introduce metabolomics and other diagnostic tools for monogenetic and multifactorial metabolic diseases. Presentations by students and a written exam are part of this week. In the second week students have to develop a new research aim in a small group (3-5 students) and present this as a poster.

Literature/study material used:
Recent reviews and original articles

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
CS&D students (max. 20)
Biology of Disease students (max. 20) and other GSLS students
The maximum number of participants in total is 40.

Mandatory for students in Master’s programme:
CSDB: can be part of the 15 EC Theoretical Courses
BoD students: This course is one of the specific cardiovascular BoD-courses. Additional to the mandatory Kick off course, BoD students should accomplish 12 EC with specific (cardiovascular) BoD courses.

Optional for students from other GSLS Master's programmes:
Yes, but only when the maximum enrolment of 40 has not yet been reached.

Prerequisite knowledge:
A bachelor degree in Biomedical Sciences or equivalent. The student must have thorough knowledge of basic biochemistry, cell biology and physiology. Basic concepts of metabolism will be recapitulated at the beginning of the course. Students should be proficient in English, and be able to quickly grasp the main points of a research paper.

Model Organism

Period: 8 April - 12 April 2019
Please note: this course is only given once per 2 years.

Lecturer(s):
Name, faculty/department, participation (%) in course
Prof. dr. Rik Korswagen, Hubrecht Institute and Department of Biology, Faculty of Science, UU
Dr. Catherine Rabouille, Hubrecht Institute and UMC Utrecht
Dr. Matilde Galli, Hubrecht Institute
Invited speakers

Description of contentGenetic analysis in model organisms is a powerful approach to gain detailed insight into biological processes. In this course, we will highlight research in model organisms that cover a wide range of topics in biomedical research: cell cycle studies in yeast, cell and developmental biology in C. elegans and Drosophila, stem cell biology and regeneration in planarians and organ development and tissue homeostasis in the mouse. The aim of the course is to provide a basic understanding of how genetics in these organisms can be used to unravel important biological processes. In addition, the course teaches a variety of skills that are important for every researcher, including critical reading and oral presentation.

Each day of the course, a different model organism will be discussed, with a basic introductory lecture in the morning and a research seminar in the afternoon. The lectures and seminars will be given by local as well as invited international speakers.

In addition to the lectures and seminars, the students will read selected papers on the different topics, discuss these papers with the course organizers and the invited speakers and present these papers in a formal presentation at the end of the course.

Literature/study material used:

Recent articles featuring the model organisms covered in the course.

Registration:
www.CSnD.nl/courses

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Given the low number (20) of students that can be accepted, preference will be given to students of the CS&D.

Prerequisite knowledge:
BSc BMW / Biology

Introduction Biomolecular Mass Spectrometry

Short course description (max. 50 words – for studyguide app):
This one-week course aims to give an overview of techniques used in proteomics, particularly mass spectrometry, along with examples of their application to biological research.

Extended course description (for Osiris):
Over the past few years, mass spectrometry has become a powerful technique for the identification and characterization of single proteins, but also in the analysis of complex mixtures (e.g. protein complexes, proteins in organelles and entire cells). With recent developments in mass spectrometry, but also in separation science (such as gel electrophoresis and peptide chromatography), proteomics increasingly finds its place among established biochemical techniques. More importantly, it has proven itself as a discovery tool in many biological and biomedical applications. This one-week course aims to give an overview of techniques used in proteomics, particularly mass spectrometry, along with examples of their application to biological research. Topics that will be covered in the course are:
· principles of mass spectrometry
· protein identification by MS
· protein separation techniques
· peptide separation techniques, including (multidimensional) chromatography
· large scale proteomics
· bioinformatics
· quantitative proteomics
· analysis of protein networks
· analysis of protein posttranslational modifications (including phosphorylation)
Applications of these techniques will be illustrated by invited speakers who will show examples of mass spectrometry applied to biological problems in developmental biology, cell biology and immunology. An important part of the course is practical and hands-on training in the interpretation of experimental data (manual and automated interpretation of spectra, database searching, bioinformatics). In addition, a lab-demo will be organized at the Dept. of Biomolecular Mass Spectrometry to show various instruments in action.

Literature/study material used:
Research articles and presentations provided by lecturers

This course is not for chemistry or MLS students who did already the course SK-B2MSPR

General courses

Academic Writing

Period (from – till): This course will be given three times a year. See dates below for start and end dates of the course editions. FacultyCourse coordinator: Eva Herold, MSc, programme advisor BMS, UMC Utrecht, - If you have any questions regarding the content of the course, please contact the lecturer.Lecturer: Frans van Dam, Lecturer science communication, Faculty of Science

Course description
This mini-course will focus on the demands of ‘academic’ writing in English, and will include topics such as writing strategies, text plans, revision and structure. It is particularly helpful for students embarking on a research thesis or an internship report.

Registration
This course is (in first instance) open to all second year Master’s students of the Graduate School of Life Sciences. It is important that you are already experienced or starting with writing an internship report or Master's thesis.
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide and placement for the course is on a "first come, first served" basis.
The maximum number of participants is 15, the minimum 6.
Course datesGroup 1 Dates 12 Sept 2019 – 31 Oct 2019 (Osiris Student starting block: BMS_P1_A):
Meeting 1: Thursday 12 September 2019 - 10:00 – 13:00h
Meeting 2: Thursday 26 September 2019 – 9:30 – 12:30h
Meeting 3: Thursday 10 October 2019 – 9:30 – 12:30h
Meeting 4: Thursday 31 October 2019 – 9:30 – 12:30h

Group 2 dates will follow at a later stage
Meeting 1:
Meeting 2:
Meeting 3:
Meeting 4:

Group 3 dates will follow at a later stage
Meeting 1:
Meeting 2:
Meeting 3:
Meeting 4:
Literature/study material used
Will be handed out during the meetings.
Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Yes.
Testimonials
"This short course is very useful and instructive"
"The teacher is very enthusiastic"
"You work on your own report"
"Useful advise about the writing process and common pitfalls"
"Eye-opener"

Basics of Biostatistics

Period (from – till): 11 November 2019 - December 2019

Programme:
The more detailed programme of the course (including the exact enddate) will follow when available.
Faculty
Paul Westers, GNK (coordinator)
Cas Kruitwagen, GNK (weblecturer)
Rebecca Stellato, GNK (weblecturer)

Course description
Please note:Basic of Biostatistics is a 'Blended course'. The lectures of this course are offered online via Elevate and are self-studies. During the course there are some optional face-to-face meetings with the lecturers. These meetings are held at UMC Utrecht.

