EU-US Training 2012 Agenda

Time

18.06.2012

19.06.2012

20.06.2012

21.06.2012

22.06.2012

8.30-10.00

Lecture

Research II, lecture hall

Welcome

Matthias Ullrich

Jennifer Biddle

Frank Oliver Glöckner

Introduction biological data databases

Sequence comparison similarity, identity substitution matrices

FOG

Multiple alignments patterns, profiles databases

FOG

Introduction to InterPro

Alex Mitchell,

EBI

Lucas Stal, Netherlands

"What's so special about Marine Microbiology?"

10.00 – 10.30

Break

Break

Break

Break

Break

10.30-12.00

Demonstration/ Hands-on

Research I, PC-lab

Set up of accounts

Introduction to computer facilities

Achim Gelessus

Linux for beginners I

CQ, JG

Linux for beginners II

CQ, JG

Linux for beginners III

CQ, JG

Contextual (meta)data:   The Genomic Standards Consortium

Dawn Field, UK

12.00 – 13.00

Lunch break

Lunch break

Lunch break

Lunch break

Lunch break

13.00 – 15.00

Hands-on

Research I, PC-lab

Flash talks and poster presentation by participants

Important databases Navigation, retrieval

PLB, IK

Multiple alignment tools, MAFFT, Muscle

PLB, IK

InterPro member databases & search algorithms

Alex Mitchell,

EBI

Contextual data: Tools & submission

Pelin Yilmaz, Germany

15.00 – 15.30

Break

Break

Break

Break

Break

15.30 - 17.00

Research I, PC-lab

Lecture on ecological theory, statistics and experimental design

Alban Ramette

BLAST [n,p,x] Command line BLAST output parsing,

PLB, IK

MAFFT, Muscle

PLB, IK

MEMI Metagenomics portal

Chris Hunter, EBI

Adam Martiny, USA

"Integrating oceanographic data"

Break

Dinner in Servery

Dinner in Servery

Visit of EU US Task Force

17:30 Board Bus to Bremen

Evening lectures

19:00-20:00

Research II

18:00

All participants BBQ

Jennifer Biddle, USA

Daniel Vaulot, France Eukaryotes

Guy Cochrane, EMBL-EBI/ENA Data at EBI/ENA

Visit of Bremen

together with Task Force

Time

25.06.2012

26.06.2012

27.06.2012

28.06.2012

29.06.2012

8.30-10.00

Lecture

Research II, lecture hall

ARB & SILVA

Jörg Peplies,

Frank Oliver Glöckner, Germany

Introduction to Phylogeny

QIIME

Luke Ursell, USA

High-troughput microbial ecology

MG-RAST Andreas Wilke,

Folker Meyer,

USA

CAMERA & Megx.net Shulei Sun USA,   Renzo Kottmann, Germany

Course Evaluation

Hands-on work in PC-lab

10.00 – 10.30

Break

Break

Break

Break

Break

10.30-12.00

Demonstration/ Hands-on

Research I, PC-lab

Aligner & Alignment

Tree reconstruction

JP, PY

Processing sequencing reads and preparing metadata

IK, AW

Navigating MG-RAST

MYgenes

Comparisons

IK, AW

CAMERA website,   GIS query, advanced data query

IK, AW

Finish own work

12.00 – 13.00

Lunch break

Lunch break

Lunch break

Lunch break

Lunch break

13.00 – 15.00

Hands-on

Research I, PC-lab

Navigating SILVA & ARB

Import of sequences

Alignment

JP, PY

OTU picking, taxonomic assignment, and tree visualization

IK, AW

Get familiar with MG-RAST

Download subsets

IK, AW

CAMERA workflow and results

IK, AW

Discussion about needs, obstacles, future plans.

Recommen-dations

Wrap up

15.00 – 15.30

Break

Break

Break

Break

Break

15.30 - 17.00

Research I, PC-lab

Phylogenetic tree reconstruction

Filters

JP, PY

Phylogenetic diversity analysis and visualization

IK, AW

Compare samples Statistics

IK, AW

Data sharing User submitted workflows

IK, AW

Wrap-up

Dinner in Servery

Dinner in Servery

Dinner in Servery

Break

Farewell

Evening lectures

19:00-20:00

Research II

Christopher Quince, UK Denoising

Hanno Teeling, Metagenomics Binning

Groupfoto 18:00

BBQ