FH-Prof. Mag. Dr. Alexandra Graf Research Staffalexandra.graf@fh-campuswien.ac.at T: +43 1 606 68 77-3602 F: +43 1 606 68 77-3609 Room: MUT.02 Muthgasse 11/2 1190 WienPersonal WebspaceLectures 2021/22Applied Life Sciences> Molecular Genetics and Straindevelopment VO Bioengineering moreMolecular Genetics and Straindevelopment VOLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Ing. DI (FH) Dr. Harald Kühnel, MSc2SWS4ECTSLecture contentsKnowledge on basics of molecular genetics: What are living organisms made of - in a biochemical sense - what molecules - which compartments and structures? How are these molecules, compartments and structures passed on to offspring? How do living organisms function in a chemical and physical sense? How is this live "steered"? How identical are offspring to their parents, or how different? How is genetic and biological relationship explained on the molecular level? Topics in the Basics part: - Historical perspective - Genomics, Transcriptomics, Proteomics - Differences between Eukaryota, Porkaryota, Archaea, and Viruses - Replication - Transcription - Translation - Mutations and Recombination Methods included in this part: - Sequencing technologiesAssessment methodsMoodle examTeaching methodsLectureLanguageGerman> Bioinformatics VO Bioengineering moreBioinformatics VOLector: FH-Prof.in Mag.a Dr.in Alexandra Graf0.5SWS1ECTSLecture contentsIntroduction to the working environment with Linux, R and Python. Introduction to concepts of version control with Git and working on a Linux Server environment.Assessment methodspractical programming taskTeaching methodslecture (powerpoint) practical work using computersLanguageGerman> Bioinformatic Data Analysis (Statistics) UE Bioengineering moreBioinformatic Data Analysis (Statistics) UELector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS2ECTSLecture contentsIntroduction in Programming with R and the analysis of biological datasets: R topics: - Data types - Control structures - Functions - Packages - PlotsAssessment methodsExercises in DataCamp and through MoodleTeaching methodsLecture and Exercise. Accesss to DataCamp.LanguageGerman-English> Programme Design, Automation, Bachelor Thesis SE Bioengineering moreProgramme Design, Automation, Bachelor Thesis SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Mag. Alexander Hirner, Bakk., Monika Waldherr, MSc5SWS10ECTSLecture contentsThe lecture is meant to support the students in their bachelor thesis, the content is dependent on the topic the student has selected. Python (Norbert Auer): Based on the programming lectures so far, this lecture finalizes important programming concepts with Python. Practical examples from different areas, such as functions, class hierarchies, polymorphism, interfaces, exceptions, modules, and file in/output, are presented and practiced.Assessment methodsThis lecture is the basis for the bachelor thesis and will be appraised together with it.Teaching methodsPresentation and dialogs, interactive work and studies, practice on our notbooksLanguageGerman> Transcriptomics and Genomics ILV Bioinformatics moreTranscriptomics and Genomics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Eric Schinogl, BSc2SWS4ECTSLecture contents1) Acquire knowledge on selected bioinformatics chapters (Next Generation Sequencing, ChIP-Seq, RNA-Seq) ans 2) Application of relevant bioinformatics tools for the analysis of associated data 3) using script languages under Linux, such as Bash, awk and perl.Assessment methods40 % Hands on exercise: Hand in a short program which solved a given task 60% Lecture: Written examTeaching methods- Introductions and explanations (lecture) - Exercises using the computerLanguageGerman> Selected Chapters of Bioinformatics SE Bioinformatics moreSelected Chapters of Bioinformatics SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, DI (FH) Anton Grünberg1SWS2ECTSLecture contentsThe seminar is meant to give students an overview over the various fields of bioinformatics. Experts from different fields will be invited to talk about their experiences and projects.Assessment methodsWritten exam at the end of the course.Teaching methodsSeminar Talks and DiscussionsLanguageGerman-English> Data Analysis Laboratory LB Bioinformatics moreData Analysis Laboratory LBLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Ing. DI (FH) Dr. Harald Kühnel, MSc, Katharina Seiberl, BSc MSc, Monika Waldherr, MSc2SWS4ECTSLecture contents-) Introduction to the Oxford Nanopore sequencing technology -) Sequencing of DNA samples using MinION in the wet lab -) Development of suitable quality control -) Development of suitable analysis pipeline -) Interpretation and discussion of resultsAssessment methodsImmanent examination, protocol of the results of the practical exercises, final examTeaching methods-) Presentation -) practical exercises in the wet-lab and in-silicoLanguageGerman> Master Thesis Preparation SE Bioinformatics moreMaster Thesis Preparation SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf0.5SWS1ECTSLecture contentsForm and features of the