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Course

BioExcel / EuroCC workshop

Nov 26-28, 2024
Coimbra, Portugal
Register

Course

BioExcel / EuroCC workshop

Nov 26-28, 2024
Coimbra, Portugal
Fee: 50 euros

About Event

Upcoming 2.5-Day Hands-On Workshop: Hybrid Learning Experience

Jointly organized by BioExcel and supported by National Competence Centres in Portugal, France, Spain, and Ireland, this hydrid workshop will offer participants the chance to engage both on-site and online. The workshop will focus on the use of BioExcel core codes such as GROMACS, HADDOCK, PMX, BioBB, and AlphaFold, with a strong emphasis on hands-on practical sessions and guidance from leading experts in the field.

In addition to in-depth tutorials, the event will feature an exciting on-site GROMACS competition.


Key Topics Covered:

  • Molecular Dynamics Simulations:
    • Focus on GROMACS, including membrane-protein simulations;
    • Performing alchemical transformations with GROMACS (e.g., solvation free energy calculations);
    • GROMACS performance optimization.
  • Biomolecular Docking:
    • Using HADDOCK modeling Antigen-Antibody and Protein-DNA interactions.
  • Free Energy Calculations:
    • Advanced methods for calculating amino acid mutations and more.
  • AlphaFold Tutorials:
    • Practical sessions for Hands-on sessions covering both AlphaFold2 and AlphaFold3.
  • BioBB Workshop:
    • Protein conformational transitions, calculations, and automatic ligand parameterization.

Participants will receive personalized guidance from software developers and experts throughout the workshop. On-site attendees will enjoy enhanced support and in-person interaction with the trainers. Please note that online attendees will have access to the lectures, but additional support will not be available in the virtual format.

  • Nov 26-28, 2024
  • Department of Life Sciences, University of Coimbra
  • Fee Icon   60 Euros for on-site, free online
  • 40 On-site Seats For PhD and post-docs
  • Additional Seats Available for Online Participation
  • 10 Speakers
Register

Who is this course for?

The BioExcel workshop is designed for intermediate to advanced researchers particularly PhD students and post-doctoral fellows, who are currently using or planning to incorporate biomolecular modeling and simulation into their research projects.

Ideal Participants Will Have:

  • A working knowledge of Linux.
  • Basic familiarity with molecular modeling software.

What Will I Learn?

Utilize GROMACS software in a Conda environment, with Jupyter Notebook support, virtual machines, and easy-to-use web portals such as Open OnDemand for streamlined computational workflows.

Miniconda3/Anaconda3 with the latest BioBB version, utilizing remote display tools and cloud resources for visualization.

Miniconda3/Anaconda3 with the latest HADDOCK version, leveraging remote display and cloud resources for visualization, along with PyMol Educational for 3D molecular rendering, and Docker for streamlined deployment and environment management.

Miniconda3/Anaconda3 with the latest GROMACS version, and access to install PMX for advanced molecular simulations.

Learn structure prediction using AlphaFold2 and AlphaFold3 for protein folding simulations.

Gain the opportunity to participate in a GROMACS competition, which requires access to a supercomputer. The competition includes GROMACS installation, system validation, and assistance with SLURM script configuration for efficient job scheduling.