The four week course(4,5 ECTS, 32 hours per week) provides an introduction to statistical methodology and supplies a number of statistical techniques important for practical data analysis. Examples from the medical and biological fields will be used in exercises. Datasets will be analyzed on the computer using the statistical package SPSS. The first part covers the "Basics of Biostatistics", statistical testing for one and two samples, confidence intervals, simple linear regression and correlation, one way analysis of variance, binomial distribution and proportions, analysis of contingency tables and non-parametric statistics. The second part covers an "Introduction to Modeling" and introduces the most important regression models used in biomedical research, that can be used in the study of the relation between a number of explanatory variables on the one hand, and the occurrence of an outcome on the other: multiple regression and logistic regression.
Note: Some basic statistical notions will be assumed known, such as measures of location (mean, median) and scale (variance, standard deviation), the normal distribution, standard error of the mean. They will not explicitly be repeated in the course, but will be used implicitly. If necessary, participants should refresh their knowledge using a statistics book used in previous courses, or using the statistics e-books.

Literature/study material used:
During the course all the course material will be online available. Besides this online material you can use also one of the following statistical books:

  • W.W. Daniel, Biostatistics: Basic Concepts and Methodology for the Health Sciences, International student version, 9th Edition. John Wiley & Sons, 2010;
  • P. Armitage, G. Berry and J.N.S. Matthews, Statistical Methods in Medical Research, 4th edition. Wiley-Blackwell, 2001;
  • M.C. Whitlock and D. Schluter. The Analysis of Biological Data. Roberts and Company Publishers, 2009;
  • J.H. Zar, Biostatistical Analysis, 5th Edition. Pearson Education International, 2010.

The first two books have more medical examples, whereas the last two books more biological examples. These reference books remain useful long after you have completed the course. They can be obtained from scientific bookstores. You are not obliged to use any of these books during the course.
Brief manuals of SPSS are included in the workbook of the course. If you are interested in more detailed manuals we recommend one of the following books:

  • A. de Vocht, Basishandboek SPSS 16, Bijleveld, 2008;
  • A. Field, Discovering Statistics Using SPSS, 3rd edition. SAGE Publications Ltd, 2009;
  • The very extended help function of SPSS itself.

An overview of all kinds of statistical hyperlinks (books, applets, software et cetera) on the internet is also given in the online course manual.

Examination
The examination consists of two parts, namely:

  1. a case study (25% of final grade)
  2. a final test (75% of final grade) consisting of open and multiple choice questions.

The grades for both parts should be at least 5the final test must be at least 5. To pass for the course the final grade should be at least 5.5. If the final grade is lower than 4 it is not allowed to do the re-exam, except if there is a permission from the exam committee.
Furthermore active (online) attendance is mandatory.

Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Students will be dived into four groups. The number of students per group is limited to 15 (60 students in total).
Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Yes.
Prerequisite knowledge
Although active statistical knowledge is not a prerequisite, we assume some basic knowledge on statistics and mathematics acquired through, for example, courses in biostatistics in the bachelor programme or self study.

The basic knowledge we assume are:
1) the concepts of population and sample;
2) histogram, boxplot, frequency table, scatterplot, contingency table;
3) mean, median, mode;
4) variance, standard deviation, range, interquartile range, standard error of the mean;
5) probability, probability distributions (especially the normal distribution).

If you want to refresh your basic knowledge we recommend one of the following sources of information (see also study material):

  • Chapters 1 till 5 of the book of W.W. Daniel;
  • Chapters 1 till 3 of the book of P. Armitage, G. Berry and J.N.S. Matthews;
  • Chapters 1 2, 3, 5 and 10 of the book of M.C. Whitlock and D. Schluter;
  • Chapters 1 till 6 of the book of J.H. Zar;
  • Module A and B of the Dutch E-learning software COSO (ComputerOndersteund StatistiekOnderwijs). It requires the (free) software authorware to run;
  • Module I, II, III, V of the very advanced online textbook Online Statbook;
  • Modules 1 and 2 (e-book) and/or module 1 (exercises) of CAST (Computer-Assisted Statistics Textbooks) that consists of a collection of electronic textbooks (e-books).

Several weeks before the start of the course there will be a test available for testing your basic knowledge on statistics and mathematics. It is then also possible to ask questions with respect to the basic knowledge to the lecturers. Both will be features of the Elevate environment of this course.

Bio-inspiration Essentials

The subjects being addressed
This is a course that introduces the field of Bio-Inspiration. We start to elucidate the philosophical and historical roots of the concept of bio-inspiration. We will touch upon movements like: deep ecology and permaculture and illustrious predecessors such as, Leonardo da Vinci, Buckminster fuller, Viktor Schauberger, Jay Harman and Bill Mollison.
Next, we will give an overview of the main bio-inspired approaches, being: biomimicry, bionics, nature inspired design, natural capitalism, biophilia, Circular Economy and CtoC. Moreover, you will learn to see similarities and differences, by to comparing and classifying different bio-inspired approaches.
Finally, we will address Design as a discipline and process. In this way you can start to formulate and explore possibilities for innovation as a product, process or systems innovation.
You learn how to define the function you want to ‘biologize’. By doing so, you will describe the scope and hoped-for-outcome in such a way that a biologist can deliver the information as an important co-creative step in an innovation process.

This is an online course stretching over 10 weeks with a study load of approximately 7 hours per week. The course consists of web lectures as well as articles, group assignments, individual assignments, peer feedback and feedback from teachers. During the course you interact with other participants through assignments and discussions. The course is moderated actively by a professional moderator and teaching staff.

