Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades - Agenda

(Agenda as of 2024/04/30-15:55 CEST)

Monday, 7 March 2022
CET: 13:00 UTC: 12:00	Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades This workshop is part of the EBRAINS RI trainings. Registration to the training is now closed. Dial in: If you registered, you can find the meetings dial-in on your personal meeting page Material: for registered meeting attendants material is available in this Collab drive .
CET: 13:00 UTC: 12:00	Session 1: Introduction and OMICs data
CET: 13:00‑13:30 UTC: 12:00‑12:30 (30 min)		Welcome & introduction Introduction and overview of the HBP and EBRAINS. Talk slides	Rebecca Wade (HITS, Germany), Giulia D'Arrigo (HITS, Germany), Giulia Rossetti (FZJ, Germany), Jeanette Hellgren-Kotaleski (KTH, Sweden)
CET: 13:30‑14:30 UTC: 12:30‑13:30 (60 min)		Lecture and Hands-on: Synaptic Proteome Database (Overview and Demo) Please find material in this Collab drive in the Synaptic Proteome Database (Overview and Demo) directory	Douglas Armstrong (UEDIN, UK), Oksana Sorokina (UEDIN, UK)
CET: 14:30‑15:00 UTC: 13:30‑14:00 (30 min)		Break
CET: 15:00‑16:30 UTC: 14:00‑15:30 (90 min)		Lecture and Hands-on: Working with Molecular Data slides	Sven Cichon ( UNIBAS, Switzerland), Thoman Mühleisen (FZJ, Germany), Dominique Hilger (FZJ, Germany), Nicola Palomero-Gallagher (FZJ, Germany)
CET: 16:30‑17:30 UTC: 15:30‑16:30 (60 min)		Case studies discussion	Rebecca Wade (HITS, Germany), Giulia D'Arrigo (HITS, Germany), Giulia Rossetti (FZJ, Germany), Jeanette Hellgren-Kotaleski (KTH, Sweden)

Tuesday, 8 March 2022
CET: 13:00 UTC: 12:00	Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades, day II
CET: 13:00 UTC: 12:00	Session 2: Molecular data and molecular dynamics simulations
CET: 13:00‑13:30 UTC: 12:00‑12:30 (30 min)		Lecture: GRALL (database of allosteric modulators of the Glycine receptor) Talk slides	Jean-Pierre Changeux (IP, France), Marco Cecchini (UNISTRA, France), Adrien Cerdan (UNISTRA, France)
CET: 13:30‑13:55 UTC: 12:30‑12:55 (25+5 min)		Hands-on: GRALL (database of allosteric modulators of the Glycine receptor) Material: knime-workflow-grall.tar.gz	Marco Cecchini (UNISTRA, France), Adrien Cerdan (UNISTRA, France)
CET: 14:00‑15:30 UTC: 13:00‑14:30 (90 min)		Lecture and Hands-on: CNS ligands/MoDel/Setting up/running molecular dynamics simulations Talk slides	Adam Hospital (IRB, Spain)
CET: 15:30‑16:00 UTC: 14:30‑15:00 (30 min)		Break
CET: 16:00‑16:30 UTC: 15:00‑15:30 (30 min)		Lecture tauRAMD calculations of protein-ligand dissociation rates Talk slides	Giulia D’Arrigo (HITS, Germany)
CET: 16:30‑18:00 UTC: 15:30‑17:00 (90 min)		Hands-on: tauRAMD calculations of protein-ligand dissociation rates Tutorial slides	Giulia D’Arrigo (HITS, Germany), Rebecca Wade (HITS, Germany)

Wednesday, 9 March 2022
CET: 13:00 UTC: 12:00	Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades - day III
CET: 13:00 UTC: 12:00	Session 3: Further molecular simulation techniques (Brownian dynamics and QM/MM)
CET: 13:00‑15:00 UTC: 12:00‑14:00 (120 min)		Lecture and Hands-on: QM/MM interface to compute protein-ligand binding kinetics Setup guide	Davide Mandelli (FZJ, Germany), Andrea Rizzi (FZJ, Germany), Katya Ahmad (FZJ, Germany), Paolo Carloni (FZJ, Germany)
CET: 15:00‑15:30 UTC: 14:00‑14:30 (30 min)		Break
CET: 15:30‑17:30 UTC: 14:30‑16:30 (120 min)		Lecture and Hands-on: Brownian dynamics simulations with SDA to compute association rates Talk slides and tutorial slides	Abraham Muniz Chicharro (HITS, Germany), Stefan Richter (HITS, Germany) & Rebecca Wade (HITS, Germany)

Thursday, 10 March 2022
CET: 13:00 UTC: 12:00	Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades - day IV
CET: 13:00 UTC: 12:00	Session 4: Subcellular modelling and simulation
CET: 13:00‑14:00 UTC: 12:00‑13:00 (60 min)		Lecture and Hands-on: Subcellular toolset Talk slides	Olivia Eriksson (KTH, Sweden) & Federica Milinanni (KTH, Sweden)
CET: 14:00‑15:30 UTC: 13:00‑14:30 (90 min)		Lecture and Hands-on: Subcellular App Files for the hands-on part Talk slides	Andrey Stepaniuk (EPFL, Switzerland)
CET: 15:30‑16:00 UTC: 14:30‑15:00 (30 min)		Break
CET: 16:00‑17:30 UTC: 15:00‑16:30 (90 min)		Lecture and Hands-on: SSB framework Talk slides: SSB toolkit: from molecular structure to subcellular networks Talk slides: hands-on	Alejandro Giorgetti (University of Verona, Italy) and Rui Ribeiro (FZJ, Germany)
CET: 17:30‑18:00 UTC: 16:30‑17:00 (30 min)		Closing discussion	Rebecca Wade (HITS, Germany), Giulia D'Arrigo (HITS, Germany), Giulia Rossetti (FZJ, Germany), Jeanette Hellgren-Kotaleski (KTH, Sweden)
CET: 18:00 UTC: 17:00	End of the workshop

Contact: martina.schmalholz@kip.uni-heidelberg.de