Schedule

14:00 to 15:00

26 Nov 2024



Introduction to GROMACS: from basis to advance features

Alessandra Villa

KTH, Stockholm, Sweden

Anfiteatro, DCV

15:15 to 16:45

26 Nov 2024



GROMACS Tutorial

Alessandra Villa &
Andrey Alekseenko

KTH, Stockholm, Sweden

Anfiteatro, DCV

17:00 to 17:45

26 Nov 2024

Theoretical part: GROMACS performance

Only for physical attendees

Andrey Alekseenko

KTH, Stockholm, Sweden

Anfiteatro, DCV

18:00 to 19:00

26 Nov 2024

GROMACS performance Tutorial & Competition

Only for physical attendes

Alessandra Villa &
Andrey Alekseenko

KTH, Stockholm, Sweden

Anfiteatro, DCV

9:45 to 10:45

27 Nov 2024

Integrative Modeling of Biomolecular Complexes

HADDOCK Theoretical

Alexandre Bonvin

Utrecht University,
Netherlands

Anfiteatro, DCV

11:00 to 12:30

27 Nov 2024

Integrative Modeling of Biomolecular Complexes

HADDOCK Tutorial

Alexandre Bonvin &
Victor Reys

Utrecht University,
Netherlands

Anfiteatro, DCV

14:00 to 15:00

27 Nov 2024

Introduction into alchemical
free energy calculations

PMX Theoretical

Bert de Groot

Max Planc Institute,
Germany

Anfiteatro, DCV

15:15 to 16:45

27 Nov 2024

Alchemical free energy calculations with PMX/GROMACS

PMX Tutorial

Sudarshan Behera

Max Planc Institute,
Germany

Anfiteatro, DCV

17:00 to 18:00

27 Nov 2024


University of Coimbra Tour


Guided Tour

University of
Coimbra

20:00

27 Nov 2024


Social Dinner


University Tuna
Performance

Before dinner
(see full schedule)

Papa Restaurant

9:00 to 10:00

28 Nov 2024

AlphaFold2 and its impact on biological research

AlphaFold 2.0 Theoretical


Paulyna Magaña

EMBL-EBI, UK

Anfiteatro, DCV

10:15 to 11:45

28 Nov 2024


AlphaFold 2.0 Tutorial



Paulyna Magaña

EMBL-EBI, UK

Anfiteatro, DCV

12:00 to 12:30

28 Nov 2024


User-friendly cloud HPC with Python and the Inductiva API


Hugo Penedones

Inductiva.AI, Portugal

Anfiteatro, DCV

14:30 to 15:30

28 Nov 2024

Interoperable and reproducible biomolecular simulations workflows using BioExcel building blocks (BioBB)

BioBB Theoretical

Pau Andrio and
Pieter Zanders

IRB Barcelona, Spain

Anfiteatro, DCV

15:45 to 17:15

28 Nov 2024

BioBB interactive Jupyter Notebooks for FAIR and reproducible biomolecular simulation workflows

BioBB Tutorial

Pau Andrio and
Pieter Zanders

IRB Barcelona, Spain

Anfiteatro, DCV

Please scroll to view the schedule. If you want to see the full schedule, please click the button below.

Online Schedule

Honorable Speaker/Trainer

Alexandre Bonvin

Bonvin Lab, Computational Structural Biology, Utrech University

Bert de Groot

Computational Biomolecular Dynamics Group, Max Plank Institute

Alessandra Villa

KTH - Royal Institute of technology

Paulyna Magaña

Protein Data Bank in Europe Group @ EMBL

Hugo Penedones

Inductiva.AI, Portugal

Pau Andrio

Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Computational team @ Barcelona Supercomputing Center

Pieter Zanders

Spanish National Bioinformatics Institute (INB)/ELIXIR-ES, Computational team @ Barcelona Supercomputing Center

Victor Reys

Posdoctoral Researcher @ Bonvin Lab

Andrey Alekseenko

Researcher @ Department of Applied Physics - KTH - Royal Institute of technology

Sudarshan Behera

Postdoc @ Computational Biomolecular Dynamics Group, Max Planc Institute

To view all speakers, please hover your cursor over the section.

How to apply?

To apply, the registration process must be completed.

Register
  • As part of your application, you will need to submit the following documents:
    • CV: Up-to-date curriculum vitae highlighting your relevant experience and qualifications.
    • Motivation Letter: A statement (250 words maximum) detailing your interest in the program.
    • Research Area: Include information or a brief outline of the field of investigation you are working on or planning to explore (250 characters maximum). This should highlight your research interests, the significance of the topic, and any relevant methods or approaches you are considering.

