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

bioexcel.eu Partners Funding

BioExcel/PRACE Spring School 2017 – HPC for Life Sciences

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Vera Matser

EMBL-EBI

Center of Excellence for Computational Biomolecular Research

Training and Dissemination

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Life Science and HPC

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Atom Small Molecule Macromolecules Cell Tissue Organ Population

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Electronic structure Personalized medicine Physiology Neuroinformatics Biomarkers design Biomaterials science and nanotechnology

Biomolecular Modeling and Simulations

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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)

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Objectives of BioExcel

Excellence in Usability

• Make ICT technologies

easier to use by biomolecular researchers, both in academia and industry

• Devise efficient workflow

environments with associated data integration

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DMI Monitor DMI Enactor DMI Executor DMI Enactor Data Delivery Point Data Source Monitoring flow Data flow Service Invocation DMI Optimiser DMI Planner DMI Validator DMI Gateway DMI Gateway DMI Gateway DMI Enactor Portal / Workbench DMI Request DADC Engineer DMI Expert

Repository

Registry DMI Expert Domain Expert

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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

• f related software
• academic and commercial

resource providers

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BioExcel Center of Excellence

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BioExcel Training Programme

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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
• bjectively
• 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

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Example Competency

"Write his/her own scripts to perform tasks in context of biomolecular research"

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Knowledge Skills Behaviour Knowledge of existing commands/libraries to re-use Is able to automate the process of executing processes remotely Uses appropriate scripting languages Judges when a task should be automated Write & debug scripts

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BioExcel Competency Profile

Group related competencies together into areas

• Generic Competencies
• Scientific Competencies
• Generic Computing Competencies
• Parallel Computing Competencies

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BioExcel Competency Profile

Different types of users

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Heads up on what we are planning

Face-to-Face training events

• 3-7th 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

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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

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How to get in touch with us

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@BioExcelCoE

ask.bioexcel.eu www.bioexcel.eu

Announce updates, training courses, webinars & papers Subscribe to mailing list Company Page

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Activity - Competency

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

• f the area, generating new understanding or new technology

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www.surveymonkey.co.uk/r/bioexcel

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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

17/12/2015

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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

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Interest Groups

• Entry Level Users
• Integrative Modeling
• Free Energy Calculations
• Hybrid methods
• Workflows
• Industry
• Training

Support platforms

Forums Code Repositories Chat channel Video Channel

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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.

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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

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Free Energy Calculations

This group will discuss topics of interest related to methods for free energy calculations, which are crucial for evaluation

• f 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.

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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.

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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.

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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.

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Join Today!

www.bioexcel.eu/interest-groups

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