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.
Betreuer Course instructors
Allgemeine Informationen General Information
Credits und Arbeitsumfang Credits and work load :
12 ECTS / 10 SWS (10P/Block) = 360 working hours
Zeit (während des Semesters):
Date (during the semester):
Di + Do
Tue + Thu
13-18h: ~300h
Zeit (Block):
Date (block phase):
1-2 Wochen:
1-2 weeks:
~60h
Raum: Hiwi-Räume
Room: Hiwi-rooms + 406 Amalienstr. 17
Lernziele Aims 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.
Voraussetzungen Prerequisites
Voraussetzungen:
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.
Prerequisites:
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 Praktikums Structure/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
Vorkenntnisse Prerequisites
Grundstudium Bioinformatik (Bachelor oder Diplom) Bachelor
Bioinformatics
Programmierpraktikum Bioinformatik Bioinformatics programming
course
Praktikum Genomorientierte Bioinformatik Practical Genome-oriented
bioinformatics
Gute Programmierkenntnisse (Bachelor Level) Good programming skills
(bachelor level)
Literatur Literature
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