Join us in Amsterdam for BioExcel’s first Community Forum

A networking event with a programme of small interactive working groups aligned with the BioExcel Interest Groups

Come to talk to the core developers of GROMACS, HADDOCK and CPMD

22nd-23rd November, 2017
Lloyd Hotel & Cultural Embassy, Amsterdam
Free – Register at:

The BioExcel Community Forum provides an opportunity for members of BioExcel’s interest groups (IGs) and other members of the BioExcel community to come together for discussions and to work on issues of interest to the group. This will be an “unconference”, so it won’t just be a set of presentations; this will be a chance for you to have your voice heard and to influence the future direction of the Centre of Excellence, and will also provide you with a chance to work together with other IG members on topics that are of interest to you.


The overall schedule is shown below, followed by descriptions of parallel sessions planned by the various Interest Groups.

Planned Schedule

DAY ONE: 22nd November, 2017

13:00-13:45 Registration & Coffee
14:00-14:15 Welcome
14:15-15:30 Parallel Sessions: Session 1a
15:30-16:00 Break: Networking over Coffee
16:00-17:15 Parallel Sessions: Session 1b
17:15-18:15 Networking Reception

DAY TWO: 23rd November, 2017

09:00-10:15 Parallel Sessions: Session 2a
10:15-10:45 Break: Networking over Coffee
10:45-12:15 Parallel Sessions: Session 2b
12:15-13:15 Lunch
13:15-15:00 Parallel Sessions: Session 3
15:00-15:15 Break: Networking over Coffee
15:15-16:15 Keynote: Siewert-Jan Marrink: “Modeling the complexity of real cell membranes
16:15-17:15 Plenary: Feedback from Sessions

Exact times are provisional at this stage, and are subject to change. We hope you can join us for the full day and a half, but you are welcome to attend as many or as few sessions as you wish. You are welcome to move between the different parallel sessions.

IG-Integrative Modelling with IG-Hybrid Methods
Leads: Adrien Melquiond and Emiliano Ippoliti
22nd November (PM) – 23rd November (PM)

Over three hands-on sessions, the Integrative Modelling and Hybrid Methods Interest Groups will join forces. We will explore protein-small ligand docking using HADDOCK, followed by hybrid QM-MM simulations using CPMD, ending in analysis of results which may involve running a small MD simulation with GROMACS. Alternative analyses can be explored, depending on the interests of the people in the room.

IG-Free Energy
Leads: Bert de Groot & Vytautas Gapsys
22nd November (PM) – 23rd November (PM)

Session 1. introduction/brainstorming

We start with a brief introduction to bring everyone on the same page by providing some background and examples. Then we continue with brainstorming about issues that the participants would like to focus on, ranging form their own specific research questions to general best practice issues. (1-1.5 hours)

Session 2. practical/hands on session.
Here participants can optionally run a PMX tutorial to get to know the ins and outs of alchemical free energy calculations as well as get a first go at protein design. Alternatively, IG members are invited to bring their own research questions and work hands on on their projects. (~2 hours)

Please bringing your own laptop. The tutorial will be ran from a virtual machine which we will distribute via USB drives.

Session 3. discussion/wrap up session.
Feedback on the practical session, analyse/discuss the outcome. Q&A on issues that remained unclear, future recommendations (30-45 minutes).

Lead: Vera Matser
22nd November (PM) – 23rd November (PM)

Note: all sessions below are independent

Session 0 [continuous drop-in session 22nd and 23rd November – central platform] User Testing of the Knowledge Resource Centre – with gamification for adding new resources (run by Alba Gomez)

We are giving people a chance to try out the BioExcel Knowledge Resource Center (KRC) and give us their feedback. We are always interested in finding new courses and training resources to add to the KRC. We will be handing out BioExcel branded goodies to people who test the KRC; you can unlock higher tier goodies by adding increasing numbers of new resources to the KRC.

Session 1 (on 22nd November @14:15 to 15:30 pm and @16:00 to 17:15 pm):  Creating reference persona and use cases for BioExcel community.

In this session we will be exploring user profiles of potential BioExcel users and try to understand if we can distil generic use cases. Depending on how long the first part of the session takes we may expand into mapping to created reference user profiles to the BioExcel competency profile and explore their training needs.

Session 2/3 (on 23rd November @ 9am – 12:15 (optional extension to 15:00 to start report writing)):  Brainstorming on webinar guidelines

This session is a brainstorming exercise to create a coherent document with guidelines for webinar speakers and organisers. It should cover everything from different webinar styles, how to keep your audience engaged, and how to encourage interactivity during your webinar. We encourage attendance by webinar organisers and welcome input from webinar attendees, as well as experienced and inexperienced webinar speakers. The final document will be made publicly available, and we will organise a webinar to disseminate our results. This session is being run in collaboration with other initiatives running webinar series.

IG-Entry-Level with IG-Workflows
Leads: Adam Hospital, Stian Soiland-Reyes
22nd November (PM) – 23rd November (PM)

The Entry-Level Users IG and Workflows IG are running a combined programme. After an initial round table to find out the interests of those present, we will discuss a number of different MD tools and related workflows. This will be followed by presentation of what BioExcel is doing with such tools. The next session will be a “bring-your-own-workflow” session in which participants will discuss the MD workflows with a chance to ask experts questions and discuss potential solutions.

Additional time will be available for a final hands-on session which will allow us to dig deeper based on the interests of the group.

IG-Practical Applications for Industry
Lead: Ian Harrow
22nd November (PM) – 23rd November (PM)

The theme is sharing success stories and user experience challenges for the application of biomolecular tools. These interactive sessions will start with a brainstorm on shared success stories and challenges that are barriers for the application of biomolecular tools in industry. Next this will be analysed and discussed as a group so that we can formulate recommendations for the plenary session.

There will also be the lead code developers present from GROMACS, HADDOCK and the new QM/MM interface in CPMD who will be listening to your interests and priorities for future releases of the codes.