Lehr- und Forschungseinheit Bioinformatik



NEAP Summer of 2023: A multi-modal diease model

We want to analyse and create a multi-modal view of a disease or tissue.

Nowadays the creation of multi-modal datasets is becoming increasingly simple: the relevant techniques (e.g. 10X Genomics scRNA-seq, Visium spatial RNA-seq, etc.) are mostly commercially available, and thus easy to use by a wetlab. However, shedding light into the stack of data is extremely complicated.

Moreover, researchers aim to include different kinds of measurements: transcriptomics, proteomics and metabolomics. While gene expression and protein abundance are meant to be well correlated, the inclusion of metabolomics is a new topic when it comes to spatial analyses.
We thus want to explore and create methods for analysing multi-modal datasets, apply existing methods and shape new analysis methods. This will take place at different levels and we will have to answer (at least some) of the following questions: how do sc/snRNA-seq and bulk RNA-seq relate, how can proteomics be included, as well as how to include spatial information, e.g. from spatial transcriptomics or spatial imaging mass-spectrometry/spatial metabolomics?

This practical is very much research oriented. Experience with sc/sn/spatialRNA-seq analyses is welcome, but not required beforehands.

BetreuerCourse instructors

Allgemeine InformationenGeneral Information
  1. Credits und ArbeitsumfangCredits and work load: 12 ECTS / 10 SWS (10P/Block) = 360 working hours
  2. Zeit (während des Semesters): Date (during the semester): Di + Do Tue + Thu 13-18h: ~300h
  3. Zeit (Block): Date (block phase): 1-2 Wochen: 1-2 weeks: ~60h
  4. Raum: Hiwi-Räume Room: Hiwi-rooms + 406 Amalienstr. 17

LernzieleAims and Learning Goals
Ziele und Lernziele:
Die zu entwickelnden Methoden und Routinen bauen auf verfügbaren hochmodernen Tools für eine effiziente Analyse und komfortable Visualisierung der Ergebnisse unter Verwendung moderner Python und R Programmierumgebungen und -pakete aufbauen. Die Robustheit und Reproduzierbarkeit der Ergebnisse ist eine wichtige Voraussetzung für alle Ihre Implementierungen.
Aims and Learning Goals:
The developed pipeline will build on available state-of-the-art tools for efficient analysis and comfortable visualization of results using modern python and R programming environments and packages. Robustness and reproducibility of results is an important requirement for all implementations.

Bachelor Bioinformatik, insbesondere erfolgreicher Abschluss des GoBi-Moduls. Gute Programmierkenntnisse (Java, Python, Dash, R, Shiny). Interesse an Datenvisualisierung und komplexen menschlichen Krankheiten. Das Praktikum ist sehr forschungsnah. Erfahrung in der Analyse von sc/sn/spatialRNA-seq Data ist willkommen, aber keine Voraussetzung.
Bachelor Bioinformatics, in particular successful completion of the GoBi module. Good programming skills (java and/or python). Interest in data visualization and complex human diseases. This practical is very much research oriented. Experience with sc/sn/spatialRNA-seq analyses is welcome, but not required beforehands.

Struktur/Zeitablauf des PraktikumsStructure/Schedule

The practical will take place in a hybrid mode. Regular synchronization points are planned to take place in-persona in Amalienstr. 17 .
Meetings in-persona will (probably) take place Thursdays 14:00-16:00 .
The practical can be organized with or without consecutive/block working time.

Full remote participation can be considered individually, however, it is strongly encouraged to participate in the in-persona meetings (which are meant to happen roughly every 2 weeks).

  • Feb/Mar 2022: Kickoff meeting und Zuordnung der Projekte und Teams
  • Apr-Jul 2022: ~300h Projekt und Paper Planung, Projektarbeit, Zwischen-Präsentationen und Diskussionen
  • Jul-Aug-Sep 2022: ~60h Block Phase, Projektarbeit, Schreiben des Papers, Abschlusspräsentation und Einreichen des Papers
  • Feb/Mar 2022: Kickoff meeting and project assignment
  • Apr-Jul 2022: 300h project and paper planning, project work, presentations and discussions
  • Jul-Aug-Sep 2022: 60h block phase, project work, paper writing, final presentation and paper submission

  • Grundstudium Bioinformatik (Bachelor oder Diplom)Bachelor Bioinformatics
  • Programmierpraktikum BioinformatikBioinformatics programming course
  • Praktikum Genomorientierte BioinformatikPractical Genome-oriented bioinformatics
  • Gute Programmierkenntnisse (Bachelor Level)Good programming skills (bachelor level)


Informationen fürInformation for