• Course title: ISB103: Academic Induction
• Number of ECTS: 2
• Course code: MMCB-2
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

This introductory week consists of 3 parts:

(i) Learning about the structure and rules of your Master study line.

(ii) Familiarization with protein primary (amino acid sequence) and tertiary structure. Getting to know commonly used methods to study proteins.

(iii) A brief overview of ethics in academic writing (e.g. plagiarism), how to properly handle references, and how to structure a typical scientific report.

Understanding the structure and rules of your study line

Re-familiarize yourself with protein structures

Being able to write reports for the upcoming experimental and computational courses

Overview lecture and Q/A session to study line structure and rulesLecture and exercises to use the free protein structure visualization software Chimera.Seminar with short presentations about common protein methods.Lectures on ethics and academic writingCPE 1 title: Introduction to protein structureDescription: Learning and familiarization with proteinogenic amino acid structure. Application of the software Chimera to visualize 3D protein structure. Recognition of amino acid side chains within a protein structure.Course instructors: Daniel Abankwa, Carla DuvalCPE 2 title: Introduction to protein methodsDescription: Student seminar short presentations describing assigned methods to study proteins. Course instructors: Daniel Abankwa, Sara BottoneCPE 3 title: Introduction to academic writingDescription: This class provides a brief overview of ethics in academic writing (e.g. plagiarism), how to properly handle references, and how to structure a typical scientific report, e.g. introduction, materials and methods, and results.  Course instructors: Evan Williams 

Assessment modalityContinuous assessment

Assessment tasksType of assessmentGrading schemeWeight for final grade

Task 1Written exam20 points (0-20)Full exam 40%ObjectivesRecognize amino acids within a 3D protein structureAssessment rulesCorrect responseAssessment criteriaCounts of correct responses

Task 2Presentation20 points (0-20)10%ObjectivesPresent in 5 min an assigned method to study proteins.Assessment rulesPresentation quality judged by peers and instructorAssessment criteriaCumulative Scoring

Task 3Written exam20 points (0-20)50%ObjectivesProper citations, plagiarism identification, recognize proper scientific writing styles (e.g. objective, impersonal)Assessment rules4 quizzes in MoodleAssessment criteriaCounts of correct responses

• Course title: ISB811: Biosafety and Introduction to Cell and Molecular Biology
• Number of ECTS: 3
• Course code: MMCB-1
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

Getting an overview on working in a bioscience laboratoryAbility to design and perform experiments in modern bioscienceUnderstanding of the safety regulations in a bioscience laboratory

Safety regulations in bioscienceSterile workingOrdering reagentsPreparing solutionsDesigning and organizing experimentsAnalysis of dataPresentation of research results

Learning material   Instruction hand-outs, PDF-files of method articlesTeaching methods and assessmentObligatory attendance, summary protocol

• Course title: ISB101: Genomics / Databases
• Number of ECTS: 5
• Course code: MMCB-3
• Module(s): Module 1.1
• Language: EN
• Mandatory: Yes

This course introduces the theory and practice of current concepts in genomics and genetics, particularly to introduce the genome as the basic foundation for systems biology. Topics include overview of genomes, sequencing and mapping, comparative genomics, population genetics and genomics, basic bioinformatics, population-level and rare variation analysis (SNPs, indels), functional genomics and clinical genomics. The course familiarizes students with the tools and principles of genomics, with a focus on the requirement for efficiently processing high volumes of data. By the end of the course, students will have a working knowledge of current genomics technologies and approaches as well as the types of databases and computational tools available.

Learn the fundamentals molecular biology and biochemistry background for genetics and genomics.Obtain an overview on how current sequencing technologies work and how to analyse the data.Introduce programmatic data analysis in R.Become familiar with common, large biological databases routinely used in genomics and genetics, and how to retrieve and analyse these datasets.Learn scripting the R programming language as well as searches with regular expressions.Develop familiarity with command line interface of Unix shells for data transfer and handling.After the course, students will understand how to perform large-scale data analyses on networked computers for genomics and related disciplines.

