AquaExcel: Experimental data management from generating protocols to sharing data.

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General information

The course will deal with best practice experimental data management, including all aspects from preparing experiment protocols to sharing data. It is based on the experimental data repository system developed in FP7-AQUAEXCEL called bioWES. bioWES is a distributed, knowledge-based repository for large datasets, typically applicable in biological and related sciences. The bioWES scientific data management solution provides full control over experiments, from protocol design, through data acquisition and processing to sharing final results.

Participants will learn how to use the bioWES system for their own experimental work, using their own protocols and real experimental data. The aim is that by the end of the course, each participant will be able to install the bioWES system, create his or her own account, create unique experimental protocols based on their own specific needs, store their own experimental data, create connections between experimental protocols, cooperate with colleagues through sharing and visualize the overview of individual project steps. The participants will also be introduced to the special functionality of the system: data processing modules, plugins for communication with measurement devices and standardization support.

The course will be organized as an online training with active participation of the users. The organizers will guide the users through every single step of the bioWES system, from installation to sharing of experimental data, during three one and a half hour sessions. The participant will use their own protocols and experimental data to test theoretical knowledge on real examples. The course will be available through standard internet browser for each registered participant. It is believed that the course is particularly useful for researchers involved in AQUAEXCEL2020 TransNational Access (TNA) projects.


Day 1 (Monday 25 April 2016, 10.00-11.30hrs):
• Basic usage of the bioWES software solution
• bioWES fundamental parts explanation (protocol manager + web interface)
• General idea explanation – from protocol design, data acquisition and processing steps to sharing final protocol
• Protocol template creation
• Homework – complete the protocol template

Day 2 (Wednesday 27 April 2016, 10.00-11.30hrs):

• Protocol creation, completing experimental protocol and connect it with other protocols
• Connection, visualisation + evolution of protocol (CLONING)
• Protocol and protocol template sharing
• Protocol and protocol template visualisation chain
• Homework

Day 3 (Friday 29 April 2016, 10.00-11.30hrs):
• Web interface explanation – protocol and protocol templates visualisation
• Downloading experimental data
• Protocol and protocol template visualisation chain
• Processing modules – process your data directly in the repository
• Plugin – automatic protocol filling (information from devices: microscope, camera)
• Information about the cooperation with the ELIXIR initiative within AQUAEXCEL 2020 related to standardisation

Contact Person: AquaTT (


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, Czech Republic


Open from
1 Apr 2016 to 22 Apr 2016

Application Procedure:

E-mail your registration request to, using the official registration form on the Aquaexcel website

Please indicate the following in the subject: AQUAEXCEL2020 / training course # 1 (JU)

Deadline: Thursday 21 April 2016.


Academic level: PhD

Qualification: Master of Science
Occupations (not validated):
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