HPC for Life Sciences Center of Excellence for Computational - PowerPoint PPT Presentation

BioExcel/PRACE Spring School 2017 – HPC for Life Sciences Center of Excellence for Computational Biomolecular Research Vera Matser EMBL-EBI Training and Dissemination Funding Partners bioexcel.eu 1

Life Science and HPC Population Organ Tissue Cell Macromolecules Small Molecule Atom bioexcel.eu 2

Biomarkers design Physiology Electronic structure Biomolecular Modeling and Simulations Personalized medicine Neuroinformatics Biomaterials science and nanotechnology bioexcel.eu 3

Objectives of BioExcel Excellence in Biomolecular Science Improve the performance, efficiency and scalability of key codes • GROMACS (Molecular Dynamics Simulations) • HADDOCK (Integrative modeling of macro-assemblies) • CPMD (hybrid QM/MM code for enzymatic reactions, photochemistry and electron transfer processes) bioexcel.eu 4

Objectives of BioExcel Excellence in Usability DMI Repository DMI • Service Invocation Make ICT technologies Gateway Expert DMI Portal / Domain Data fl ow Gateway Workbench easier to use by Expert Monitoring fl ow DMI biomolecular researchers, Request both in academia and DMI Registry DADC Gateway Engineer industry DMI DMI Planner Optimiser DMI Validator • Devise efficient workflow DMI Executor DMI Monitor environments with associated data integration DMI Enactor DMI Enactor DMI Enactor DMI Data Delivery Expert Data Point Source bioexcel.eu 5

Objectives of BioExcel Competence-building among academia and industry Promote best practices and train end users to make best use of both software and computational infrastructure • academic and non-profit users • industrial users • independent software vendors (ISVs) and academic code providers of related software • academic and commercial resource providers bioexcel.eu 6

BioExcel Center of Excellence bioexcel.eu 7

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BioExcel Training Programme bioexcel.eu 9

What is a competency? A Competency is an observable ability of any professional, integrating multiple components such as knowledge, skills and behaviours. The key aspects of the competency-based approach are: • Competencies are observable, so acquisition can be validated objectively • Evidence of competency can be collected in a competency portfolio • Competencies are shared ‘currency’ applicable to learning of all types and at all career stages bioexcel.eu 10

Example Competency " Write his/her own scripts to perform tasks in context of biomolecular research " Knowledge Skills Behaviour Knowledge of existing Is able to automate Uses appropriate commands/libraries the process of scripting languages to re-use executing processes remotely Judges when a task Write & debug scripts should be automated bioexcel.eu 11

BioExcel Competency Profile Group related competencies together into areas • Generic Competencies • Scientific Competencies • Generic Computing Competencies • Parallel Computing Competencies bioexcel.eu 12

BioExcel Competency Profile Different types of users bioexcel.eu 13

Heads up on what we are planning Face-to-Face training events 3-7 th July 2017, Foundation skills for HPC in computational • biomolecular research - BioExcel Summer School, EMBL- EBI, UK • Autumn 2017, Introduction to HPC for Life Scientists (with PRACE), EPCC, UK • Early summer 2018, BioExcel Summer School bioexcel.eu 14

Online resources BioExcel webinar series • Wednesday 14:00 GMT / 15:00 CET • Video on the website afterwards http://bioexcel.eu/category/webinar/ Virtual training sessions (planning) • Subscribe to mailing list to stay informed Knowledge Resource Center (under development) • Relevant F-2-F courses (internal & external) • Relevant tutorials, courses, best practice docs bioexcel.eu 15

How to get in touch with us www.bioexcel.eu Announce updates, @BioExcelCoE training courses, webinars & papers Company Page Subscribe to mailing list ask.bioexcel.eu bioexcel.eu 16

Activity - Competency www.surveymonkey.co.uk/r/bioexcel Which user category are you? How relevant is the competency for you? Awareness: the professional appreciates what is possible in this area and how the area impacts on their own work Working knowledge: the professional has a firm underpinning knowledgebase in this area and applies it effectively in his or her day-to-day work Specialist knowledge: the professional actively contributes to advancement of the area, generating new understanding or new technology bioexcel.eu 17

Interest Groups • BioExcel aims to foster a community around computational biomolecular research and support existing communities • An important link with wider communities is through Interest Groups: Smaller groups of named individuals who have chosen to be members of the group Interest Groups are open to all: Sign up at bioexcel.eu/interest-groups. Funding available to support face-to-face meetings bioexcel.eu 17/12/2015

Interest Groups Interest Groups will: • Allow BioExcel to learn about its users • Allow members to learn from BioExcel • Aid communication between members • Lead to user-driven governance bioexcel.eu

Interest Groups • Entry Level Users • Integrative Modeling • Free Energy Calculations • Hybrid methods • Workflows • Industry • Training Support platforms Forums Code Repositories Chat channel Video Channel bioexcel.eu 20

Biomolecular Simulation Entry Level Users This group is for scientists interested in biomolecular simulations who have a basic knowledge of protein/DNA structure but little or no experience on setting up simulations. Initially, we expect the group to focus on simulations in standard conditions (NPT, explicit solvent, no ligands) which seek to address specific biochemical questions (effects of mutations in stability, simple conformational changes). This group will allow members to help each other, but it will also be joined by experienced practitioners and developers of key codes from the BioExcel project who will contribute to discussions and share their experience. bioexcel.eu 21

Integrative Modelling This 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’! Initially, this IG primarily targets HADDOCK users, but in the longer term, it will also encompass other aspects of Integrative Modelling bioexcel.eu 22

Free Energy Calculations 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. …with 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. Initially, this IG primarily targets GROMACS users. bioexcel.eu 23

Hybrid Methods for Biomolecular Systems This interest group will deal with hybrid methods in general, in order to better describe biological systems. In particular, the discussions will be concerned with methodologies and approaches to interface the different granularity of descriptions from quantum to coarse levels. Initially, the IG targets mainly CPMD users. bioexcel.eu 24

Practical Applications for Industry We’re developing a strategy for the formation and engagement of an Industry IG which will place emphasis on the practical applications of computational biomolecular research. This will consider any prior use cases of relevance to industry to show the impact and benefit of biomolecular modelling and simulations . It will determine what aspects generate the most interest and provide support for practical application through understanding the needs and challenges of this IG who are important for expanding usage and developing our sustainability plans. bioexcel.eu 25

Training IG 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. bioexcel.eu 26

Join Today! www.bioexcel.eu/interest-groups bioexcel.eu 27