Educators:
Julian Uszkoreit (BioInfra.Prot), Michael Turewicz (BioInfra.Prot) and Michael Kohl (BioInfra.Prot)

Date:
7. December 2017

Location:
Ruhr-University Bochum, Germany

Contents:
In this one day course we will show some of our tools provided in de.NBI, namely “PIA – Protein Inference Algorithms”, “PAA – Protein Array Analyzer” and CalibraCurve. PIA allows to inspect and combine the results of proteomics search engines. The main focus lays on the integrated inference algorithms for identification and quantification purposes. PAA is an R/Bioconductor software package providing a comprehensive workflow for protein microarray data analysis, especially aimed at biomarker discovery. CalibraCurve is a tool intended for the generation of calibration curves in the context of MRM (targeted proteomics) experiments. Such calibration curves are necessary for the selection of suitable transitions.

Learning goals:
Attendees of the course will learn how to use the tools PIA, PAA and CalibraCurve effectively for their daily proteomics tasks.

Prerequisites:
This course is for all researches in the field of proteomics. The attendees should have basic knowledge of LC-MS proteomics, but no prior bioinformatics skills are required. Basic knowledge of how to analyse LC-MS data are sufficient. Attendees are required to bring their own laptops. If not possible, please contact the organizers.

Keywords:
Proteomics; Data Analysis;

Tools:
PIA; PAA; CalibraCurve;

Contact:
Julian Uszkoreit
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Registration:
https://goo.gl/sd7bMc

Flyer:

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Educators:
Antje Chang, Ida Schomburg, Stefan Bietz, Sandra Placzek, Lisa Jeske (BioData)

Date:
11.10.2017 (09.00-17.00)
12.10.2017 (09.00-13.00)

Location:
TU Braunschweig, BRICS
Rebenring 56, Room 44

Content:

Introduction to BRENDA:
- History, scope and contents
- Data sources and updates
- Application areas

BRENDA web interface:
- Query engine – data access
    • Text-based queries, numerical queries
    • Genome explorer, EC explorer, Taxonomy tree explorer, Ontologies
    • Ligand query via chemical structure or substructure – molecule editor
    • Membrane proteins
    • Pathway based queries
    • Complex combination queries
- Result pages:
    • Enzyme summary page and Ligand summary page
    • Word maps
    • Pathway maps
    • Enzyme/disease relation
    • Expected taxonomic range
    • Protein 3D structure – amino acid sites
    • Enzyme functional parameters – statistical analysis
    • Text-mining results

Computer-based BRENDA access:
- SOAP
- SBML output

Introduction to ProteinsPlus:
- Experimental protein structures
- Protein-ligand interactions
- Basics and challenges of molecular modelling

ProteinsPlus server:
- Application area and computational methods behind ProteinsPlus
- Workflow and the interactive visualization concept
- Download options

ProteinsPlus applications:
- Protein-ligand binding site and hydrogen prediction
- Druggability and structure quality assessment
- Protein-ligand interaction analysis and 2D visualization
- Protein conformation analysis
- Protein-protein interface classification

Learning goals:
- Introduction to the BRENDA enzyme database and exploiting the potential
of enzyme structures in ProteinsPlus
- Learning and understanding the scope and organization of the databases
- Learning and working with the tools of the database

Prerequisites:
- Basic knowledge in biochemistry, molecular biology and microbiology
- we recommend that you bring your own laptop

Tools:
BRENDA, ProteinsPlus

Keywords:
BRENDA, ProteinsPlus

Contact, information and registration:
The training is free of charge. The participants have to cover their traveling
and hotel expenses. A list of hotels will be supplied.

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Registration Deadline: 01.10.2017

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Download Flyer here

Educators:
Malvika Sharan (HD-HuB), Konrad Förstner

Date:
04-05.09.2017

Location:
IMIB, GSLS University of Würzburg
Josef-Schneider-Str. 2, Haus D15, Room D15.00.048, 97080 Würzburg

Contents:
The aim of Software Carpentry is to enable researchers to be more productive while
producing work of higher quality. This 2-day workshop will teach the key skills
required to practice robust computational science effectively and efficiently, and
provide an overview of some of the tools and resources available for modern
computational biology.
Topics covered include:
- An introduction to scripting in Python, and using the language for scientific applications and biological data handling
- Effective use of the Unix command line
- Version control with git and GitHub

Learning goals:
This course aims to teach software writing skills and best practices to researchers in
biology who wish to analyze data, and to introduce a toolset that can help them in
their work. The goal is to enable them to be more productive and to make their
science better and more reproducible.

