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Moved BBMRI presentations to bbmri2 34b84f42.

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lectures/bbmri2_kickoff/Makefile deleted 120000 → 0
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lectures/bbmri2_kickoff/bbmri2_kickoff.tex deleted 100644 → 0
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\documentclass[slidestop]{beamer} % Add 'handout' for printable slides.
\title{e-Infra}
\providecommand{\myConference}{BBMRI-NL 2.0 Kick-Off}
\providecommand{\myDate}{Wednesday, October 7, 2015}
\author{Jeroen F.J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
\raisebox{-0.1cm}{
}
}
\providecommand{\lastRightLogo}{
%\includegraphics[height=0.7cm]{logos/bbmri_logo}
}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title page.
\bodytemplate
% First page of the presentation.
\section{Introduction}
\subsection{Goals}
% sufficient servers for our applications (catalogue, apps, warehouses,
% interoperability, etc). Keep current facilities available in collaboration
% with CIT and SURFsara. Integration of procedures and support such that
% researchers can get access to all facilities as one (e.g. RP3 can give access
% to all via clear procedure). Uniform MTA and security rules such that
% biobanks can trust the environment. Clear capacity requirements to the
% e-infra providers for 2015. Mirror the data between SURFsara to CIT and give
% permission within MTAs
\begin{pframe}
Facilities.
\begin{itemize}
\item Keep them up and running.
\item Manage access.
\item Data sharing.
\item Security and backup.
\end{itemize}
\bigskip
\pause
Realise this via:
\begin{itemize}
\item Federated authentication and authorisation.
\item Dedicated network connections (e-lan).
\item Documentation and automatic roll-out of software.
\end{itemize}
\end{pframe}
\subsection{Federated authentication and authorisation}
% Dramatically reduce the effort of maintaining users and permissions. Giving
% access is now fragmented, which is becoming a challenges with ~dozen groups
% and ~200 counts. Ideally, accounts would be managed by institutes and BBMRI
% only needs to worry about granting access. In collaboration with NFU/WP7 we
% will therefor pilot: centralized identity/group management using federated ID
% (analogous to SurfConext for websites). If that doesn’t work we will
% implement technically less advanced procedures to keep the facilities in
% sync.
\begin{pframe}
User management is difficult.
\begin{itemize}
\item Currently more than $300$ accounts from different institutes.
\item More than $10$ different groups.
\end{itemize}
\bigskip
\pause
Pilot with SURFsara to solve this.
\begin{itemize}
\item User accounts are managed by the institutes.
\item Ideally, access is managed by putting users in a certain group.
\end{itemize}
\end{pframe}
\subsection{Data sharing}
% Dramatically ease the sharing of data across compute facilities. Currently it
% is technically challenging to move access between current facilities, e.g.
% for failover or use in specific tools. Also there is unnecessary duplication
% of data because of barriers between the facilities. EUDAT and iRODS promise
% solutions to ease staging and sharing of data. In this task we will evaluate
% and document current solutions and bring into production if useful.
\begin{pframe}
The current situation results in:
\begin{itemize}
\item Complicated procedures to transfer data.
\item Long transfer times.
\item Data duplication.
\end{itemize}
\bigskip
\pause
With the e-lan we set up a fast, reliable and safe permanent connection.
\begin{itemize}
\item Only accessible from other UMCs (possibly other partners like
universities will participate).
\item In combination with the federated authentication and authorisation,
data can be kept at the hosting institute.
\end{itemize}
\end{pframe}
\subsection{Documentation and software roll-out}
% Dramatically ease the sharing of tools/pipelines across compute facilities.
% Deploy of software tools and pipelines across the central and local
% facilities is still a lot of work. In this task we will develop procedures to
% ease this process, using standard systems like ‘module’ system, puppet,
% easyinstall, VM technology, etc.
\begin{pframe}
Tools and pipelines are difficult to deploy.
\begin{itemize}
\item Dependencies.
\item Databases.
\item System configuration.
\end{itemize}
Also, making a VM has disadvantages.
\begin{itemize}
\item Difficult to separate the important bits.
\end{itemize}
\bigskip
\pause
We propose to use Ansible playbooks.
\begin{itemize}
\item Human readable.
\item Machine executable.
\end{itemize}
\end{pframe}
\section{Questions?}
\lastpagetemplate
\begin{pframe}
\end{pframe}
\end{document}
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\documentclass[slidestop]{beamer}
\author{Jeroen F.J. Laros}
\title{BBMRI2: Storage \& Compute}
\providecommand{\mySubTitle}{}
\providecommand{\myConference}{BBMRI2 taskleader meeting}
\providecommand{\myDate}{15-03-2016}
\providecommand{\myGroup}{}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\usetheme{lumc}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title slide.