The added value for the participants
For students with a chemical biological or bio-medical background it gives a first introduction into a whole new and promising field that combines economic values and methods (innovation) with nature based approaches.
For entrepreneurs, programme & project managers, policymakers, trade and industry professionals: the course will help you to understand the main concepts within bio-inspiration that allow you initiate and direct bio-inspired innovation-trajectories.

Summary of course content (max 75 words)
This course introduces a new field in Science and Design: Bio-Inspiration you will learn to look at nature as source of knowledge that will help to make our products, processes and systems part of nature, compatible with and supporting a transition to a circular economy instead of designing for the ‘dump’. After an overview of different Biologically Inspired approaches you will learn to define the scope and function of an innovation and write a first design-brief.

Cardiac Regenerative Medicine

Period (from - till): 27 January 2020 - 7 February 2020
Lecturer(s):
Lectures are provided by (guest) lecturers from the Hubrecht Institute, UMCU, and other national cardiac RM experts. Working groups are administered by guest lecturers from UMCU. Laymen and/or patients are involved in assignment(s).

Course description:
In this course the student will get acquainted with the application of regenerative medicine in cardiac diseases. Subjects like cardiac development, reprogramming, RM treatment options including non-cell based therapies and translational cardiac RM are addressed. In addition, students are introduced in the interpretation and processing of study data, and get acquainted with the impact of research on society, in particular on patients. The course consists of lectures, interactive meetings, an exam, and a group assignment, supervised by experts and laymen.

Literature/study material used:
- Primary literature
- E-module
- Textbook Medical Physiology (background information)

Registration:
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.

Mandatory for students in own Master’s programme:
For BoD students: this course is one of the specific cardiovascular BoD-courses. Additional to the mandatory Kick off course, BoD students should accomplish 12 EC with specific (cardiovascular) BoD courses.

Optional for students in other GSLS Master’s programme:
Yes. RMT and BoD students have priority for enrollment.

Prerequisite knowledge:
Bachelor in Life Sciences and basic knowledge about cell biology and cardiac physiology.

Co-create: life’s professional challenges

Period (from – till): 4 Februari - 15 Februari 2019.

Course Coordinator: Ing. Michèle Gerbrands (m.c.gerbrands@umcutrecht.nl)

Facluty and Lecturer(s):
Heleen van Ravenswaaij Msc, Biomedical Sciences.
Heleen and Michele developed this elective course in co-operation with Career Services.
A diverse groups of lecturers and professionals from the educational and corporate world will share their knowledge and skills during this elective course

Course description:
As a bachelor year 3 / master student of the University Utrecht (UU) you are not far away from graduating, taking your first steps into the professional world. You will be challenged to work with a diverse group of colleagues, co-operate, and solve complex problems that fit users and society’s needs. This implicates that you need insights in how to grow as a professional in a fast changing world, be able to attain the right knowledge and skills.
Gaining new skills implicates the ability to actively plan, reflect, learn and experience your way into these skills to keep on track in a world where ‘life-long learning’ has become the standard.

This two-week elective course offers you a challenge to create a concept for a client in co-operation and co-creation with peers from several bachelor (year 3) and master programmes and professionals from the educational and corporate world. You are offered short inspirational sessions and workshops to discover which team- and individual based (soft)skills, techniques and tools are needed to deliver a concept. At a networking event you will pitch the concept and receive feedback. Several coaches are available if you need help (on-demand coaching). You will present your final concept to the client and a jury using a pitch and a report.

You will create an elevator pitch. Being able to pitch your own unique set of skills can assist you in your future employability. Therefore, a coach will guide you through the process of making this pitch, and you will hand in a video of the pitch.

For more Information visit: www.co-challenge.comwww.co-challenge.comwww.co-challenge.com

This course is inspired on a co-creation event EduChallenge. A video of this challenge can be watched on: https://www.youtube.com/watch?v=_iyCVDV9ACw

Literature/study material used:
-

Registration:
The registration is via Osiris Student. Please find additional information about the registration on the Study Guide.
UU students need to register for the course via Osiris Student (Osiris Student starting block: BMS P3 A).
In addition, UU students need to send an email to Michèle Gerbrands (m.c.gerbrands@umcutrecht.nl) with the following information:
-Available full time (9:00- 16:30) during the course: O yes/ O No
-Short motivation (1 A4 page) why you want to participate, addressing the following topics:

  • What is, according to you, entrepreneurship?
  • What do you think you can learn from this course and what do you expect in general?
  • What do you think you can offer your peers in this course (in terms of knowledge, skills, personality etc.)?

PLEASE NOTE: the Osiris registration is closed but there are still places available. UU students can register via the registration period on 10/11 January. You can already send you motivation by email.

Other (non-UU) students who want to apply for this course, need to send an email to Michèle Gerbrands (m.c.gerbrands@umcutrecht.nl).
Please include the following information:
Surname
Initials
First name
Master/beachelor programme:
Student number
Phone number
Mail address
Available full time (9:00- 16:30) during the course: O yes/ O No
Short motivation (1 A4 page) why you want to participate, addressing the following topics:

  • What is, according to you, entrepreneurship?
  • What do you think you can learn from this course and what do you expect in general?
  • What do you think you can offer your peers in this course (in terms of knowledge, skills, personality etc.)?

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Remarks
There is a limit of 25 students. Registration is on first come, first served basis (max. 6 students per bachelor/master) if the applicant will meet the following criteria:

  • You are available (full time) during the course (9:00-16:30).
  • Short motivational letter why you want to attend this elective course.

Every master student and bachelor year 3 from the UU can participate in this elective course. The theme of this real-world problem you will be solving is Healthy Urban living. You will be developing a concept for the City of Utrecht. A detailed description of the assignment will be presented online before the start of the course and face-to-face on day 1 of the course.
The course will be offered in English.

Schedule
A detailed schedule will be online before the start of the course and handed at the first meeting. We will start every day at 09:00 a.m. with an informal activity and end around 16:30 p.m. On day 4 the day ends at 18:30 p.m. due to the networking event.

