• Escala


René Rahn, Hannes Hausewedell (CIBI)

22.03.2018 – 31.03.2018

Escala, France

The SeqAn project will hold its SeqAn3 release-retreat and an ELIXIR / de.NBI / CIBI workshop
in southern France at the end of March (22nd to 31st).
Goal of the meeting is to kickstart new projects with our collaborators from RKI, MPI, Italy, etc. and for the SeqAn core team to finalise the SeqAn3 release which will constitute a milestone in modern Bioinformatics software engineering by significantly lowering the boundaries to creating high performance C++ solutions to current challenges from computational biology.

Additionally, to working on the release of SeqAn3, the SeqAn team will offer a workshop as part of ELIXIR Germany that includes trainings and hands-on sessions so that our project partners and interested guests are the first to learn how to use our new software and related programming techniques. Those parties will be able to come to the meeting with their current research problems or existing applications and we will do our best to port these or develop new working proto-types with them on-site. Furthermore the meeting  provides a unique opportunity for those parties to present their research and  formulate expectations they have of a modern Bionformatics library/framework  and thereby influence the future development of SeqAn in a way that benefits  their work in the long run.

Below is the preliminary schedule for the week, all days will begin with one or  multiple short presentations (totaling not more than 60min per day) and have  workshops / programming sessions for the rest of the day.


**Friday 2019-03-22**
Arrival during the day; Welcome and introductory session; Poster session

Talk: SeqAn3 by Hannes Hauswedell
Workshop: Programming a read mapper in one day

Talk: Modern C++ by Hannes Hauswedell
Workshop: Hands-on training in modern C++ techniques

Talks: short research/problem/app presentations
Workshop: individual work on the presented projects assisted by SeqAn team; KNIME integration; work on SeqAn3 release by other team members

Talks: High-performance computing and parallelisation by Rene Rahn
Workshop: individual work on the presented projects assisted by SeqAn team; work on SeqAn3 release by other team members

Social and networking event
Optionally work on individual projects

Talks: short research/problem/app presentations
Workshop: individual work on the presented projects assisted by SeqAn team; work on SeqAn3 release by other team members

Talk: The DREAM framework by Knut Reinert
Workshop: individual work on the presented projects assisted by SeqAn team; work on SeqAn3 release by other team members

Evaluation of the week's results.
Gather feedback and feature requests from guests; wrap-up loose ends and create schedules for open issues

**Sunday 2019-03-31**

Learning goals:
- Software engineering and App development with SeqAn
- High-performance computing using SeqAn and the STL
- Modern C++ features like Concepts, Ranges, and many more

This tutorial is mostly suited for computational biologist and bioinformaticians with research focus on sequence analysis (e.g., genomics, metagenomics, assembly, read alignment, variant detection, etc.) Attendees must have an intermediate level of programming skills and a strong interest in C++ as well as a fundamental background in the SeqAn3 software library. Attendees must bring their own laptop. Software for the tutorial should be installed beforehand, but we will also dedicate some extra time for setting up the workstations. The following systems/software is required:

- MacOS (g++-7 or higher) or Linux or BSD (g++-7 or higher)
- Git
- Cmake-3.0 or higher

The number of participants is limited to 20. To register please write an email to the contact person below.

SeqAn3, Sequence Analysis, modern C++


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