Please ensure that your application is completed by midnight (CET) on Monday, 11 November. Incomplete applications will not be considered. Applicants will be notified of their application status (successful, waitlisted, or rejected) by 15 November.

Details

Date: 26 - 28 November 2024

Venue: Hybrid course, On-site in Coimbra, Portugal

Application deadline: 11 November

Notification date: 15 November

Participation: Applications are open to everyone, with a selection process in place. 40 participants will be chosen for the on-site course, with additional spots available for online attendees.

Registration fee: A fee of 60 Euros is required after the selection process for in-person registration. Online participation is free.

Catering and Activities: For on-site participants, lunches (Nov 27 and 28), coffee breaks, a visit to the University of Coimbra, and the social dinner (Nov 27) are included.

Contact: For inquiries, please contact us at irina.moreira _at_ cnc.uc.pt (Please replace "_at_" with "@").

ORGANIZERS

LOCAL ORGANIZERS

Pedro Alberto

UC/LCA/NCC Portugal

Irina Moreira

CNC-UC/CiBB/DCV/FCTUC

Nícia Ferreira

Researcher
Data-Driven Molecular Design Group/ MoreiraLab, UC

Marcos Gouveia

INESC-TEC

Urszula Orzel

PhD student
Data-Driven Molecular Design Group/ MoreiraLab, UC

Beatriz Caniceiro

PhD student
Data-Driven Molecular Design Group/ MoreiraLab, UC

Luana Afonso

PhD student
Data-Driven Molecular Design Group/ MoreiraLab, UC

Raquel Gouveia

PhD student
Data-Driven Molecular Design Group/ MoreiraLab, UC

Ana Amorim

PhD student
Data-Driven Molecular Design Group/ MoreiraLab, UC

  INTERNATIONAL ORGANIZERS

Alessandra Villa

KTH - Royal Institute of technology

Karim Azoum

NCC France

Marie Lhande Pincemin

NCC France

Luca Monticelli

BioExcel ambassadors of France (Collaboration)

David De Sancho

BioExcel ambassadors of Spain (Collaboration)

To view all organizers, please hover your cursor over the section.

Location & Venue

Location

Calçada Martim de Freitas

3000-456 Coimbra

Portugal

How to get there?

Access to FCTUC-DCV is quick and convenient, especially for those arriving at Coimbra-A train station. From there, it’s easy to walk or use the available public transportation. Taxis and on-demand services like Uber are also readily available.

Bus

The Municipal Urban Transport Services of Coimbra (SMTUC) provides several bus lines:
  • From the Bus Terminal: Line 5 or 28
  • From the Coimbra-A: Line 103

Taxi

Accommodation and Travel

Accommodation for the Conference:

Hotels: Coimbra offers a variety of accommodation options to suit different budgets. Several hotels are available in the city, providing convenient access to the conference venue.

Getting to Coimbra:

Airport: The closest airport is Francisco Sá Carneiro Airport (IATA: OPO) in Porto.

Train: From Porto, the easiest way to reach Coimbra is by train from Porto Campanhã station. You can get to the station via Taxi, Uber, or the metro. The cost of the train ticket typically ranges from 14 to 25 Euros. For more information and to purchase tickets, visit CP - Comboios de Portugal.

Bus: Another option to travel from Porto to Coimbra is by bus. You can check schedules and availability on Flixbus or Rede Expressos. Tickets typically cost between 8 and 18 Euros, depending on availability and time of booking.

Back to the Airport:

Airport Shuttle: From Coimbra to Lisbon Airport, the shuttle service costs around 41 Euros, and to Porto Airport, it costs around 34 Euros. For schedules and availability, visit Airport Shuttle.

If you need further information or have any questions about accommodation, feel free to contact us at irina.moreira _at_ cnc.uc.pt (Please replace "_at_" with "@").