Join A BioExcel Interest Group
BioExcel Interest Groups (IG) are designed to support groups of people with a common interest related to Computational Molecular Biology.
- Allow us to learn about your interests, challenges and priorities
- Allow us to share best practice and expertise (for example from code developers of our pilot codes)
- Provide a platform to allow you to interact and share your knowledge, challenges and news with the rest of the IG
The BioExcel project also has funds available to support face-to-face meetings of IG members.
To join an interest group, simply enter your name and email address in the form at the bottom of this page, and select the group(s) that you’d like to join.
Entry Level Users IG
This is a group for scientists working on biomolecular (proteins/nucleic acids) structures but with little or no experience of setting up simulations. That would be users who are mostly interested in simulations in standard conditions (constant temperature and pressure, explicit solvent, no ligands) seeking to solve specific biochemical questions (effects of mutations in stability, simple conformational changes) using biomolecular simulations.
The IG targets mainly users of portals for automated simulations such as those offered by IRB: MDWeb (http://mmb.irbbarcelona.org/MDWeb), a platform to setup, run and analyse protein structure molecular dynamics, FlexServ (http://mmb.irbbarcelona.org/FlexServ), to run a complete set of flexibility analyses on protein structure MD trajectories, and NAFlex (http://mmb.irbbarcelona.org/NAFlex), a platform to build, setup, run and analyse nucleic acids molecular dynamics simulations.
In addition, those IG users will have access to a set of already computed MD simulations stored in a couple of databases: MoDEL (http://mmb.irbbarcelona.org/MoDEL), with almost 2000 different protein structures trajectories and BigNASim (http://mmb.irbbarcelona.org/BigNASim), with 150 nucleic acid trajectories covering 150 µs simulation time.
For entry level users interested in small molecule docking, the SEABED web server (http://www.bsc.es/SEABED) integrates a variety of docking and QSAR techniques in a user-friendly environment, going beyond the basic docking and QSAR web tools, implementing extended functionalities like receptor preparation, library editing, flexible ensemble docking, hybrid docking/QSAR experiments or virtual screening on protein mutants.
The Integrative Modelling Interest Group is for users who have an interest in the structural prediction of biomolecular interactions combining experimental data from various sources with powerful algorithms to generate high-resolution 3D models of the macromolecular complexes. The time has come to ‘combine and conquer’.
This IG mainly targets HADDOCK users.
Free Energy IG
This group will discuss topics of interest related to methods for free energy calculations, which are crucial for evaluation of reaction paths, binding propensities (drug design), thermostability predictions, protein design, etc. There will be a particular focus on the automated, unsupervised setup of such calculations, rendering such simulations more user-friendly and accessible to the novice user as well as enabling large-scale scans for advanced users.
This IG mainly targets the GROMACS users
The Hybrid Method Interest Group will deal with hybrid methods in general, in order to better describe biological systems. In particular, the discussions will be concerned about the methodologies and the approaches to interface the different granularity of descriptions from quantum to coarse levels.
The IG targets mainly CPMD users interested to the QM/MM approaches and any other person interested in multi-scale approaches in computational biology.
The Workflows Interest Group is for users (and potential users) of Scientific Workflow systems for data analysis and pipe-lining of biomolecular simulation and modelling tools; in particular using Galaxy, Apache Taverna, KNIME, COMPSs and Common Workflow Language.
Covering pros and cons of these workflow system, practical workflow design and setup, discussion in this group also covers deployment questions on HPC/cloud infrastructure, like the use of Docker for packaging command line codes.
The Training IG has the following aims:
- Improve visibility of training initiatives and individual courses/resources. Members of the Training IG will be able to act as liaisons to other training initiatives.
- Facilitate collaboration between projects to promote best practice and efficient use of resources.
- Improve communication between “computational trainers” and “life science trainers”.
- Promote the importance of high quality training
The Training IG is for you if you are responsibility for or have an interest in training within your institute or project or are a training professional (trainer, coordinator, lecturer) in a life sciences and/or computational field.