Schedule

All times in CET!

9:15 - 09:30 Getting Connected, All

9:30 - 09:45 Address of Welcome and Introductions, Eduard, Jonas

9:45 - 09:55 Get to know activity, All

9:55 - 10:30 Speed-dating, All

Break 10:30 - 10:40

10:40 - 11:00 Kahoot quiz, All

11:00 - 11:20 How do you feel at the start of your PhD?, All

11:20 - 11:35 Future communication in the network: Channels, Tools, Formats, Frequencies, Eduard, Jonas

Break 11:35 - 11:45

11:45 - 13:10 Team Game, All

13:10 - 13:30 Wrap Up and Questions, All

End of Day 1

All times in CET!

9:30 - 10:10 Lecture: Introduction to the data-dependent acquisition proteomics workflow, Eduard Sabidó, CRG

10:10-10:15 Break

10:15-10:55 Lecture: Introduction to data-dependent acquisition proteomics data, Jürgen Cox, MPIB

11:00-11:30 Tutorial: Assignment Introduction – Tutorial on raw data access, spectra annotation and visualization, Christian Panse, FGCZ

11:30-15:00 Break

15:00-17:00 Hands-on Workshop, all ESRs

17:00-17:40 Tutorial: Assignment revision - Tutorial on raw data access, spectra annotation and visualization, Christian Panse, FGCZ

17:45-18:25 Lecture: Introduction to the top-down workflow, Michal Sharon, WIS

All times in CET!

9:30 - 10:10 Lecture: Algorithms for automatic spectra interpretation, Ralf Gabriels, VIB/UGENT

10:10-10:15 Break

10:15-10:55 Lecture: Statistics for peptide identification and protein inference, Nina Demeule-meester, VIB / UGENT

11:00-11:30 Tutorial: Assignment Introduction – Manual spectra annotation and automatic database/library search, Viktoria Dorfer, FHOOE

11:30-15:00 Break

15:00-17:00 Hands-on Workshop, all ESRs

17:00-17:40 Tutorial: Assignment revision - Manual spectra annotation and automatic database/library search, Viktoria Dorfer, FHOOE

17:45-18:25 Lecture: Algorithms for identification and localization of post-translational modifications, Marie Locard Paulet, UCPH

All times in CET!

9:30 - 10:10 Lecture: Introduction to experimental strategies of proteome quantification, Odile Schiltz, CNRS-IPBS

10:10-10:15 Break

10:15-10:55 Lecture: Algorithms for proteome quantification, Lukas Käll, SciLifeLab

11:00-11:30 Tutorial: Assignment Introduction – Tutorial on quantitative proteomics and results visualization, David Bouyssié, CNRS-IPBS

11:30-15:00 Break

15:00-17:00 Hands-on Workshop, all ESRs

17:00-17:40 Tutorial: Assignment revision - Tutorial on quantitative proteomics and results visualization, David Bouyssié, CNRS-IPBS

17:45-18:25 Lecture: Statistical methods for studies of biomolecular systems, Olga Vitek, Northeastern

All times in CET!

9:30 - 10:10 Lecture: Introduction to the data-independent acquisition proteomics workflow, Eduard Sabidó, CRG

10:10-10:15 Break

10:15-10:55 Lecture: Machine learning algorithms in predicting peptide fragmentation, Mathias Wilhelm, TUM

11:00-11:30 Tutorial: Assignment Introduction – Tutorial on the generation of a retention time prediction model with tensor flow, Mathias Wilhelm, TUM

11:30-15:00 Break

15:00-17:00 Hands-on Workshop, all ESRs

17:00-17:40 Tutorial: Assignment revision - Tutorial on the generation of a retention time prediction model with tensor flow, Mathias Wilhelm, TUM

17:45-18:25 Lecture: AI-driven Deep Visual Proteomics defines cell identity and heterogeneity, Andreas Mund, UCPH

All times in CET!

9:30 - 10:10 Lecture: Big data Proteomics Projects: ProteomicsDB – a multi-omics and multi-organism resource for life science research, Mathias Wilhelm, TUM

10:10-10:15 Break

10:15-10:55 Lecture: GrandPep, a novel software for computational reconstruction of ancient protein sequences, Petra Guten-Brunner, MPIB

11:00-11:30 Closing Lecture: Intact nd native proteomics, Albert Heck, Utrecht Univ.

11:30-11:40 Break

11:40-12:00 Wrap Up and feedback round, All

All times in CET!

9:30 - 10:10 Lecture: Introduction to Open and Responsible Research, Michela Bertero, CRG

Break 10:10 - 10:15

10:15 - 10:55 Lecture: Transparent Publishing & Open Science: how to share reproducible data, Bernd Pulverer, EMBO

Break 10:55 - 11:00

11:00 - 11:30 Lecture: Proteomics repositories: PRIDE and ProteomeXchange, Juan Antonio Vizcaíno, EMBL-EBI

Break 11:30 - 11:40

11:40 - 12:30 Lecture: Reuse of public proteomics data, Lennart Martens, VIB/ UGENT

All times in CET!

9:30 - 10:45 Hands-on Workshop: Healthy and Constructive Supervision Part 1, Joanna Harney, Trinity College Dublin

Break 10:45 - 11:00

11:00 - 12:20 Hands-on Workshop: Healthy and Constructive Supervision Part 2, Joanna Harney, Trinity College Dublin

Break 12:20 - 12:25

12:25 - 12:40 Hands-on Workshop: Introduction to Career Development Plans, Brian Cahill, Leibniz Information Center for Science and Technology, Germany

All times in CET!

9:00 - 10:30 Hands-on Workshop: Open and Responsible Research Hands-on Part 1, Celine Carret, EMBO solutions

Break 10:30 - 10:40

10:40 - 11:45 Hands-on Workshop: Open and Responsible Research Hands-on Part 2, Celine Carret, EMBO solutions

Break 11:45 - 11:55

11:55 - 13:30 Hands-on Workshop: Open and Responsible Research Hands-on Part 3, Celine Carret, EMBO solutions