The course consists of half-day lecture segments on genetics and genomics technologies and five half-day lecture segments data analysis in R in the first week. The second week introduces a project to be conducted in groups that revisits key elements of the lectures in practical.

Total grade is composed of graded exercises in R, (30%), a graded report (35%) and written exam on genomics (35%).

Key words: databases, genomics, next-generation sequencing (NGS), single-nucleotide polymorphism (SNP), genome-wide association studies (GWAS), R, data analysis

• Course title: ISB201: Gene Regulation / Transcriptomics
• Number of ECTS: 5
• Course code: MMCB-4
• Module(s): Module 1.2
• Language: EN
• Mandatory: Yes

Week 1: After DNA replication, certain parts of the genome are transcribed into mRNA. This process is extremely well regulated and coordinated to allow for cell- and situation-dependent expression of necessary gene products. MISB201 is teaching a solid understanding of how gene expression works in mammalian cells and how it is regulated at all known levels. Week 2: An introduction into the most common language R to analyse high throughput gene expression data coming from various RNA Seq or single cell Seq. Explanations and hands-on exercises to learn to use: Data retrieval, Database use, Data formatting, Statistics QC of RNA Seq data, RNA Seq data analysis, and Sc Seq data analysis.Overview of transcriptomics (first week)

Learn critical thinking and approaching complex contents in a relatively short period of time, enhance self-study skills to repeat and recap the taught material. Interactive group exercises in class are included to enhance interactions and understanding.Have a solid understanding of how gene expression works in a mammalian cells, how it is regulated at the various cellular levels, which types of RNA are generated and what functions they have in the cell, how gene expression can be measured and manipulated and how the data retrieved from high throughput technologies are handled and analysed.

1.  The topic and putting gene transcription into a general context of cellular life cycles;2.  Epigenetic mechanisms involved in gene expression; 3. Transcription machinery assembly at the promoter and the transcriptional process itself;4.  Post-transcriptional regulatory mechanisms (fine-tuning the amount of expressed genes);5.  Types of transcribed RNAs with a focus on lnc and miRNAs;6.  Technologies to measure and quantify gene expression.7.   R to analyse high throughput gene expression data coming from various RNA Seq or single cell Seq8.   Data retrieval, Database use, Data formatting, Statistics QC of RNA Seq data, applications of up-to-date bioinformatics tools and packages (as these are changing, this will be updated regularly) 

Written exam           

• Course title: ISB301: Protein Structure and Function
• Number of ECTS: 5
• Course code: MMCB-5
• Module(s): Module 1.2
• Language: EN
• Mandatory: No

Solid knowledge of how proteins function as ‘molecular machines’Understand general ‘rules’ and common principles in protein activity regulationUnderstand the generic architecture of proteins and protein mediated processes (enzyme catalysis, signalling)Learn about the evolutionary principles that are exploited to create the diversity of proteinsApply knowledge to the difficult question of drug discovery

In the main lecture we will use a mix of classical theory- and methods-focused lectures, flipped classroom teaching, Kahoot-formative testing and exercises to provide you with an intensive training in modern protein biology.We will start by reviewing basics of chemistry that apply to protein biochemistry and repeat the fundamentals from amino acids to secondary structures. Next we have a look at the basic building blocks of proteins, domains, and learn how these combine to form new functional entities. Then we look at how proteins react as enzymes and with each other, how they are modified, and which factors determine how fast they react. In the fourth section, we look at how major signalling pathways function on the protein-structural level, before we in the fifth section look at drug discovery. We learn about basics in drug discovery and will apply our knowledge from all the sections in group exercises to formulate steps necessary in drug discovery.These theoretical sections are supported by method focused lectures, where we learn about common tools in protein biochemistry. This includes, the structure and application of antibodies e.g. in Western blotting, bio/physical techniques to study protein-protein interactions in vitro and in cells, basics of protein structure determination and common assays in drug discovery.Additional lectures and exercises will introduce you to the use of protein databases and computational protein structure analysis.In an accompanying seminar you will elaborate a presentation on a protein science topic and present it to the class.Last but not least, you will gather hands on experience in a practical that will introduce you to basic techniques of protein biochemistry, such as Western blotting.

