Computer Practicals "Data management in practice" Advanced Lecture Course on Systems Biology, March 8, 2014, Innsbruck, Austria
Sharing well-annotated research data helps the systems biology process.
This practical is about how to easily structure your experimental data such that it becomes well annotated, standard compliant, reproducible, and re-usable (also for others). While much big data travels from machine to machine without human intervention, we will focus on exchange of small data describing experiments which is (to our experience) mostly handled via MS Excel and similar tools. First we give an outline talk about (potentially) deadly sins to avoid when describing data for later use with computers. Then we will build (together) an Excel templates for use with an experimental data of different types. Finally we will introduce you to off-the-shelf tools applied to realistic experimental data to improve its quality before uploading it to the data management system SEEK.
We target experimental biologists, no prior informatics training is assumed, own data can be used in this course
Tools to be used:
http://www.seek4science.org/ https://www.sysmo-db.org/rightfield http://openrefine.org/ Software: Please download and preinstall Rightfield and OpenRefine for this practical.
SEEK ID: https://demo.fairdomhub.org/assays/32
Experimental assay
Projects: SysMO DB
Investigation: Methods for interrelating 'omics data
Study: hidden item
Assay position:
Assay type: Experimental Assay Type
Technology type: Technology Type
Organisms: No organisms
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Created: 25th Feb 2014 at 13:06
Last updated: 26th Oct 2017 at 09:57
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Projects: SysMO DB, FAIRDOM training
Institutions: HITS gGmbH
I am a researcher at the Scientific Databases and Visualization Group at Heidelberg Institute for Theoretical Studies (HITS) , one of the developers of SabioRK - System for the Analysis of Biochemical Pathways - Reaction Kinetics (http://sabiork.h-its.org/) . I am working on design and maintenance of the information systems to store, query and analyse systems biology data; definition and implementation of methods for the integration of data from multiple sources. In SySMO-DB project ...
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO is to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB
Web page: http://sysmo.net/
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
- facilitates and maximises the potential for data exchange between SysMO research groups;
- maximises the ‘shelf life’ and ...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
This Investigation was performed by SySMO DB team together with PALS in order to crete methods and best practices for capturing experimental data.
Submitter: Katy Wolstencroft
Studies: No Studies
Assays: Computer Practicals "Data management in practice" Advanced Lecture Cours..., Transcriptional profiling
File to use as an example for OpenRefine computer paractical
