Workshop Info

General information:

Topic: Experimental data and metadata management

Organizers: University of South Bohemia in České Budějovice, dataPartner ltd.

Status: ICSB2013 workshop


Location: Technical University of Denmark

Anker Engelunds Vej 1

Building and room number will be specified later

2800 Kongens Lyngby


Tel.:+45 45 25 25 25

Technical University of Denmark


Date: August 29 – 30, 2013



August 9 – abstract submission

August 16 – abstract acceptance/rejection decision


The workshop is focused on the system of experimental data and metadata management and processing and analysis of mass spectrometry data.

  • The first part of the workshop will present the solution in the field of experimental data and metadata management. The solution is developed in the frame of the BioWes ( project and tries to cover all aspects of data management, including experimental and data analysis protocols. The general philosophy of the project is an assumption that the plan of the experiment is based on extended background information which is not fully intelligible from the resulting dataset. The aim of the workshop is to introduce the solution for experimental data and metadata standardization, storage, and sharing along with the tools for data processing.  (August 29, 9:00 – 12:00)
  • The second part of the workshop will discuss the data processing and analysis of mass spectrometry measurements based on a probabilistic approach, automation of the steps, and interpretation of the confidence level. (August 29, 13:15 – 18:00)
  • In the third part of the workshop, the participants will present their own contribution to the workshop topics. (August 30, 13:00 – 18:00). The candidates for the presentation should send the abstract until August 9, to Jan Urban Ph. D.( The abstract should not exceed one page A4 and should be written in English. The committee will select the best abstracts for the oral presentation until August 16. Possible topics are data management, metadata, mass spectrometry, time alignment and multivariate data analysis.


Notebooks: The presentation of the experimental data management (see the program below) will include the active testing of the system by the participants of the workshop. A notebook, slate PC or tablet (Windows XP, Windows Vista, Windows 7 or 8) will be needed for the testing. Several extra notebooks will be availaible on request (please use “Contacts” to apply). Please see also Danish plug/outlet info (e.g. AC power plugs and sockets on Wiki) to check your adapter compatibility.


Food and Drinks:

Coffee breaks: (coffee and cookies) will be provided by workshop organizers.

Lunch: Lunch is not provided for the participants. There is a restaurant within 5 minutes from the workshop venue.


Workshop Programme:

9:00 – 9:15 Welcome speech (Prof. Dalibor Štys, MSc., Ph.D.)

9:15 – 10:30 Experimental data and metadata management, protocol generator

  1. Motivation
  2. General overview of the system
  3. Individual parts of the system
    1. How to create protocol template
    2. Put protocol into database
    3. Use protocol for experiments, Plug-in system
    4. Store data and metadata into database
    5. Share the protocol
    6. Check the experiment
    7. Next processing of the experiment
    8. Explore past experiments
    9. Use old protocol template to create new experiment
    10. Share experiment

10:45 – 12:00 Interactive presentation of the system, the participants can test the system

  1. Participants will be able to create their own protocol and upload it to the database.
    1. Create the protocol template using protocol designer
    2. Upload the protocol template to the local database
    3. Find the protocol template  in database
    4. Fill the protocol using protocol generator
    5. Share the protocol
  2. Minimal requirements
  3. Project  timeline
  4. Marketing

12:00 – 13:15 – lunch

Data processing and analysis of mass spectrometry measurements based on a probabilistic approach, automation of the steps, and interpretation of the confidence level (Jan Urban)

13:15 – 14:30

  1. Information flow in LC/GC- MS
  2. Processing vs. analysis
  3. Abstract model
  4. File formats, BioWes mAssistent converter
  5. Visualization
  6. Omics

14:30 – 14:45 – coffee break

14:45 – 16:15

  1. Processing and analysis steps
  2. Preprocessing, precision in value
  3. Resolution, resolving power, discriminability, and distinguishability

16:15 – 16:45 – coffee break

16:45 – 18:00

  1. Noise filtration
  2. Chromatographic peaks deconvolution
  3. Peak compositions
  4. Time alignment
  5. Multivariate data analysis
  6. Expertomica metabolite profiling

Friday, August 30

9:00 – 13:00 Symposium of the participants´ presentations

Possible topics: Data management; Metadata, Mass spectrometry, Time alignment, Multivariate data analysis