de.NBI Systems Biology Service Center (de.NBI-SysBio)
The staff of the Service Center "de.NBI Systems Biology Service Center" (de.NBI-SysBio)de.NBI Services offered by de.NBI-SysBio de.NBI Training offered by de.NBI-SysBio
About
The "de.NBI-Systems Biology" Service Center located at HITS (Heidelberg Institute for Theoretical Studies) offers software and support for FAIR data and model management (SEEK, FAIRDOMHub) as well as curated kinetic data (SABIO-RK database). In 2016 the partner project de.NBI-ModSim was established consisting of two research groups from Heidelberg University and MPI Magdeburg. These partners provide world-wide recognized tools for mathematical modeling, simulation and analysis of biological networks (COPASI and CellNetAnalyzer) thus enabling de.NBI-SysBio to serve the entire systems biology cycle..
Services
The mission of de.NBI-SysBio is to serve the systems biology community by providing data management solutions for all kinds of projects as well as resources, services and developments for systems biology modeling. The services address different profiles of users: Application users (experimentalists and modelers) get easy access to manually curated and enriched kinetic data; they can use a sharing platform to search, store and exchange their data, models and standard operating procedures (SOPs); they receive support in encoding and publishing their results in a reproducible manner. Additionally, modelers get support in model construction and analysis by provided software and trainings. Developers are guided to deploy their own data management instance for their projects and are enabled to extend the current open source software SEEK. They get assistance in implementing systems biology standards in their own simulation and analysis tools. Expert data analysts benefit from web services for automated data search, upload and integration into, e.g., modeling and simulation tools; and they gain better access to reproducible modeling results. Workshops and hands-on trainings are organized regularly for all types of users.
Developments
Developments in this unit focus on establishing and maintaining a sustainable, reliable and scalable infrastructure for systems biology data management. Additionally, we are working on further facilitating the integration of our tools into existing workflow systems such as KNIME and Galaxy. In particular we are interested in workflows, where collecting data early on facilitates curation. Future developments of COPASI and CellNetAnalyzer include integration of the tools with existing resources of de.NBI and improving compliance with model standardization and annotation schemes propagated by the de.NBI-SysBio node.
Project Management
HITS Website
PD Dr. Wolfgang Müller (Coordinator)
Scientific Databases and Visualization (SDBV)
Heidelberg Institute for Theoretical Studies (HITS gGmbH)
Schloß-Wolfsbrunnenweg 35
69118 Heidelberg
SEMS Website
Dr. Dagmar Waltemath (Partner)
Simulation Experiment Management for Systems Biology (SEMS)
Department of Systems Biology and Bioinformatics
Universität Rostock
Ulmenstraße 69
18057 Rostock
Partner Project Management
de.NBI-ModSim
Prof. Dr. Ursula Kummer (Deputy Coordinator)
Modeling of Biological Processes
Ruprecht-Karls-Universität Heidelberg
INF 267
69120 Heidelberg
de.NBI-ModSim
Dr.-Ing. Steffen Klamt
Analysis and Redesign of Biological Networks
Max Planck Institute for Dynamics of Complex Technical Systems
Sandtorstraße 1
39106 Magdeburg
Posters