Communicating Life Sciences

Period (from – till): 12 September 2019 – 21 November 2019.
Faculty
Course coordinator: Eva Herold, Msc, programme advisor BMS, UMC Utrecht, - If you have any questions regarding the content of the course, please contact the lecturer.
Lecturer: Connie Engelberts, MSc, science editor, UMC Utrecht
Course description
During this course, the participants will write and edit articles for three editions of a digital newsmagazine from the Graduate School of Life Sciences. The course starts with three meetings in which the students learn to identify interests of their target group, practice interview techniques and exercise in popular science writing. In the second half of the course, the students will form an editorial board and write at least three popular science articles about Utrecht life sciences research. The course is available for 4-10 students.

Previous issues of Master for life magazine can be found here.

Programme12-9-2019Thursday13:1517:0019-9-2019Thursday13:1517:003-10-2019Thursday13:1517:0017-10-2019Thursday13:1517:0031-10-2019Thursday13:1517:0021-11-2019Thursday13:1517:00
Literature/study material
N.A.
RegistrationYou can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Registration is on a "first come, first served" basis. The maximum number of participants is 10, with a minimum of 4.

Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Yes.

English for Academic Purposes

Period (from – till): Seven times a year. The exact dates are displayed in the table below. Dates for groups 1 and 2 available, other groups to be announced.
Faculty
Teachers from Babel Talen, Utrecht

Course description
The Babel Language Institute organises an 'English for academic purposes' course specifically for Life Sciences students. You can take this course as part of your elective component, if your programme coordinator agrees.

This English for Academic Purposes course focuses on giving academic presentations and writing an academic paper. The students’ own subjects will be used as a basis for language work. We will consider some essential elements of a presentation: opening, closing, signposting the organisation, referring to visuals, handling questions, adopting the right body language, and involving the audien­ce. Students will learn how to give feedback and will improve their oral fluency and their vocabulary throughout the course.Furthermore, we will focus on language aspects relating to writing an academic paper. We will analyse its information and look at language conventions. Moreover, we will discuss some issues involving punctuation, formal and informal English, wordiness and the use of linking words. This course aims to develop and improve the writing and presenting skills students need in their master programme. In addition, students will activate and expand their vocabulary and improve their fluency in English.

The course length is 10 meetings of 2 hours. Students need to invest 3-5 hours of self-study per week. Students will pass the course if they attend at least nine meetings, have given a presentation, and have handed in a paper.
Literature/study material used
Textbook (writing and presenting scientific papers) and loose-leaf material will be handed out during the meetings.
RegistrationRegistration is on a "first come, first served" basis. Registration for the courses will be through OSIRIS Studet. In the table below the corresponding registration periods for each edition have been added under the group number, to indicate which one you should use when registering via Osiris Student. More information about the registration procedure can be found here on the Studyguide.The maximum number of participants per group is 10, the minimum 6.
Mandatory for students in Master’s programme
N.A.

Optional for students in other GSLS Master’s programme:
Yes.

Prerequisite knowledge
The English proficiency is of an upperintermediate to advanced level.

Teaching Schedule:
The course is taught from 19:15-21:15 in the Hijmans van den Bergh building.Group:
Osiris:group 1
BMS_P1_Agroup 2
BMS_P1_Bgroup 3
tbagroup 4
tbagroup 5
tbagroup 6
tbagroup 7
tba mondaytuesday 12-9-20193-9-2019 29-9-201910-9-2019 316-9-201917-9-2019 423-9-201924-9-2019 530-9-20191-10-2019 67-10-20198-10-2019 714-10-201915-10-2019 821-10-201922-10-2019 928-10-201929-10-2019 104-11-20195-11-2019 reservetbatba reservetbatba

Essentials of Neuroscience

Period (from – till):
Essentials of Neuroscience Face-to-face course: 20 January 2020 - 31 January 2020
Essentials of Clinical Neuroscience Online course: 11 November 2019 following through Period 2.
Faculty
Ramakers, Adan, Burbach, Pasterkamp, Hol; UMC Utrecht Brain Center, Department of Translational Neuroscience.
Course descriptionOverall aim
The aim of the course is to provide sufficient background in molecular and cellular neuroscience to understand mechanisms underlying psychiatiric and neurological diseases.

Description of the Essentials of Neuroscience Face-to-face course:
This intense two weeks course is intended for non-neuroscience master students who want to get more background into neuroscience. The lectures during the course cover a broad range of neuroscience topics from gene to neurological disease and include neuro-anatomy, neurodevelopment, synaptic plasticity, neurogenetics and diseases. The lectures are given by experts from the UMC Utrecht Brain Center. During the afternoons the students will work in couples on an assignment on a neurological disease. This assignment will results in a scientific presentation of a research proposal on the disease, which will discuss all aspects covered in the lectures, ranging from clinical symptoms and treatment, to molecular and cellular mechanisms, to genetic studies and genes involved. These presentations will be held on the last Friday during a symposium.

Description of the Essentials of Clinical Neuroscience Online course:
This online course gives you a unique opportunity to study the state of the art insights in Neurosciences, discover the research strengths of UMC Utrecht and experience our educational philosophy.With participants from all over the world you will follow weblectures by top UMC Utrecht neuroscientists, discuss recent developments in this field and make assignments and group projects online. This course gives you a unique opportunity to study the state of the art insights in Neurosciences, discover the research strengths of UMC Utrecht and experience our educational philosophy. Wherever you are, whenever you are available you can join our academic community of eager, young minds from behind your computer!
The course will consist of web lectures by renowned experts as well as articles, group assignments, individual assignments, peer feedback and feedback from teachers. During the course you will interact with other participants through assignments and discussions. The course will be moderated actively by professional moderators and teaching staff of the Brain Center Rudolf Magnus of UMC Utrecht.

Literature/study material used:
Parts of Neuroscience (Purves et al., Sinauer Ass.Inc., Sunderland, Massachusetts, 4e editie, 2004 (ISBN 978-0-87893-697-7)) and recent reviews and original articles.

Registration:
Essentials of Neuroscience Face-to-face course: You can register for this course via Osiris Student via BMS_P2_B. More information about the registration procedure can be found here on the Studyguide. The maximum number of participants is 40.
Essentials of Clinical Neuroscience Online course: You can register for this course via Osiris Student via BMS_P2_A. More information about the registration procedure can be found here on the Studyguide. The maximum number of participants is 16.