Final written examTwo Quick Tests during the lectureReport and contribution to practical (TP)Seminar presentation

BibliographyHow proteins work (Mike Williamson) Garland Science, ISBN-10: 9780815344469https://www.amazon.com/How-Proteins-Work-Mike-Williamson/dp/0815344465/

• Course title: ISB302: Proteomics
• Number of ECTS: 5
• Course code: MMCB-6
• Module(s): Module 1.2
• Language: EN
• Mandatory: No

Students trained in this course will be able to design a basic cellular experiment that involves proteomic profiling using LC-MS/MS. Students will be able to differentiate various technologies (instrumentation, enrichment strategies, protein identification and quantification) in the field of proteomics, and be able to compare their capabilities and limitations for biomedical research. Home work and quiz will focus on data interpretation using mass spectra acquired from peptides, from which students will be able to identify proteins (both by de novo sequencing and using a database search engine). We introduce reverse-phase protein array (RPPA) as a cross validation technology. Students will understand the principle of protein microarrays and be able to compare the analytical aspects of RPPA and LC-MS in phosphoproteomics.

Biological mass spectrometryMass spectrometry-based proteomicsAnalytical strategies for proteins (enrichment, separation, identification and quantification)PhosphoproteomicsProtein microarray

(1) Biological mass spectrometry and its application- Mass spectrometry- Liquid chromatography- Protein chemistry for MS-based proteomics- Peptide sequencing- Protein identification- Protein quantification- Proteome profiling and sample preparation- PTM studies- Proteomics in biomedical research- Proteomics in clinic- Proteogenomics(2) A case study of phosphoproteomics- Introduction of phosphoproteomics- Phospho-enrichment and biochemical processing (wet-lab)- LC-MS/MS (MS lab) and data analysis(3) Cross-validation of phospho signaling- Introduction of protein arrays- Protein extraction (wet-lab)- RPPA (protein lab) and data analysis

Attendance (10%), Home Work (20%), Quiz (30%), and Report (40%)

Support:Handout: A booklet prepared by lecturers will be provided.

• Course title: ISB202: Practicals in Gene Regulation
• Number of ECTS: 5
• Course code: MMCB-7
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Practical approach to transcriptomics: experimental manipulation of gene expressionLearning to manipulate gene expression in cancer cellsAnalysis of transcriptomic high throughput data and selection of interesting target genes for validationPerturbation of gene expression of selected target genesExtraction of RNA from cultured and manipulated cancer cellsMeasuring gene expression levels by qPCRPerforming wet lab experiments

Understanding principles of practical gene level perturbationAnalyse and select high throughput data (RNAseq) to identify single targets of interestExperiencing and performing tissue culture, cancer cell treatment/stimulation, RNA extraction + quantification and qPCR to measure affected gene expression levels: standard measure to quantify gene expressionUnderstanding principles, data analysis and QC aspects of qPCRGenerating and critically analysing own dataAnalysing other, supplied data (Western Blot) in relation with generated dataDesigning own qPCR experiment with all relevant controlsWorking in a team in a wet lab environmentWriting a detailed scientific report

Practical work in teaching lab, lectures, data analysis:Melanoma tissue cultureTreatment of cells with cancer drugs (targeted therapy)RNA extraction and quantificationReverse TranscriptionqPCR with data analysis of own resultsIntroductory lecture on the course (theory and practical details), lectures on RNA+RNA extraction and qPCR data analysisBioinformatic analysis of RNAseq data generated in Signal Transduction lab