written thesis. Presentation techniques.Assessment methods-Teaching methodsTalk - discussionLanguageGerman-English> Bioinformatics ILV Molecular Biotechnology moreBioinformatics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf3SWS3ECTSLecture contentsIn this lecture we talk about what Bioinformatics is and why we need it today. The studients will be introduced to basic programming and can play around with simple practical examples. We will go through specific topics of Bioinformatics and discuss the available applications. The topics include: - Why did Bioinformatics develop and what is it. - Human Genome Project and its consequences - Biological sequences, sequence comparison and database search. - Pattern search - Structure of biological sequences and structure prediction - High throughput technologies and data analysis Programming: - practical examples in R and a short introduction in PythonAssessment methodsExercises to be handed in using the Moodle Platform, and short mulitple choice tests also on the Moodle platform.Teaching methodslecture, powerpoint presentation, discussion and hands on exercisesLanguageGerman-English> Programming and Bioinformatics ILV Bioengineering moreProgramming and Bioinformatics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Martina Salzmann, BSc, BSc1SWS3.5ECTSLecture contents1. In this lecture we talk about what Bioinformatics is and why we need it today. 2. Basic concepts of programming will be discussed and with hands on exercises illustrated. We will go through specific topics of Bioinformatics and discuss the available applications. The topics include: - Why did Bioinformatics develop and what is it. - Human Genome Project and its consequences - Biological sequences, sequence comparison and database search. - Pattern search - Structure of biological sequences and structure prediction - High throughput technologies and data analysisAssessment methodsExercises and short test at end of the lectureTeaching methodslecture, powerpoint presentation, discussion and hands on exercises> Biotechnological Seminar SE Bioinformatics moreBiotechnological Seminar SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, FH-Prof. DI Dr. Michael Maurer0.5SWS1ECTSLecture contentsAs an example from biotechnology, students will work in the brew lab to create a beer, following a recipe. Students will be introduced into the topic of brewing and will have the chance to see an automated solution and investigate the data produced by the equipment. Additionally to the work in the lab, students are required to design a label for their beer and create a website with the recipes they worked on. The students will work in groups of 3-4 persons.Assessment methodsStudents will be graded on their performance in the lab and the design of the label and web page.Teaching methodsPresentation, praktical lab exerciseLanguageGerman> Metagenom Analysis ILV Bioinformatics moreMetagenom Analysis ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS2ECTSLecture contentsIntroduction to the production and analysis of metagenome/microbiome data.Assessment methodsPresentation of a practical task.Teaching methodsVortrag, Diskussion und praktisches Beispiel.LanguageGerman-English> Master Thesis Supervision AP Bioinformatics moreMaster Thesis Supervision APLector: FH-Prof.in Mag.a Dr.in Alexandra Graf0SWS1ECTSLecture contentsMethodology for the implementation of the diploma thesis: clarification of the procedure through individual presentations of the thesisAssessment methodsAssessment of the presentationTeaching methodsPresentationsLanguageGerman> Master Thesis Seminar SE Bioinformatics moreMaster Thesis Seminar SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS1ECTSLecture contentsIn the course each student presents his/her Master thesis. Progression of the thesis and potential setbacks and problems will be discussed in the group.Assessment methodsPresentationTeaching methodsPresentation, discussionLanguageGerman> Bachelor Thesis - Supervision - BVT ILV Bioengineering moreBachelor Thesis - Supervision - BVT ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf2SWS2ECTSLecture contentsIn the lecture students will be supported in the research into the biological topic of their bachelor thesis. The written format of the bachelor thesis will be explained and the scientific process of writing a thesis will be introduced.Assessment methodsFinal presentation by the studentsTeaching methodsPresentation, discussionsLanguageGerman> Transcriptomics and Genomics Practice UE Bioinformatics moreTranscriptomics and Genomics Practice UELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Eric Schinogl, BSc1.5SWS3ECTSLecture contentsThe exercise should give students the option of working with software and programs introduced in the lecture Transcriptomics and Genomics.Assessment methodsPractical examplesTeaching methodsMoodle, Linux server, example scriptsLanguageGermanPublications The publications of Alexandra Graf written at FH Campus Wien can be found in our publication database, others in the personal web space.
