| Wednesday, 21 June 2023 |
CEST: 13:00
UTC: 11:00
| Second HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades
2nd Training Workshop on Tools for Molecular
Simulation of Neuronal Signaling Cascades
The human brain is one of the most complex and fascinating structures. It is still far from understood and therefore considered one the last biological frontiers. Its function is the result of intricate signal transmission networks and reactions occurring within and between neurons. To model and simulate such complexity, multiscale models are required that are aimed at reproducing brain function through a bottom-up approach, from the molecular to the whole brain level. This workshop will provide training in some of the computational tools developed in the Human Brain Project that enable brain simulation and modelling at the molecular and subcellular levels. This workshop is intended to offer an overview of these tools and their application and provide students and young researchers with the necessary theoretical background and practical experience to enable them to apply them in their own research. There will be a mix of lectures and practical session as well as discussions of case studies and the participants' own research problems.
This workshop is part of the EBRAINS RI trainings.
Registration to the training is now closed.
Venue for the Hybrid Event
- on site: Mathematikon (Building A -entrance from the Klaus Tschira platz), 3rd Floor computer pool, Im Neuenheimer Feld 205, Heidelberg, Germany see map
- online: zoom
Material
- for registered meeting attendants material is available in this Collab drive
|
CEST: 13:00
UTC: 11:00
| Session 1: OMICS and Subcellular Simulations |
CEST: 13:00‑13:30
UTC: 11:00‑11:30
(30 min) | | Welcome & introduction
Introduction and overview of the HBP and EBRAINS.
Talk slides
| Rebecca Wade (HITS gGmbH) |
CEST: 13:30‑14:30
UTC: 11:30‑12:30
(60 min) | | Lecture and Hands-on
Synaptic Proteome Database (Overview and Demo)
Talk slides & Tutorial files
Video
| Douglas Armstrong (UEDIN, UK), Oksana Sorokina (UEDIN, UK) |
CEST: 14:30‑15:00
UTC: 12:30‑13:00
(30 min) | | Break |
CEST: 15:00‑16:00
UTC: 13:00‑14:00
(60 min) | | Lecture and Hands-on:
Subcellular toolset
Talk & Tutorial Slides
Video
| Olivia Eriksson (KTH, Sweden) & Federica Milinanni (KTH, Sweden) |
CEST: 16:00‑17:30
UTC: 14:00‑15:30
(90 min) | | Lecture and Hands-on:
Subcellular App
Tutorial slides
Video
| Andrey Stepaniuk (EPFL, Switzerland) |
CEST: 17:30‑18:00
UTC: 15:30‑16:00
(30 min) | | Case studies discussion | All tutors |
| Thursday, 22 June 2023 |
CEST: 13:00
UTC: 11:00
| 2nd HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades, day II |
CEST: 13:00
UTC: 11:00
| Session 2: Molecular Data and Simulations |
CEST: 13:00‑14:30
UTC: 11:00‑12:30
(90 min) | | Lecture and hands-on:
CNS ligands/MoDel/Setting up/running molecular dynamics simulations
Talk & Tutorial Slides
Video
| Adam Hospital (IRB, Spain) |
CEST: 14:30‑14:45
UTC: 12:30‑12:45
(15 min) | | Break |
CEST: 14:45‑15:15
UTC: 12:45‑13:15
(30 min) | | Lecture:
tauRAMD calculations of protein-ligand dissociation rates
Talk slides
Video
| Giulia D'Arrigo (HITS gGmbH) |
CEST: 15:15‑16:45
UTC: 13:15‑14:45
(90 min) | | Hands-on:
tauRAMD calculations of protein-ligand dissociation rates
| Giulia D’Arrigo (HITS, Germany) |
CEST: 16:45‑17:00
UTC: 14:45‑15:00
(15 min) | | Break |
CEST: 17:00‑18:30
UTC: 15:00‑16:30
(90 min) | | Lecture and Hands-on:
SSB toolkit: from molecular structure to subcellular networks
Video
| Alejandro Giorgetti (University of Verona, Italy) and Rui Ribeiro (FZJ, Germany) |
| Friday, 23 June 2023 |
CEST: 09:00
UTC: 07:00
| 2nd HBPMolSim Training Workshop on Tools for Molecular Simulation of Neuronal Signaling Cascades - day III |
CEST: 09:00
UTC: 07:00
| Session 3: Further Molecular Dynamics Simulations Techniques |
CEST: 09:00‑11:00
UTC: 07:00‑09:00
(120 min) | | Lecture and Hands-on:
QM/MM interface to compute protein-ligand binding kinetics
Set up guide & Tutorial files
Video
| Davide Mandelli (FZJ, Germany), Emiliano Ippoliti (FZJ, Germany) & Mirko Paulikat (FZJ, Germany) |
CEST: 11:00‑11:15
UTC: 09:00‑09:15
(15 min) | | Break |
CEST: 11:15‑13:15
UTC: 09:15‑11:15
(120 min) | | Lecture and Hands-on:
Brownian dynamics simulations with SDA to compute association rates
Talk slides & Tutorial files
Video
| Abraham Muniz Chicharro (HITS, Germany), Stefan Richter (HITS, Germany) & Rebecca Wade (HITS, Germany) |
CEST: 13:15‑13:45
UTC: 11:15‑11:45
(30 min) | | Lunch Break |
CEST: 13:45
UTC: 11:45
| Session 4: Molecular Data |
CEST: 13:45‑14:30
UTC: 11:45‑12:30
(45 min) | | Lecture:
ACRALL (Nicotinic Acetylcholine Receptor Allosteric Ligand Library
Talk slides
Video
| Jean-Pierre Changeux (IP, France), Marco Cecchini (UNISTRA, France) |
CEST: 14:30‑15:00
UTC: 12:30‑13:00
(30 min) | | Case studies discussion | All tutors |
CEST: 15:00‑15:15
UTC: 13:00‑13:15
(15 min) | | Break |
CEST: 15:15
UTC: 13:15
| HBP BRAVE Partner project - Open Workshop
The BRAVE project addresses the problem of COVID-19's impact on the brain by tackling COVID-19 brain inflammation by computer-aided molecular design.
The aim of the project is to block SARS-CoV-2 mediated neurodegeneration and brain damage by inhibiting the activation of the NLRP3 inflammasome, which is responsible for neuroinflammation in several neurodegenerative conditions such as Alzheimer's disease and long COVID-19. The results of this project will be presented and discussed in this workshop.
|
CEST: 15:15
UTC: 13:15
| Session 1: Presentations of project achievements |
CEST: 15:15‑16:15
UTC: 13:15‑14:15
(60 min) | | Lecture:
Project Introduction and Results, part 1: COVID-19 and neuroinflammation. Identification of new molecules to target neuroinflammation and neurodegeneration.
Talk slides
Video
| Francesca Spyrakis (Turin, Italy) |
CEST: 16:15‑17:15
UTC: 14:15‑15:15
(60 min) | | Lecture:
Project Results, part 2: NLRP3 monomer Functional Dynamics: from the Effects of Allosteric Binding to Implications for Drug Design
Talk slides
Video
| Giorgio Colombo (Pavia, Italy) |