Assessment modality Combined assessmentAssessment tasks Type of assessment Grading scheme Weight for final gradeTask 1 Take-home assignment20 points (0-20)75Objectives Final reportAssessment rules Written reportAssessment criteria Quality of report writing, presentation of scientific results generated in the wet lab course, understanding of the results and interpretation, troubleshooting capacity, correctness of scientific results and provided tasksTask 2 Written exam Knowledge test during the course20 points (0-20)10Objectives Testing knowledge of provided course material and scripts, standard wet lab calculationsAssessment rules Written testAssessment criteria PerformanceTask 3 Active participation Practical lab work20 points (0-20)       10Objectives practically planning and performing molecular biological experiments; generating interpretable scientific data; observing safety rules and punctualityAssessment rules Presence in the lab, active participation, pipetting skills, level of understanding of required tasksAssessment criteria Motivation, performance (wet lab skills)Task 4 Active participation High throughput data analysis20 points (0-20)5Objectives Bioinformatic analysis of transcriptomic high throughput dataAssessment rules Active participationAssessment criteria Performance, finding the requested target genes           

• Course title: ISB701: Introduction to Systems Biology
• Number of ECTS: 5
• Course code: MMCB-8
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Getting an overview on the elements of systems biology and its concepts and applications; Ability to analyze biological processes by systems biology methods and concepts; Understanding of the principles of systems biology, such as topology, stochiometry and kinetics

Recall and apply key procedures and methods in mathematics and bioinformatics; Differentiate the key principles of bottom-up systems biology; Integrate basic understanding of bottom-up systems biology by designing, creating and analyzing models

Definition of systems biology; Basic concepts in systems biology; Biophysical basis of enzyme reactions; Math recap: Matrices; Linear Equations and Ordinary Differential Equations; Balancing and Modelling; Model Analysis (Steady States, Stability, Phase Portrait, Bifurcation plot); Network motifs; Application examples

Combined assessmentWritten exam

Detailed Course Handbook including links to deepening youtube videos, as a basis for independent studying during this flipped-classroom course.

• Course title: ISB702: Pharmacokinetics
• Number of ECTS: 5
• Course code: MMCB-9
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Getting an overview on the elements of pharmacology & pharmacokinetics (PK) and its concepts and applications; Ability to model and analyze simple PK processes; Develop, run and present own PK model based on ordinary differential equations

Recall and apply key procedures and methods in modelling and model analysis; Understand and Differentiate the key principles of PK; Integrate basic understanding of PK applying dynamical modelling within the Matlab framework

 Courses content:Introduction to Pharmacology and Pharmacokinetics:Definition of pharmacology and PK; Basic concepts in PK: ADME – Absorption, Distribution, Metabolism, Elimination; PK models and application examples;  Safety pharmacologyPharmacokinetic modelling:Introduction IQMtoolbox within Matlab; Modelling case studies ; Modelling project: Develop, run and present own project idea, with the help of tutors

Continuous assessment

Week 1

Written exam Multiple choice

Week 2

Written exam Multiple choice

Presentation

Pitch and present own project

• Course title: ISB104: Translational biomedical research in neurodegeneration – from bed-to-bench-to-bedside
• Number of ECTS: 5
• Course code: MMCB-10
• Module(s): Module 1.3
• Language: EN
• Mandatory: No

Introduction to clinical and translational medicine Introduction into precision medicine Practical experience of recruitment of study participants Processing of patient’s bio-samples for molecular profiling (RT-QuIC)Patient-derived cellular disease modelsLab automation  Use of patient derived cellular disease models for phenotypic drug screening Designing of a Clinical Study including arms, events and Case Report Forms (CRFs) Introduction to Electronic Data Capturing (EDC) system – REDCap Cross-talk between clinician, data scientist and lab scientistFAIR principles and data FAIRification of data (making data Findable, Accessible, Interoperable and Reusable) Clinical data curation, harmonization and basic analysis Different types of clinical trials and expected outcomesBiomarkers for precision medicine Translation into care and prevention 

