Bioinformatics

The GDC can support your bioinformatics needs in many ways.

Please contact Stefan Zoller if you would like to discuss the possibilities.

Technologies and Analysis we support:

Next Generation Sequencing data analysis

- deNovo assembly (for genome, transcriptome, and metagenome data)
- re-sequencing / reference-mapping
- RAD sequencing
- transcriptome analysis (RNA-seq), including differential expression analysis
- microsatellite marker development from NGS data sets (primer development).
- SNP detection and marker development
- sequence annotation
- gene prediction
- installation/support of genome browser software
- general support of NGS data analysis
- support for experimental design
- support on how to use NGS tools on the GDC Linux servers
- library validation

Gene expression analysis from microarrays

(commercial or custom made arrays, including design of arrays).

- statistical and functional analysis (differential expression, functional groups, pathways)
- design of custom microarrays (Agilent platform)

Phylogenetic analysis

- improvement of alignments
- phylogenetic analysis, model testing, MP, ML and Baysian methods using the ETH cluster (parallel computing) or the GDC servers.
- design and support of experiments 

Linux and cluster computing

- support of application installation on the ETH brutus cluster.

- installation of special software on our Linux servers or ETH cluster (brutus)
- hands-on introduction to Linux/Unix and analysis tools- writing special shell,  perl or python scripts to support cluster usage

General data analysis

- support in design phase of experiments with special regard to data analysis
- support of general data analysis or data handling with custom-made R-, Perl-, Python scripts or Java programs. For example for filtering, quality control, data transformation, data set combining.

Databasing, webapps

- installation and maintenance of databases for general usage (e.g., Blast) 
- installation and population of custom-made databases on GDC Linux servers
- programming of custom-made web interface to databases
- installation of project specific wikis or data repositories
- installation and population of open-source webapps (e.g., IGV, GBrowse) on the GDC web server

Workshops and training for PhD students, Postdocs and staff

- on request special workshops and trainings can be arranged on any of above subjects or on e.g., Linux command line usage, ETH compute cluster usage, Perl/BioPerl programming, Java, Python, R, or any other data analysis related topic.

Possible support scenarios:

• Support of data analysis with open source and commercial software.
• Automating data handling and transformation steps currently done manually.
• Automating analysis steps and pipelines currently done manually or semi-automated.
• Implementing algorithms or statistical analysis procedures.
• Support with installation, testing and running of programs on the ETH cluster (brutus cluster)
• Creation of custom software tools (command line or with graphical user interface or web-application).
• Creation of data-bases or data-collections. Building of user interfaces to these data-bases.
  

Some examples of our experience:

• Assembly of next generation sequencing data (genome, transcriptome, RADseq)
  
• Annotation, Visualization, data warehousing of next gen sequencing data (e.g., with GMOD tools)

• Creation of server/client application for the secure transformation and transfer of data
• Development of microsat primers from NGS data sets and published draft genomes.
  
• Gene expression analysis with commercial tools and open source R.
• Phylogenetic analysis with raxml, mrbayes, of nt and AA data.
  
• Data transformation scripts to extract data from RT-PCR runs.
• Design of custum gene expression microarray.
• Design and implementation of web application to analyze expression data.
• Databases for storing sequence data, and array probes.
  
• Probe viewer application to visualize probe location on genes.
  
• Simulation studies on phylogenetic algorithms.