Using SEEK and I-S-A structure to integrate experimentation and mathematical modelling

Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. By connecting fields such as genomics, proteomics, bioinformatics, mathematics, cell biology, genetics, mathematics, engineering and computer sciences, Systems Biology enables discovery of yet unknown principles underlying the functioning of living cells. At the same time, testable and predictive models of complex cellular pathways and eventually of whole cells and organisms are generated as tools for research. Our workshop will provide a hands-on experience in integrating experimentation and mathematical modelling.

DOI: None

Zenodo URL: None

Created at: 26th May 2021 at 07:23

Contents

Experimental study for hands on session

Experimental study for hands on session

How to use templates to structure experimental data

Here we will use JERM templates with embedded ontologies to describe and annotate example data

Master template

Master template for hands on session

  • MASTER_exampleBlank2.xls

Transcriptomics Template (ArrayExpress Format)

An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment).
This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)

  • microarray_example_newformat.xls

Extraction and quantitative analysis of proteins from FFPE tissue

A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.

  • STORE_SOP_Extraction_and_quantitative_analysis_of_proteins_from_FFPE_tissue.pdf

How to use templates to structure experimental data 222

Here we will use JERM templates with embedded ontologies to describe and annotate example data 222

0804_shake-flask-sigB-starvation

Data sheet generated in Greifswald to measure the response of sigB activity in response to different media composition.

  • 0804_starvation-sigb-wt.xls

3455

No description specified

Extraction and quantitative analysis of proteins from FFPE tissue

A Standard Operating Procedure (SOP) is a document consisting of step-by-step information on how to execute a task. An existing SOP may need to just be modified and updated.

  • STORE_SOP_Extraction_and_quantitative_analysis_of_proteins_from_FFPE_tissue.pdf
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Created: 26th May 2021 at 07:23

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