> Molecular Genetics and Straindevelopment VO Bioengineering moreMolecular Genetics and Straindevelopment VOLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Ing. DI (FH) Dr. Harald Kühnel, MSc2SWS4ECTSLecture contentsKnowledge on basics of molecular genetics: What are living organisms made of - in a biochemical sense - what molecules - which compartments and structures? How are these molecules, compartments and structures passed on to offspring? How do living organisms function in a chemical and physical sense? How is this live "steered"? How identical are offspring to their parents, or how different? How is genetic and biological relationship explained on the molecular level? Topics in the Basics part: - Historical perspective - Genomics, Transcriptomics, Proteomics - Differences between Eukaryota, Porkaryota, Archaea, and Viruses - Replication - Transcription - Translation - Mutations and Recombination Methods included in this part: - Sequencing technologiesAssessment methodsMoodle examTeaching methodsLectureLanguageGerman
> Bioinformatics VO Bioengineering moreBioinformatics VOLector: FH-Prof.in Mag.a Dr.in Alexandra Graf0.5SWS1ECTSLecture contentsIntroduction to the working environment with Linux, R and Python. Introduction to concepts of version control with Git and working on a Linux Server environment.Assessment methodspractical programming taskTeaching methodslecture (powerpoint) practical work using computersLanguageGerman
> Bioinformatic Data Analysis (Statistics) UE Bioengineering moreBioinformatic Data Analysis (Statistics) UELector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS2ECTSLecture contentsIntroduction in Programming with R and the analysis of biological datasets: R topics: - Data types - Control structures - Functions - Packages - PlotsAssessment methodsExercises in DataCamp and through MoodleTeaching methodsLecture and Exercise. Accesss to DataCamp.LanguageGerman-English
> Programme Design, Automation, Bachelor Thesis SE Bioengineering moreProgramme Design, Automation, Bachelor Thesis SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Mag. Alexander Hirner, Bakk., Monika Waldherr, MSc5SWS10ECTSLecture contentsThe lecture is meant to support the students in their bachelor thesis, the content is dependent on the topic the student has selected. Python (Norbert Auer): Based on the programming lectures so far, this lecture finalizes important programming concepts with Python. Practical examples from different areas, such as functions, class hierarchies, polymorphism, interfaces, exceptions, modules, and file in/output, are presented and practiced.Assessment methodsThis lecture is the basis for the bachelor thesis and will be appraised together with it.Teaching methodsPresentation and dialogs, interactive work and studies, practice on our notbooksLanguageGerman
> Transcriptomics and Genomics ILV Bioinformatics moreTranscriptomics and Genomics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Eric Schinogl, BSc2SWS4ECTSLecture contents1) Acquire knowledge on selected bioinformatics chapters (Next Generation Sequencing, ChIP-Seq, RNA-Seq) ans 2) Application of relevant bioinformatics tools for the analysis of associated data 3) using script languages under Linux, such as Bash, awk and perl.Assessment methods40 % Hands on exercise: Hand in a short program which solved a given task 60% Lecture: Written examTeaching methods- Introductions and explanations (lecture) - Exercises using the computerLanguageGerman
> Selected Chapters of Bioinformatics SE Bioinformatics moreSelected Chapters of Bioinformatics SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, DI (FH) Anton Grünberg1SWS2ECTSLecture contentsThe seminar is meant to give students an overview over the various fields of bioinformatics. Experts from different fields will be invited to talk about their experiences and projects.Assessment methodsWritten exam at the end of the course.Teaching methodsSeminar Talks and DiscussionsLanguageGerman-English
> Data Analysis Laboratory LB Bioinformatics moreData Analysis Laboratory LBLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Ing. DI (FH) Dr. Harald Kühnel, MSc, Katharina Seiberl, BSc MSc, Monika Waldherr, MSc2SWS4ECTSLecture contents-) Introduction to the Oxford Nanopore sequencing technology -) Sequencing of DNA samples using MinION in the wet lab -) Development of suitable quality control -) Development of suitable analysis pipeline -) Interpretation and discussion of resultsAssessment methodsImmanent examination, protocol of the results of the practical exercises, final examTeaching methods-) Presentation -) practical exercises in the wet-lab and in-silicoLanguageGerman
> Master Thesis Preparation SE Bioinformatics moreMaster Thesis Preparation SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf0.5SWS1ECTSLecture contentsForm and features of the written thesis. Presentation techniques.Assessment methods-Teaching methodsTalk - discussionLanguageGerman-English