This course focuses on the introduction to translational biomedicine, a rapidly growing discipline across different biomedical research discipline. It aims to (i) identify unmet needs together with people with Parkinson’s disease, (ii) to accelerate the transfer of knowledge generated on the bench (laboratory) to be translated back to bedside (clinical trials and care). This course will introduce the clinical and translational medicine field, addressing its evolution and fundamental concepts including (i) domain expertise, (ii) interdisciplinary collaboration and (iii) outreach and communication, with concrete examples in the context of neurodegenerative diseases e.g. Parkinson’s disease (PD). Students will have the opportunity to visit the Parkinson’s Research Clinic (PRC) at CHL (Centre Hospitalier de Luxembourg) and experience the daily clinical research routine and recruitment of people with PD for clinical studies. This course will also include hands-on laboratory practice of how researchers process the collected bio-samples from people with PD and make them available for subsequent molecular (e.g sequencing) and cellular (e.g. induced pluripotent stem cells) profiling and drug screening. In addition, this course will also introduce into biocomputational expertise, i.e. how to design a case report form (CRF), capture data from a clinical study using an electronic data capturing system (e.g. REDCap), how to curate and FAIRify (making data Findable, Accessible, Interoperable and Reusable) the collected data and finally analyze the curated data for unlocking the potential of deep phenotypes patient cohorts for an earlier diagnosis and a better treatment.  Overall the course integrates biocomputational, biological and medical expertise for a comprehensive translational concept.

First sessionWritten exam (50%)Report of laboratory work (50%)Retake examOral exam

The Fundamental Characteristics of a Translational Scientist DOI: 10.1021/acsptsci.9b00022Electronic Data Capturing (EDC) system – REDCap short video (5min)FIAR principles publication

• Course title: ISB501: Practicals in Advanced Cell Biology (ex 502)
• Number of ECTS: 4
• Course code: MAISB-12
• Module(s): Module 2.1
• Language: EN
• Mandatory: Yes

– Getting an overview on the methods of cellular biology and physiomics- Learning and applying central methods in advanced cellular biology and physiomics- Ability to plan and perform projects in cellular biology and physiomics

Modulating tools for gene expression: knock-in and knock-out technologies, siRNA Cellular imaging techniques Organ and animal models

Protocol of work done

Instruction hand-outs, PDF-files of method articles

• Course title: ISB502: Advanced Cell Biology (ex 501)
• Number of ECTS: 4
• Course code: MAISB-11
• Module(s): Module 2.1
• Language: EN
• Mandatory: Yes

Getting an overview on cellular structure und functionAbility to relate signal transduction pathways with cellular structure, growth, differentiation and deathDetailed understanding of the central mechanisms in cell, tissue and organism biology

Evaluation: Presentations and ExercisesThis course focuses on recent developments in cell biology. In particular we will focus on organoids from various tissues. An organoid can be defined as an artificially grown mass of cells or tissue that resembles an organ. This term has grown in use within the research field over the past few years as a result of advances in two distinct directions: the isolation and propagation of adult stem cell niches in 3D, and the adaption of 3D culture conditions for the directed differentiation of pluripotent stem cell (PSC) lines towards specific developing tissues.Organoids have now been used to model disease, screen drugs, increase our understanding of normal human development and even interrogate biophysical principles of self-organisation. Organoids formed from patient-derived cell types are now in use for the evaluation of drug sensitivities and to validate disease-causing genomic variations. There is no doubt that organoid studies will act as stepping stones to more advanced regenerative medicine approaches, as well as to a better understanding of development, especially human development. Indeed, the field of organoid biology has grown at such a pace, and attracted such attention, that we have devoted this entire course to showcase organoid biology.In this course we will use several recent publications concerning organoids. The publications will be presented and analysed with various approaches.

Exam

Lecture slides, PDF-files of review articles

Presence in the complete course is mandatory

• Course title: ISB403: Microscopy and Computervision
• Number of ECTS: 4
• Course code: MAISB-47
• Module(s): Module 2.1
• Language: EN
• Mandatory: Yes

• Course title: ISB401: Metabolomics and Metabolism
• Number of ECTS: 4
• Course code: MAISB-20
• Module(s): Module 2.2
• Language: EN
• Mandatory: Yes

– Getting an overview on the biochemical pathways involved in cellular metabolism and the regulation thereof- Understanding how metabolomics is done in theory and in practice- Understanding how enzymology and metabolomics can be used to study cellular metabolism and related diseases

– Understanding how cellular metabolism connects to health and disease and how it can be experimentally studied in a comprehensive way- Ability to generate, analyze and interpret metabolomics data sets in the context of biomedical research