Mandatory for students in own Master’s programme:
BoD students: This course is one of the specific cardiovascular BoD-courses. Additional to the mandatory Kick off course, BoD students should accomplish 12 EC with specific (cardiovascular) BoD courses.
This is not applicable for the online variant of this course.

Optional for students in other GSLS Master’s programme:
Yes, except for NSCN students.

Prerequisite knowledge:
No special requirements.

Fundamentals of Biofabrication, online course

Note: this is an online course stretching over 9 weeks with a study load of approximately 10 hours per week. The course contains weekly deadlines for group and individual assignments, as well as constant participation and peer interactions in group discussions. Students should take this into account when registering for the course based on other workload (courses/internships).

Period: 18 November 2019 - 2 February 2020 (2-week Christmas holiday)

Course coordinator: Prof. dr. ir. Jos Malda
Lecturer: Paulina Nunez Bernal, MSc. (p.nunezbernal@umcutrecht.nl)

Course content
Biofabrication combines advanced 3D fabrication techniques with biological systems to create designed tissue constructs, which can be applied for tissue engineering, as 3D in vitro biological models or as medical therapeutic products. This e-­course aims to provide the student with the fundamental knowledge on the various aspects of biofabrication, including 3D printing techniques, biomaterials, tissue engineering, applications, translation and ethics.

The subjects being addressed:

  • 3D printing history, techniques, applications
  • CAD/CAM, 3D modelling, STL, G-code
  • Medical imaging to printing
  • 3D printing techniques: additive manufacturing, robotic
    dispensing, fused deposition modelling, electrospinning,
    stereolithography, powder printing
  • 3D printing in the clinic: devices and implants
  • Biomaterials: polymers, bioinks, tissue­-derived matrices
  • Cells and stem cells
  • Cell printing
  • Applications: cartilage, liver, cardiovascular system,
    organ­-on-­a-­chip, in vitro models
  • Translation, bench-­to­-bedside
  • Automation, implementation, and regulation of these technologies
  • Ethics

The added value for the participants:
This course provides fundamental knowledge on biofabrication and is developed by a leading research group within the biofabrication field. Weblectures are given by experts in the fields of tissue engineering, materials science, mechanical engineering, medicine, biology and ethics.

Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.
Students must send a short motivation letter (200-300 words) before the 29th of September, describing their reasons for taking the course, as well as their willingness to participate in its discussions and assignments and to meet deadlines. Please send this letter in an email to p.nunezbernal@umcutrecht.nl after completing the registration process via OSIRIS.

Entry requirements
None

History of Medicine and the Biomedical Sciences

Period (from – till): 14 February 2019 - 18 April 2019
Faculty:
Prof. dr. F.G. Huisman, Julius Centre UMC Utrecht
Course description:
This is a nine-week course that is part of the Research Master History and Philosophy of Science, offered by the Descartes Centre for the History and Philosophy of the Sciences and the Humanities. In principle, it is open to all MA students of the Graduate School of the Life Sciences.
Modern biomedical science and modern medicine originated - both epistemologically and institutionally – in the period between 1850 and 1950. The epoch not only witnessed the birth of the modern hospital and the laboratory, but there was a growing awareness that the state had an important role to play in public health as well. Taken together, the hospital, the laboratory and the caring state can be considered as the symbols of modernity.

Over the course of time, the medical scientist and the clinician have become valuable citizens, who transformed our health care system profoundly. At the same time, scientific progress has come with problems and drawbacks. In order to understand modern medicine and health care, it makes sense to take a look at its historical roots.
This course is an introduction to the birth of modern medicine, looking at developments over the course of the ‘long nineteenth century’. After an introduction of five weeks, you are expected to choose a topic that particularly interests you and write a paper about it. Topics may be chosen from any period between Classical Antiquity and contemporary biomedicine.
You will find out that history is not about presenting dry facts about the past, but rather about reflecting the human condition. Medical history is thinking about the ways in which man is dealing with health and illness, with pain and death – both in the past and in the present.

Literature/study material used:
- W.F. Bynum, Science and the practice of medicine in the nineteenth century (Cambridge: Cambridge University Press, 1994).
- M. Jackson ed., The Oxford handbook of the history of medicine (Oxford: Oxford university press, 2011):
* R. Cooter, ‘Medicine and modernity’ (pp. 100-116)
* H.J. Cook, ‘Medicine in western Europe’ (pp. 190-207)
* M. Gorsky, ‘The political economy of health care’ (pp. 429-449)
* R. Bivins, ‘Histories of heterodoxy’ (pp. 578-597)
- Chr. Hamlin, Cholera: the biography (Oxford UP, 2009).

Schedule:
PART 1
Week 7 (Thursday 14/2/2019)
Week 8 (21/2)
Week 9 (28/2)
Week 10 (7/3)
Week 11 (14/3)

PART 2
Week 12 (21/3)
Week 13 (28/3)
Week 14 (4/4)
Week 15 (11/4)
Week 16 (18/4) – Tuinzaal, all day

Time and location
Time: on Thursdays, 13.15-17.00 (= 1.15 p.m. to 5 p.m.).
Location: Heijmans van den Bergh Building (HvdB), Uithof (to be reached by bus no. 12 or 28). Rooms differ (power point facilities are available everywhere).

Registration:
The maximum number of participants is 15. Please register via Osiris Student in Period 3 (Please note that this is a small exception in regards to start dates and corresponding Period. Use starting block BMS P3 A). More information can be found here in the Study guide.

Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
This course is an elective course for all Master’s student of the Graduate School of Life Sciences. It is open to all students enrolled in the Research Master History and Philosophy of Science.

Prerequisite knowledge:
Bachelor’s degree and admission granted to a GSLS Master’s programme or Research Master History and Philosophy of Science.

