Bio-Informatics workshops

Find out how much is possible with your genome data

Bio-Informatics has become a major tool in modern microbiology and fermentation research. NIZO food research operates at the forefront of developing and applying Bio-Informatics technologies for fast and targeted innovations in food and health related research. That is why we organize Bio-Informatics workshops together with clients to show you how you can benefit and to inform you how NIZO can contribute.
 
The one-to-one workshops are confidential and will be held with NIZO experts. They will present you with the most recent advances in Bio-Informatics and together with them you will get insight and hands-on experience on how these technologies can help your company to innovate. 

What 
- The 2½-hours events include a presentation from NIZO experts and 2 interactive workshops/live demonstrations of your choice and discussion with representa-tives from your company only.
- In order to keep the workshop interactive and efficient, we limit the number of people to 5. 

When & Where
Contact us  to set a date and to determine the areas of your interest. Then we will tailor the programme of the workshops, to be held at our laboratories in Ede,  to your needs. 

Choose
You can choose two workshops of your interest (see below) and make an appointment with Koos Oosterhaven 

 1. Genome sequencing
The costs of DNA-sequencing have decreased substantially in recent years. Sequencing your model organism(s) may already be within reach. However, how do you deal with the flood of generated sequence data? At NIZO we assist by communicating with the sequencing company, and perform sequence assembly, gene annotation and inter-pretation of your (bacterial) genome. This workshop will  deal with these issues as well as touch upon the possibility of comparing different genotypes
(before vs. after adaptation, different strains) in order to find the chromosomal or plasmid differences that explain the phenotypes.
Benefit: 
- Know the metabolic potential of your production strain
- Get an indication whether you have a safe strain.

2. Metagenome sequencing
The availability of deep sequencing technologies has paved the way for sequencing large parts of complex eco-systems such as those found in the GI tract, in biofilms, on the skin or used as starter cultures for fermented foods. Handling the sequence data resulting from such a metagenome or 16S pyrosequencing effort requires dedicated hardware and software and knowhow of to apply which technique. Bioinformatics and molecular biology expertise to interpret the data obtained (e.g. visualization of overrepresented bacterial phyla) is also needed. At NIZO we have access to such services and personnel, enabling us to assist in the processing and analysis of your metagenome data for interpreting pyrosequencing data. In this workshop we will guide you through the possible results using various tools.
Benefit:
- Profiling the impact of your pre/probiotic product on the composition of the GI tract microbiota
- Identification of the composition of an undefined complex culture used in industrial fermentation processes

3. Statistical analysis of genomics data to identify target genes
This workshop focuses on how to identify the target genes/metabolites that relate to the differences observed between different strains or your test and control condition(s). Genomics data obtained from different 'omics' technologies (e.g. transcriptomics, proteomics, metabolomics) often measure many different parameters (gene expression levels, protein levels, metabolites) under one single condition in parallel.
We will show you the added value of the NIZO approach over traditionally used methods.
Benefit:
- Identification of key genes for particular functionalities (probiotic activity, flavour formation, sugar conversion, etc.)

4. Data management
The workshop on data management will focus on systems used within NIZO to store experimental data and the possibility to implement these in your company. All data generated with genomics techniques (transcriptome, sequencing data) requires the availability of database systems that allow storage, as well as easy access of the data generated. In addition to the storage of data a wiki-based system for storage of (bioinformatics) protocols and analysis pipelines will be shown.
Benefit:
- Get the most out of your precious genomics data
- Appreciated the added value of a linked data-base structure for your ‘omics’ data
- Secure the storage and access of your data from large-scale genomics experiments

5 Metabolic modeling
The genome sequence of an organism provides information about the metabolic potential of your production organism. This information can be used to construct a metabolic network  model of the organism. With this network it is possible to perform calculations on (efficiency of) growth given the composition of the medium. It is also possible to predict the optimal medium composition or alternative (cheaper) substrates for growth. Two real case examples will be given.
Benefit:
- Optimise the yield in your own fermentation process
- Discover new metabolic functions in your pet organisms
- Speed-up innovation by reducing research time
 
6. Making data analysis tools securely accessible via the web
Within NIZO food research a platform is available that helps to create webtools for bioinformatics or data analysis that can be accessed in a secure and standardized way by non-experts. With the platform, (newly) developed (command line-based) bioinformatics or data analysis scripts can be translated into a web framework, transforming the scripts into user-friendly web-accessible tools. We assist in setting up such a framework or providing a personalized web-access framework at NIZO food research.
Benefit:
- On-demand access for your own experts to state-of-the-art bioinformatics tools