– Overview on metabolic pathways and their regulation – Principles of enzymology- Principles of mass spectrometry based metabolomics- Principles of omics data analysis and integration- Metabolomics in the context of enzyme discovery and inborn errors of metabolism- Metabolomics in the context of diabetes mellitus- Microbial cultivation for protein/metabolite extraction and analysis- Metabolic enzyme assays- Metabolomics data analysis

Written exam

Support:Lecture slides, Scripts for tutorials and practicalsLiterature:PDF-files of review articles

• Course title: ISB705: Advanced Systems Biology II
• Number of ECTS: 4
• Course code: MAISB-41
• Module(s): Module 2.2
• Language: EN
• Mandatory: Yes

–       Principal concepts of constraint-based modeling, including metabolic network reconstruction and flux balance analysis

–       Profound understanding of the concepts of constraint-based modeling

–       Understanding the difference between automated reconstructions and manual curations

–       Overview of available methods and tools for flux balance analysis and metabolic network reconstructions

–       Use of the cobra toolbox for flux balance analysis

–       Ability to understand current research in the field

–       Revision of linear algebra, biochemistry, MatLab-       E. coli core model-       Reconstruction of metabolic networks –       Properties of the stoichiometric matrix-       Flux balance analysis-       The mitochondrial metabolic network & associated project-       Refinement of genome annotations-       Automated reconstructions-       Integrating Omics Data with Metabolic Models-       Introduction to the human metabolic reconstruction-       Application of the human metabolic reconstruction

Attendance, project report, exam

Literature :

Systems Biology: Properties of Reconstructed Networks by Palsson, Bernhard Ø. published by Cambridge University Press (2006)

Support : –       Power point presentations-       Hand-outs

• Course title: ISB102: Practicals in Bioinformatics
• Number of ECTS: 4
• Course code: MAISB-26
• Module(s): Module 2.3
• Language: EN
• Mandatory: Yes

• Course title: ISB704: Top-Down Systems Biology
• Number of ECTS: 4
• Course code: MAISB-17
• Module(s): Module 2.3
• Language: EN
• Mandatory: Yes

• Obtaining an overview of the methods for top-down systems biology analyses• Understanding the principles behind statistical analysis of large datasets, network analysis, text-mining and data integration• Obtaining experience in analyzing large biological datasets integratively via pathway and network analyses

• Statistical methods for integrative omics data analysis• Data processing, filtering and quality control approaches• Retrieving data from public biomedical databases• Cellular pathway analysis of omics data• Molecular network analysis of omics data• Machine learning analysis of omics data• Biomedical literature / text mining analysis• Visualization of high-dimensional biological data• Preparing a short research proposal in a team

Protocol of work done, graded essay 

Support:Lecture slides, PDF-files of recent papers, Exercise sheets, Analysis scripts

• Course title: ISB801: Bioscience Seminar Series
• Number of ECTS: 2
• Course code: MAISB-1
• Module(s): Module 2.4
• Language: EN
• Mandatory: Yes

Getting an overview on recent research topics in modern bioscience

Ability to discuss results from recent research topics in modern bioscience

Understanding of the relation of own projects with recent research topics in modern bioscience

Recent research topics in modern bioscience presented by experts in the field

Obligatory attendance and active participation in discussion. Written exam on content of presentations.

• Course title: ISB601: Molecular Medicine I
• Number of ECTS: 4
• Course code: MAISB-30
• Module(s): Module 3.1
• Language: EN
• Mandatory: Yes

Getting an overview on the molecular basis of neurodegenerative diseases (in particular Parkinson’s disease). Ability to link understanding of biochemical pathways with the molecular mechanisms of the discussed complex diseases Understanding of the genes, proteins and regulatory pathways involved in the discussed complex diseases.

The Molecular Medicine course focuses on neurodegenerative diseases. The cellular and molecular mechansims of neurodegenerative diseases as well as therapeutic strategies for treatment of these disease will be addressed. 

