Technical help sheet
Technical requirements for data analysis
You will require the following tools for executing the practicals in this course:
Protein Identification, from Lennart Martens, Harald Barsnes and Tine Clays
- Java JRE between 1.8 and 1.15 – https://adoptopenjdk.net/releases.html
- SearchGUI – http://compomics.github.io/projects/searchgui
- PeptideShaker – http://compomics.github.io/projects/peptide-shaker
- ThermoRawFileParserGUI – https://github.com/compomics/ThermoRawFileParserGUI
Introduction to MaxQuant, from Christoph Wichmann, Peli Kyriakidou and Daniela Ferretti
- .NET Framework 4.7.3 or higher – https://dotnet.microsoft.com/download/dotnet-framework
- MaxQuant latest version – https://maxquant.org/maxquant/
- Perseus latest version – https://maxquant.org/perseus/
- .net core 2.1 – https://dotnet.microsoft.com/download/dotnet/2.1
Integration using Cytoscape and Network Interference, from Kalpana Panneerselvam, Birgit Meldal and Eliot Ragueneau
- Cytoscape version 3.8.2 – https://cytoscape.org/
- Apps in Cytoscape: IntAct app – https://apps.cytoscape.org/apps/intactapp
- MCODE – https://apps.cytoscape.org/apps/intactapp
- ClueGO (needs liscence) – https://apps.cytoscape.org/apps/intactapp