\makeTitleSlide{\hspace{-2cm}\includegraphics[width=5.5cm]{logos/bbmri_logo}}
% Proposed structure:
%
% - Summary of deliverables until now, if possible with a small demo
% - Summary of next steps (next 3 months)
% - What links do you have with other tasks of WP's?
% - Are there any issues preventing you to deliver the next steps as planned
% First page of the presentation.
\section{Introduction}
\makeTableOfContents
\subsection{Goal}
\begin{pframe}
A clear definition of the BBMRI computational environment.
\bigskip
Example use cases:
\begin{itemize}
\item A researcher wants to use a BBMRI pipeline.
\begin{itemize}
\item With \emph{exactly} the same settings, reference files, etc.
\end{itemize}
\item An analysis needs to be redone.
\begin{itemize}
\item To obtain removed intermediate files for example.
\end{itemize}
\end{itemize}
\bigskip
Requirements:
\begin{itemize}
\item Virtual cluster.
\item Data access mechanisms.
\end{itemize}
\end{pframe}
\begin{pframe}
Projects:
\begin{itemize}
\item Pipeline infrastructure.
\begin{itemize}
\item One or more \emph{virtual machines} in cluster configuration.
\end{itemize}
\item Federated research network.
\begin{itemize}
\item Fast and secure access to BBMRI data.
\end{itemize}
\item Federated authentication and authorisation.
\begin{itemize}
\item No need to make accounts at other institutes.
\end{itemize}
\end{itemize}
\end{pframe}
\section{Deliverables 2016 Q1}
\subsection{Ongoing activities}
\begin{pframe}
Three deliverables for the first quarter:
\begin{itemize}
\item Inventory pipeline infrastructures.
\begin{itemize}
\item Dependencies, hardware requirements, etc.
\end{itemize}
\item Inventory of facilities and virtual machines.
\begin{itemize}
\item Capacity, security, users and roles, etc.
\end{itemize}
\item Inventory management systems.
\begin{itemize}
\item Puppet, Ansible, easybuild, etc.
\end{itemize}
\end{itemize}
\bigskip
All of these tasks are done in collaboration with the \emph{Pipelines}
taskforce.
\end{pframe}
\begin{pframe}
Other tasks that have been started:
\begin{itemize}
\item e-LAN.
\begin{itemize}
\item Dedicated secure network between UMCs.
\end{itemize}
\item Virtual cluster nodes in the cloud.
\begin{itemize}
\item Pilot to test performance.
\end{itemize}
\item Federated SSH access.
\begin{itemize}
\item Authenticate with SURFconext to upload a \emph{public key}.
\item SSH server uses this central database of keys for authentication.
\item Working test setup.
\end{itemize}
\end{itemize}
\end{pframe}
\section{Next steps}
\subsection{Deliverables 2016 Q2}
\begin{pframe}
On the agenda:
\begin{itemize}
\item Pilot pipeline deployment.
\begin{itemize}
\item Virtual machine in the cloud with working BBMRI pipeline.
\end{itemize}
\item First fully managed virtual machine.
\begin{itemize}
\item Automated installation (Ansible, Puppet, etc.).
\end{itemize}
\end{itemize}
\bigskip
Other tasks:
\begin{itemize}
\item Finish testing e-LAN.
\item Finish testing virtual cluster nodes.
\item Start virtual head node (completing virtual cluster).
\item Start federated SSH access on virtual cluster.
\end{itemize}
\end{pframe}
\section{Links to other tasks / WP's}
\subsection{Current collaborations}
\begin{pframe}
Started collaboration:
\begin{itemize}
\item WP5: Pipelines (Leon Mei).
\begin{itemize}
\item Inventory.
\item Pipeline deployment.
\end{itemize}
\end{itemize}
\bigskip
Investigating collaboration:
\begin{itemize}
\item WP5: Operations (Rita Azevedo).
\begin{itemize}
\item Possible connections to analysis portal.
\item Offering downloadable package of virtual BBMRI environment.
\end{itemize}
\end{itemize}
\end{pframe}
\section{Issues}
\subsection{Foreseeable difficulties}
\begin{pframe}
Currently no blockers.
\bigskip
We foresee problems with the implementation of federated authorisation.
\begin{itemize}
\item Identity management.
\item Group management.
\item Access control.
\end{itemize}
\end{pframe}
% Make the acknowledgements slide.
\makeAcknowledgementsSlide{
\begin{tabular}{lll}
Pieter Neerincx & Leon Mei & Morris Swertz\\
Freerk van Dijk & Peter van 't Hof & Jan-Willem Boiten\\
Hans Brouwers & Rita Azevedo & Jeroen Beli\"en\\
Irene Nooren & Paul van Dijk & Edith Adriaanse\\
Martijn Vermaat & Maarten Kooyman\\
Jonathan Vis\\
Guy Allard\\
Michel Villerius\\
\end{tabular}
\bigskip
\vspace{-1.2cm}\hfill\includegraphics[height=2cm]{logos/bbmri_logo}\\
}
\end{document}
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