SeqAn UGM 2016

We are happy to announce the 2016 SeqAn user meeting supported by the CIBI (Center for integrative Bioinformatics), a member of  of the de.NBI (German Network for Bioinformatics infrastructure).

The meeting will take place at FU Berlin from March 30th to April 1st 2016. The SeqAn user meeting is addressing bioinformatics students and professionals who want to develop efficient applications for NGS analysis based on an efficient, well-maintained C++ library. In the meeting you will hear talks from groups who actively use SeqAn in their daily work, you will hear about how some of the SeqAn apps work and how they were developed, and finally you get hands-on tutorials to get you started with developing your own SeqAn apps and include them into workflow systems such as KNIME.

Please sign up using this form. The deadline was March 14th 2016 and is now closed.

The meeting will be at the
Freie Universität Berlin,
Institute for Computer Science,
Takustrasse 9, 14195 Berlin,
Room SR 005 (ground floor).

Contact:
Prof. Knut Reinert – knut.reinert (at) fu-berlin.de
Secretary’s Office – anja.kasseckert (at) fu-berlin.de

Below you can see a preliminary schedule.

Time\Date

Wednesday
30th

Thursday
31st

Friday April
1st

09:00-10:30

 Welcome and Introduction
Knut Reinert 

App session 1:  Mason
Manuel Holtgrewe

App session 2: Imseq
Leon Kuchenbecker

Tutorial 1:  CLP
Svenja Mehringer

Tutorial 2: Sequences/Iterators
Jongkyu Kim

Tutorial 7: Basic File I/O
Rene Rahn

Tutorial 8: Advanced File I/O
Hannes Hauswedell

10:30-11:00

Break

Break

Break

11:00-12:30

Invited talk 1: Whole-genome sequence analysis of 20,000 Icelanders
Birte Kehr (deCode)

Invited talk 2: IsomiR-SEA: A new powerful profiling tool reveals novel biological miRNAs and isomiRs features hidden in small RNA-Seq samples.
Gianvito Urgese (Turin)

App session 3: Lambda
Hannes Hauswedell

App session 4:
deCode BAM tools
Birte Kehr

App session 5:  Stellar
Chenxu Pan

Talk to Developers

Tutorial 3:
Alignment representation
Marcel Ehrhardt

Tutorial 4:
Alignment algorithms
Rene Rahn

Tutorial 9: Q-Nexus workflow: Extending with KNIME nodes
Temesgen Dadi

Tutorial 10: Q-Nexus workflow: Developing a new SeqAn node
Temesgen Dadi

12:30-14:00

Lunch

Lunch

Lunch

14:00-15:30

SeqAn technical talk
(Hannes Hauswedell)

Introduction to KNIME
(Oleg Yasnev, KNIME)

 

App session 6: iPec
Arthur You

App session 7: KNIME and SeqAn
Temesgen Dadi

Tutorial 5: Indices 1
Christopher Pockrandt

Tutorial 6: Indices 2
Christopher Pockrandt

Tutorial 11: KNIME integration of SeqAn nodes 1
Temesgen Dadi

Tutorial 12: KNIME integration od SeqAn nodes 2
Temesgen Dadi

15:30-16:00

Break

Break

End of meeting

16:00-18:00

Introduction tutorial

 

Social Event: Tapas Bar

 

Posted in Research, Teaching.

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