International Genetically Engineered Machine Competition

Period (from – till): February - November

Course coordinator: Prof. Niels Geijsen (n.geijsen@hubrecht.eu)

Faculty:
Prof. Niels Geijsen (n.geijsen@hubrecht.eu)
Dr. Margot Koster (M.C.Koster@uu.nl)
Prof. Dr. Guido van den Ackerveken
Prof. Dr. Roos Masereeuw
Dr. Ton Peeters
Course description:The iGEM (international Genetically Engineered Machine competition), http://igem.org/Main_Page, is an international organization that stimulates students to work together to solve real-world challenges by building genetically engineered biological systems with standard, interchangeable parts. The competition already involves more than 100 teams from many universities and institutes. This course offers students the unique possibility to work in an interdisciplinary team on a very challenging project. The students do not only have to design and build a genetically engineered biological system, but also need to get sponsors, attract media attention and finally present their work on different occasions, including the iGEM jamboree in November in Boston.

Assessment is based on participation, the quality of the final report and an individual report to be judged by at least two instructors/teachers.
Literature/study material:
N.A.

Registration
For application and or information you can contact Prof. Niels Geijsen or Dr. Margot Koster. Deadline for the application is February 1. The team is selected from motivated students in a face-to-face interview. (July-august min. 75 % availability is required). For application and or information you can contact Prof. Niels Geijsen (n.geijsen@hubrecht.eu ) or Dr. Margot Koster (M.C.Koster@uu.nl).

Mandatory for GSLS students.
No.
Optional for students from other GSL Master's programmes:Yes.

Prerequisite knowledge:
N.A.

Laboratory Animal Sciences

Period (from – till): several times a year.
Faculty
Teachers from the Department of Animals in Science and Society , Faculty of Veterinary Medicine, Universiteit Utrecht

NOTE: There are different courses offered please read the information on the websites carefully. You should take the laboratory animal sciences course only if you need it for your research project; you must have permission from your supervisor and your programme coordinator.

You can find the exact course dates and information for the English taught course here.
More information about the Dutch taught course can be foud here.
Course description
This course is a requirement for conducting animal experiments and teaches you the basics on animal research.
The objective of the course is to present basic facts and principles that are essential for the humane use and care of animals and for the quality of research. From the beginning of the course, emphasis is placed on the fact that the scientist is the central person in the design and performance of animal experiments, and that he/she has specific responsibilities with respect to the welfare of the animals used. It is made clear that the use of animals can be accepted only under a set of strict conditions. Among these are that the experiment must be approved by an ethics committee, and must be conducted by persons who are fully competent.Please note:

  • You should take the laboratory animal sciences course only if you need it for your research project; you must have permission from your supervisor and your programme coordinator.
  • Because this course is expensive, you need to fill the rest of your elective component with modules which are free of extra costs, in exceptional cases more than one course may be allowed. You have to ask prior approval from the Board of Examiners if you want to take more than one of these courses.

Registration:

  • For BMS students BIFM, BIDM, CSND, EPIM, IMIF, NSCN, RMTM, TXEH: please use the registration form which can be found in the here.
  • For students from ENVB, MCLS, SBM and DINN: please use the standard form of the LAS course which you can find here.

Fill out the form and first hand it in at your Master's programme’s administration desk for approval. You need a signature and financial account number in order to have the form accepted at the LAS administration. In order to get approval from the Board of Examiners please add a signed statement of your examiner that this course is mandatory for your researchproject. After obtaining the approval you can sent the form to the LAS administration.
Mandatory for students in GSLS Master’s programme
No.

Optional for students in GSLS Master’s programme
Yes.
More information in Dutch: click here, in English: click here.

Career Orientation & Professionalisatio

This course is in Dutch only!De mastercursus Loopbaanoriëntatie en Professionalisering is een cursus voor masterstudenten van de Utrecht University, Graduate School of Life Sciences. De cursus wordt sinds 2001 gegeven door Jan van den Broek, managementtrainer en o.a. werkzaam bij de Bètafaculteit van de Radboud Universiteit Nijmegen.
Cursusomschrijving
De student analyseert zichzelf en de arbeidsmarkt en stelt een plan van aanpak op om zijn/haar doel te bereiken. Daarnaast wordt een aantal managementvaardigheden getraind. De cursus beoogt zelfreflectie en externe oriëntatie actief te stimuleren, o.a. door presentaties van individuele competentieprofielen, beroepsprofielen, netwerkervaringen, zoekrichtingen en actieplannen. Verder biedt de cursus de mogelijkheid om kennis, inzicht en vaardigheden met betrekking tot een aantal algemene professionele functievereisten (verder) te ontwikkelen: o.a. multidisciplinair samenwerken, projectmanagement, probleem solving, persoonlijke effectiviteit en leren omgaan met belangentegenstellingen (onderhandelingstechnieken en conflicthantering). De cursus wordt gegeven in het Nederlands. De cursusdagen zijn 7 hele dagen (9.00-17.00).
De cursus kent geen tentamen maar wordt afgerond met een persoonlijk werkstuk. Studenten ontvangen een beoordeling in de vorm van een cijfer. Mandatory for students in Master’s programme: NO.
Optional for students in other Master’s programmes GS-LS: Optional for all GSLS students who have a good command of the Dutch language.

Wat reacties van studenten na afloop van de cursus vorig jaar:
“In deze cursus heb ik geleerd hoe ik mijzelf moet presenteren, hoe ik professioneel overkom. Zelfreflectie vond ik een belangrijk onderdeel. Door deze cursus is mijn koers duidelijker geworden.”
“Ik liep te twijfelen over wat ik kon doen na mijn studie. Deze cursus heeft inzicht gegevens in wat ik wil, wat ik kan en wat ik waard ben op de arbeidsmarkt. Dankzij deze cursus heb ik het aangedurfd op meerdere posities te solliciteren en heb ik een geweldige baan in het bedrijfsleven gevonden”.

Nanomed

Characteristics of nanoparticles such as size, surface area and internal composition make them attractive candidates for use in therapeutic and diagnostic applications. The aim of this course is to provide an overview of the nanomedicine field. Every week a theme will be discussed in which nanomedicine is involved: therapeutics (both synthetic and bio-inspired) and diagnostics. We will focus on the applications of nanomedicine in cardiovascular disease and cancer.
 