Prerequisites:
This is a course for Graduate students of the University of Würzburg who are using computers for their
analyses, even if not full time. The target student will know a little bit of command
line/programmatic computer usage, but not consider themselves an expert. A target
student will have written a for loop in some language before, but will not know what
git is (or at least not be very comfortable with advanced git usage).

Registration:
This course is open for the Graduate students of the University of Würzburg for free.

Schedule:
https://swcarpentry-wuerzburg.github.io/2017-09-04-wuerzburg/

Keywords:
Programming; Bioinformatics; Data Analysis; Python; Unix; Git; GitHub;

Tools:
Python; Unix; Git; GitHub; SnakeMake; Jupyter notebook;

Contact:
Malvika Sharan  This email address is being protected from spambots. You need JavaScript enabled to view it.

Educators:
Stefan Albaum, Sebastian Jünemann, Nils Kleinbölting, Alexander Sczyrba (BiGi), Daniel Wibberg (CAU), Björn Usadel (GCBN), Jörn Kalinowski, Christian Rückert (CeBiTec)
 
Date:
22 - 24 November 2017
 
Location:
Bielefeld University, Universitätsstraße 25, 33615 Bielefeld
 
Content:
Aim of this workshop is to familiarise the participants with the Nanopore sequencing technology, its applications and the "Best Practice" bioinformatics workflow. The Nanopore technology have greatly facilitated the assembly of prokaryotic and eukaryotic genomes. Therefore, the workshop is focused on the establishment of finalized genome sequences.

This workshop will be composed of different talks including introductions to the Nanopore sequencing technology and working in the de.NBI cloud as well as different hands-on sessions. During the talks, the advantages and pitfalls of Nanopore sequencing will be discussed. The hands-on sessions will illustrate the typical workflow from the Nanopore sequencing to the final assembled genome.
 
Learning goals:
This workshop aims to teach basic skills and best practices to researchers working with Nanopore data. The final goal is to enable them to use the resulting reads for a de novo assembly.
 
Prerequisites:
This workshop is intended for PhD students and postdocs with molecular biology background in genomics. Good understanding of command line tools is a plus, but not required. 
 
Tool:
Canu, Pilon, Albacore, Porechop, Metricor, Poretools
 
Keywords:
Nanopore sequencing, genome assembly, genomics
 
Contact & Registration:
Daniel Wibberg 
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More Information:

Educators:
Daniel Lang (Helmholtz Center, Munich)
Maxim Messerer  (Helmholtz Center, Munich)

Date:
11-12.09.2017

Location:
Helmholtz Center Munich
German Research Center for Environmental Health (GmbH)
Ingolstädter Landstr. 1
85764 Neuherberg

Contents:
The workshop explains genefamily concepts and resources. It enables researchers to place their sequence of interest into a genefamily context to compare sequence data and to transfer knowledge from well studied genes.
1. Selecting homologs -how to find members of your gene family
(BLAST und PFAM)
2. Multile alignments - Creation and Modification
3. Phylogenetic tree calculations
4. Interpretation of trees - "What kind of *log is it"? (paralog, ortholog, ...)

Schedule:
Day 1
10:00 Introduction
11:15 Coffee break
11:30 Auswahl vonomologen - Mitglieder der Genfamilie identifizieren
13:00 Lunch
14:00 Multiple alignment -  Creation and Modification (part 1)
15:30 Coffee break
15:45 Multiple alignment -  Creation and Modification (part 1)
17:00 end day 1

Day 2
10:00 Phylogenetic tree calculation (part 1)
11:15 Coffee break
11:30 Phylogenetic tree calculation (part 2)
13:00 Lunch
14:00 Interpretation of phylogenetic trees (part 1)
15:30 Coffee break
15:45 Interpretation of phylogenetic trees (part 1)
17:00 end day 2

Prerequisites:
1.  A gene family or sequence of interest for which the phylogenetic tree will be created
(FASTA/sequence identifier).
2. Laptop
3.  skills: Browser, Excel, BLAST

Keywords:
genefamily, multiple alignment, phylogenetic tree, ortholog, paralog

Contact and Registration:
Maxim, Messerer   This email address is being protected from spambots. You need JavaScript enabled to view it.