> Bioinformatics ILV Molecular Biotechnology moreBioinformatics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf3SWS3ECTSLecture contentsIn this lecture we talk about what Bioinformatics is and why we need it today. The studients will be introduced to basic programming and can play around with simple practical examples. We will go through specific topics of Bioinformatics and discuss the available applications. The topics include: - Why did Bioinformatics develop and what is it. - Human Genome Project and its consequences - Biological sequences, sequence comparison and database search. - Pattern search - Structure of biological sequences and structure prediction - High throughput technologies and data analysis Programming: - practical examples in R and a short introduction in PythonAssessment methodsExercises to be handed in using the Moodle Platform, and short mulitple choice tests also on the Moodle platform.Teaching methodslecture, powerpoint presentation, discussion and hands on exercisesLanguageGerman-English
> Programming and Bioinformatics ILV Bioengineering moreProgramming and Bioinformatics ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Martina Salzmann, BSc, BSc1SWS3.5ECTSLecture contents1. In this lecture we talk about what Bioinformatics is and why we need it today. 2. Basic concepts of programming will be discussed and with hands on exercises illustrated. We will go through specific topics of Bioinformatics and discuss the available applications. The topics include: - Why did Bioinformatics develop and what is it. - Human Genome Project and its consequences - Biological sequences, sequence comparison and database search. - Pattern search - Structure of biological sequences and structure prediction - High throughput technologies and data analysisAssessment methodsExercises and short test at end of the lectureTeaching methodslecture, powerpoint presentation, discussion and hands on exercises
> Biotechnological Seminar SE Bioinformatics moreBiotechnological Seminar SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, FH-Prof. DI Dr. Michael Maurer0.5SWS1ECTSLecture contentsAs an example from biotechnology, students will work in the brew lab to create a beer, following a recipe. Students will be introduced into the topic of brewing and will have the chance to see an automated solution and investigate the data produced by the equipment. Additionally to the work in the lab, students are required to design a label for their beer and create a website with the recipes they worked on. The students will work in groups of 3-4 persons.Assessment methodsStudents will be graded on their performance in the lab and the design of the label and web page.Teaching methodsPresentation, praktical lab exerciseLanguageGerman
> Metagenom Analysis ILV Bioinformatics moreMetagenom Analysis ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS2ECTSLecture contentsIntroduction to the production and analysis of metagenome/microbiome data.Assessment methodsPresentation of a practical task.Teaching methodsVortrag, Diskussion und praktisches Beispiel.LanguageGerman-English
> Master Thesis Supervision AP Bioinformatics moreMaster Thesis Supervision APLector: FH-Prof.in Mag.a Dr.in Alexandra Graf0SWS1ECTSLecture contentsMethodology for the implementation of the diploma thesis: clarification of the procedure through individual presentations of the thesisAssessment methodsAssessment of the presentationTeaching methodsPresentationsLanguageGerman
> Master Thesis Seminar SE Bioinformatics moreMaster Thesis Seminar SELector: FH-Prof.in Mag.a Dr.in Alexandra Graf1SWS1ECTSLecture contentsIn the course each student presents his/her Master thesis. Progression of the thesis and potential setbacks and problems will be discussed in the group.Assessment methodsPresentationTeaching methodsPresentation, discussionLanguageGerman
> Bachelor Thesis - Supervision - BVT ILV Bioengineering moreBachelor Thesis - Supervision - BVT ILVLector: FH-Prof.in Mag.a Dr.in Alexandra Graf2SWS2ECTSLecture contentsIn the lecture students will be supported in the research into the biological topic of their bachelor thesis. The written format of the bachelor thesis will be explained and the scientific process of writing a thesis will be introduced.Assessment methodsFinal presentation by the studentsTeaching methodsPresentation, discussionsLanguageGerman
> Transcriptomics and Genomics Practice UE Bioinformatics moreTranscriptomics and Genomics Practice UELector: FH-Prof.in Mag.a Dr.in Alexandra Graf, Eric Schinogl, BSc1.5SWS3ECTSLecture contentsThe exercise should give students the option of working with software and programs introduced in the lecture Transcriptomics and Genomics.Assessment methodsPractical examplesTeaching methodsMoodle, Linux server, example scriptsLanguageGerman