After an introductory lecture on a specific theme, you will have an interactive meet up with two experts of the cardiovascular and cancer field, respectively. During the week you will work on an assignment together with one of the other students. During the course you will write a research proposal, present a paper and present the unique selling point of a nanomedicine company.  

Philosophy of Neuroscience

Period (from - till): June 2020

Course description
This course is offers compact, rigorous and practical journey in the philosophy of neuroscience, the interdisciplinary study of neuroscience, philosophy, cognition and mind. Philosophy of neuroscience explores the relevance of neuroscientific studies in the fields of cognition, emotion, consciousness and philosophy of mind, by applying the conceptual rigor and methods of philosophy of science. The teaching will start with the basics of philosophy of science including the work of Popper, Lakatos, Kuhn and Feyerabend, and use a methodological evaluation scheme developed from this work that allows rigorous evaluating neuroscientificresearch as science or pseudoscience. Furthermore, there will be attention for the historical routes of neuroscience starting with Aristotle, and the conceptual problems in neuroscience, methodological confusions in neuroscience, dualism and fysicalism. The main aim of the course is provide wide-ranging understanding of the significance, strengths and weaknesses of fields of neuroscience, which helps in critical thinking, creativity, methodological precision and scientific writing.

Literature/study material used
Book Chapters and Articles on Neurophilosophy and Philosophy of Neuro(science).
Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide. Max. 40 students.

Mandatory for students in own Master’s programme:
No

Optional for students in other GSLS Master’s programme:
Yes

Radiation Safety 5B

Period (from – till): Several times a year. The exact dates will be published on the website of TU Delft.
Faculty
W.F. Wiersma, PhD, head of the training centre/tutor in Utrecht, NCSV
Course description
This course can be followed in English and in Dutch. Go to the website for detailed information (select the 2,5 day course. PDF with details available).
Unfortunately there seems to be no English page available. If anything is unclear, please contact the person under "informatie" in the PDF with details on the website via the link above.

The radiation safety course 5B level is open to MSc students who need it for their research project. You must have permission from your supervisor and your programme coordinator.
Please note: Because this course is expensive, you need to fill the rest of your elective component with modules which are free of extra costs. The costs of the radiation safety course at level 4B will not be reimbursed.
The course Health Physics expert level 5B is meant for radiation experts in situations where radioactive sources with a low risk of exposure are used. The course offers a useful introduction in working with ionizing radiation for all kinds of radiation workers, such as laboratory personnel, technical staff, medical personnel and workers in industry. Because of the diversity in work environment of the participants, the course will not focus on one specific radioisotope.
A Virtual Learning Environment (VLE) is used for this course. Participants will have to study before the start of the training. This can be done independently and all students are fee to choose their own study moments.
The course level 5B is open to MSc students who will have to work with radioactive material during their research project. You must have permission from your supervisor and your program coordinator.
The exam consists of 50 multiple choice questions. After passing this exam, you will receive the certificate Health Physics expert level 5B and are allowed to work independently with radioisotopes.

The courses will be taught at the Ornstein Laboratory, Princetonplein 1, De Uithof, Utrecht.
More information, contact details and registration form can be found in the PDF mentioned above in the course description.
Literature/study material
Practical Radiation Protection (J. van den Eijnde, M. Schouwenburg)
(in the course fee included)

Registration
To register:
1. Fill in the General application form for electives;

After approval fill in the from of the TU Delft found via the links in the PDF
2. Go to the website for detailed information (select the 2,5 day course., select the PDF with details, select the registration form and fill it in for the course at the dates you want to participate).

Mandatory for GSLS students.
No.
Optional for students from other GSL Master's programmes:Yes.

Prerequisite knowledge:
The course is based on participants with a technical, medical or scientific education on university level. A good knowledge of physics, chemistry and mathematics is necessary.

Science and Society

Period (from – till): 11 January 2019 - 7 June 2019
Note: The Course schedule is: January 11, February 22, March 15, May 17, June 7 and optional date November 22 (a lecture from the PhD course open for students of this course), 2019. The exact schedule of lectures is available in the detailed desciption through the link below.
Faculty
Prof. dr. F.G. Huisman, Julius Centre UMC Utrecht;
Dr Annemieke Meijer
Guest lecturers
Course description
A detailed description of the course can be found here on the Study Guide.

In modern life, science is everywhere. The products of biomedical science and technology may help achieve a healthy society and economic progress. They may even prolong life and make it more agreeable at the same time. But how much do we really know about the production, implementation and evaluation of scientific knowledge? What, exactly, is the basis for our belief in science? What sets it apart from common knowledge? Who should we trust in case two scientists disagree in a hotly debated issue? Is science a vocation or just another profession? Is scientific knowledge something special to be emulated, or ‘just another opinion’? Are scientific facts discovered or socially constructed? How are science and technology embedded in society and how do they change over time?

Whoever wants to become a scientist, should be aware of these and similar questions; (s)he should not just know about the contents of scientific knowledge, but about its context as well. This course sets out to create that awareness. Until recently, it was only available to PhD students. Now, an abridged version is offered to graduate students. In six Friday afternoon sessions, the historical, philosophical, sociological and ethical dimensions of the biomedical sciences will be discussed.

For those of you who are interested in a public debate that is now going on with regard to science and the university, see www.scienceintransition.nl and http://www.wetenschapsagenda.nl/.

The course will be assessed by means of a writing assignment: you will be asked to submit a 1500 word paper on any topic, related to the theme of the course.

You will write an argumentative essay: one in which you discuss a controversial issue, take up a position and give supporting arguments aimed to persuade your readers to accept your claim(s). It is different from the types of text that you may be used to writing (lab reports, research papers) in that the writer has a clear voice – he or she is present in the text, which allows for (or indeed, requires) a considerable amount of creativity and personal choice. You may use a variety of sources, both scholarly and popular (newspapers, magazine articles).