Presentations, Course participation, Exam

Literature will be distributed within in the coursePresence in the complete course is mandatory

• Course title: ISB602: Molecular Medicine II
• Number of ECTS: 4
• Course code: MAISB-31
• Module(s): Module 3.1
• Language: EN
• Mandatory: Yes

Getting an overview on the molecular basis of immune system- and nutrition-related diseases, such as infectious diseases, autoimmune diseases, obesity, atherosclerosis and neoplasms of the immune systemAbility to link understanding of biochemical pathways with the molecular mechanisms of the discussed complex diseasesUnderstanding of the genes, proteins and regulatory pathways involved in the discussed complex diseases

– Immunology of infectious diseases- Autoimmune diseases and chronic inflammation- Heamatopoiesis in health and disease- Neutrophils, Neutrophilia and Neutropenia- Obesity / Metabolic syndrome- Atherosclerosis- Hepatocellular Carcinoma

Written exam

• Course title: ISB902: Research practical
• Number of ECTS: 18
• Course code: MAISB-42
• Module(s): Module 3.2
• Language: EN
• Mandatory: Yes

Collect experience in a research lab, start a first own research project, learn new methods, approaches and scientific concepts. Prepare for the final Master Thesis project

Understand of the design and execution of an own research project in the Systems Biology field

Before the course starts the students need to find a hosting lab. It is recommended find such a lab as early as possible (already in May/June of the year) and agree with the lab on a project. Any university level research group in the field of systems biology in Luxembourg or abroad is acceptable. In case of doubt, this can be discussed with the course coordinator. Ideally the research project shall prepare for the following Master Thesis. The projects as such  should be in the field of systems biology. The details depend on the student and the hosting lab, they shall be determined individually. 

End-of-course assessment

 Presentation : 

20 points (0-20). 

Weight for final grade : 50

 

Objectives

Explain the research question of the chosen project a well as the results.

Assessment rules

Based on the presentation all attending MISB teachers can assess.

Assessment criteria

Clarity of the presentation, particularly the understanding of underlying scientific concepts.

Project report

 : 

20 points (0-20). 

Weight for final grade : 50

Objectives

Summarize the conduced work in chapters Introduction, Materials and Methods, Results and Discussion.

Assessment rules

Assessment is done by the Course coordinator.

Assessment criteria

Quality of the report in terms of completeness, scientific maturity, clarity, discussion of available literature as well as presentation and interpretation of the obtained results.

 

 

 

Literature list :

 

Depends on the chosen project and should be obtained from the project supervisor at the start of the project.

• Course title: ISB703: Advanced Systems Biology I
• Number of ECTS: 2
• Course code: MAISB-16
• Module(s): Module 3.3
• Language: EN
• Mandatory: Yes

 · Understand coarse grained and stochastic approaches to biochemical network modeling· Express abstractions in mathematical terms, implement a mathematical model on a computer and interpret the results of numerical simulations· Use Matlab and R packages for the simulation of Boolean and stochastic models

Knowledge of Boolean modeling (deterministic and probabilistic), and simulation techniques for stochastic models. Solve theoretical problems using these approaches and their applications.

• Quantitative vs. qualitative modeling of biological networks • Boolean networks, Random Boolean networks, Noisy Boolean networks and their Markov chain representation, Piece-wise linear equations • Practical with Matlab: implementation of the theoretical concepts • Introduction to stochastic modeling, Probability models of biochemical networks: discrete and continuous Markov processes • Stochastic simulations: Monte Carlo integration, Gillespie algorithm • Practical with R: Use of R functions for simulation and numerical integration of the considered examples   

Written exam

• Course title: Academic Writing Workshop
• Number of ECTS: 3
• Course code: MAISB-53
• Module(s): Module 3.4
• Language: EN
• Mandatory: Yes

• Course title: ISB901: Master Thesis
• Number of ECTS: 30
• Course code: MAISB-29
• Module(s): Module 4.1
• Language: EN
• Mandatory: Yes

Getting an overview on scientific working in a specific field of bioscience

Ability to perform experiments in an own research project

Detailed understanding of the background in own research project

Studying literature in the fieldPerforming own research projectAnalysis of data and creation of figuresWriting a master thesis

Writing own M.Sc. thesis.