Your essay will be graded on the basis of the following criteria:

  • information: detailed, accurate, relevant
  • structure: rigorously argued, logical, easy to follow
  • interpretation: evidence of independent thought and critical analysis
  • use of evidence: key points supported with evidence, critically evaluated
  • academic referencing: good use of academic referencing conventions
  • style & use of language

Literature/study material used:
Three articles, taken from the Golem-series by Harry Collins and Trevor Pinch:

- ‘Introduction: the Golem’ and ‘The Germs of Dissent: Louis Pasteur and the Origins of Life’ in: Collins and Pinch, The Golem. What You Should Know about Science (Cambridge UP 1993), 1-3 and 79-90.
- ‘ACTing UP: AIDS Cures and Lay Expertise’ in: Collins and Pinch, The Golem at Large. What You Should Know about Technology (Cambridge UP 1998), 126-150.
- ‘Vaccination and Parents’Rights. Measles, Mumps, Rubella (MMR), and Pertusis’ and ‘The Themes Revisited’ in: Collins and Pinch, Dr. Golem. How to Think about Medicine (The University of Chicago Press 2005), 180-204 and 205-224.

In addition to these articles, speakers will provide one or two articles on the topic of their lecture. When possible, we will send an email with these attachments before the meetings, so that you can prepare the topics to be discussed. Students should print the documents themselves.

Registration:
The Course schedule is: January 11, February 22, March 15, May 17, June 7 and optional date November 22 (a lecture from the PhD course open for students of this course), 2019.
Please register via Osiris Student in Period 3 (Please note that this is a small exception in regards to start dates and corresponding Period. Use starting block BMS P3 A) Please also be aware that the course starts on January 11th and therefore the re-registration for this course is only available on January 10th since afterwards the course has already started. More information can be found here and by sending an email before November 25th 2018 to Ms M. van Dijk-Okla: m.vandijk-okla@umcutrecht.nl, including the following information:

  • Name
  • Email address
  • Home Address
  • Zip code and City
  • A short motivation

The maximum number of students is 25.
All Master’s students of the Graduate School of Life Sciences are welcome to attend the course. There is, however, a maximum capacity of 25 participants. Should there be more applicants, the final 25 will be selected on the basis of their application letter.
You are expected to be an active participant, i.e. to prepare the topic and to take part in the general discussion.

Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Yes.

Prerequisite knowledge:
Bachelor’s degree and admission granted to a GSLS Master’s programme

Societal Challenges for Life Science Scientists: Exploring Interdisciplinarity

Period (from - till): 9-20 December 2019

Course coordinators:
Dr. ir. M.E.G.L. Lumens
Dr. G.M.J. Ramakers

Course description:
One overarching interdisciplinary theme will be chosen each year. This year the theme is Food and health. In the first few days, lecture/discussion will be organized with experts in the field to help students familiarize with the topic, get an overview of the current debate, and the problems to solve. In the meantime, students will be instructed on the principles of interdisciplinary research.
Students form interdisciplinary groups of 3/4 and develop a research question within the theme that captured their interest. After presenting their plans and receiving (peer) feedback on the feasibility of their plans, students make a concrete plan for the rest of the course period and divide tasks. Each team has a supervisor.

Examination:AssessmentDescriptionWeightONDERZResearch proposal40%OPDRACHTAssignment30%PRESENTPresentation30%
Literature/study material used:
-
Registration
You can register for this course via Osiris Student. More information about the registration procedure can be found here on the Studyguide.

Mandatory for students in own Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Yes.
Prerequisite knowledgeStudents should be enrolled in a master's programme of the Graduate School of Life Sciences.

Vascularized Tissue Engineering online course

Period (from – till): 4 February - 31 March 2019
Note: this is an online course stretching over 7 weeks with a study load of approximately 9-10 hours per week. Please take into account that the studyload is divided over the week so you will need to be able to login on various moments (taking into account vacation days).
The e-moderator will keep track of your progression. He/she will score the quality of the content and your responses on all required activities. This results in ‘insufficient, ‘sufficient’ or ‘good’. You need at least a 5.5 for all three individual components to pass the course. ​

Course coordinator: Dr. Caroline Cheng/Dr. Joost Fledderus
Lecturer: Merle Maas-Krebber, MSc

Course description:
Tissue engineering (TE) is an ever-growing multidisciplinary scientific field aiming at replacing injured, missing or damaged tissue. Current researchers in the field use different principles, knowledge and techniques from (stem) cell biology, vascular biology, medicine, biomaterials and bioengineering. Vascular and vascularized tissue engineering take prominent places within this field. The construction of blood vessels is both an independent target for replacement therapy as well as an integral part of larger constructs. A crucial challenge in obtaining large sized functional TE scaffolds (>1 milimeter in any dimensional space) is how to introduce a complex vascular tree that supplies a steady medium and blood stream for the expanding tissue to meet oxygen en nutrient demands.
This course teaches Master students’ in-depth and hands-on knowledge on developmental and adult blood vessel formation in health and disease and the current clinical treatments for which vascular(ized) TE is thought to be eligible. Moreover, we will address state of the art techniques of vascular(ized) TE, including the use of biomaterials and cell sources for bioreactor-cultured and in situ applications.

This course teaches fundamental knowledge on vascular and vascularized tissue engineering, adding significantly to the currently available curriculum concerning angiogenesis, vascular repair and remodeling, regenerative medicine and cardiovascular disease. Participants in this e-course will benefit from the flexible work hours, enabling participation parallel to writing a thesis or doing an internship abroad. This course was developed using collaborative partners leading in regenerative medicine and cardiovascular disease. Grading of this course will be based on handing in a graphical abstract (group assignment), an individual assignment and on individual participation during the course and in discussion forums.

Required Materials:
N.A.

Mandatory for students in Master’s programme:
N.A.

Optional for students in other GSLS Master’s programme:
Open as an elective to GSLS students from the programmes RM&T, BFAB & BOD.

Registration:
Please register via the Study guide. Deadline for registration is January 25th. The maximum of participants is 16.
Students from outside the Graduate School of Life Sciences can register for this course by sending an email to m.m.krebber@umcutrecht.nl (link sends e-mail). Please include your name, student number, Master’s programme and the course code.

Prerequisite knowledge:
Master student RMT, BOD, Biofab