TY  - JOUR
AB  - Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database. BioSankey is a valuable tool to visualize different data elements from single or dual RNA-seq datasets and additionally enables a straightforward exchange of results among collaboration partners.
AU  - Platzer, A.*
AU  - Polzin, J.*
AU  - Rembart, K.*
AU  - Han, P.P.*
AU  - Rauer, D.
AU  - Nussbaumer, T.
C1  - 53649
C2  - 44930
TI  - BioSankey: Visualization of microbial communities over time.
JO  - J. Integr. Bioinform.
VL  - 15
IS  - 4
PY  - 2018
ER  - 

TY  - JOUR
AB  - Using the lac operon as a paradigmatic example for a gene regulatory system in prokaryotes, we demonstrate how qualitative knowledge can be initially captured using simple discrete (Boolean) models and then stepwise refined to multivalued logical models and finally to continuous (ODE) models. At all stages, signal transduction and transcriptional regulation is integrated in the model description. We first show the potential benefit of a discrete binary approach and discuss then problems and limitations due to indeterminacy arising in cyclic networks. These limitations can be partially circumvented by using multilevel logic as generalization of the Boolean framework enabling one to formulate a more realistic model of the lac operon. Ultimately a dynamic description is needed to fully appreciate the potential dynamic behavior that can be induced by regulatory feedback loops. As a very promising method we show how the use of multivariate polynomial interpolation allows transformation of the logical network into a system of ordinary differential equations (ODEs), which then enables the analysis of key features of the dynamic behavior.
AU  - Franke, R.*
AU  - Theis, F.J.
AU  - Klamt, S.*
C1  - 4180
C2  - 28153
TI  - From binary to multivalued to continuous models: The lac operon as a case study.
JO  - J. Integr. Bioinform.
VL  - 7
IS  - 1
PB  - IMBio, Informationsmanagement in der Biotechnologie e.V.
PY  - 2010
ER  - 

TY  - JOUR
AB  - The informative value of biomolecular networks has shifted from being solely information resources for possible cellular partners (whether these embody proteins, (ribo)nucleic acids or small molecules) towards becoming models for the functional connectivity within a cell. These models are increasingly exploited to make quantitative predictions about the cell?s functional organization as well as about the functionality of individual elements in the network. A large number of concepts and methods have been proposed in order to interpret experimental data mapped to cellular networks these systems and to make use of the rich source of information they represent. We will present a system for the Comprehensive Analysis of Biomolecular Networks (CABiNet), capable of integrating available network analysis methods. Integration is done by classifying each method into one of four separate categories using standardized interfaces that encapsulate the functionality of the method in a distinct component with standardized in- and output. These components can be accessed individually or in an integrated form using a processing pipeline for semi-automatic analyses. Additionally, the system can be used to query both biomolecular networks as well as the derived results of network analysis methods, such as clustering algorithms, in order to provide a service for researchers who are focused towards the functional context of any particular cellular entity. CABiNet is designed in an easy-to-use and easy-to-extend software framework that allows a straightforward integration of novel components. We will demonstrate the capabilities of the system by introducing several use cases. The CABiNet suite can be accessed at http://mips.gsf.de/genre/proj/CABiNet. Source code including additional components that can be accessed using the API is available upon request.
AU  - Oesterheld, M.
AU  - Mewes, H.-W.
AU  - Stuempflen, V.
C1  - 4041
C2  - 24912
TI  - Analysis of integrated biomolecular networks using a generic network analysis suite.
JO  - J. Integr. Bioinform.
VL  - 4
IS  - 3
PB  - IMBio, Informationsmanagement in der Biotechnologie e.V.
PY  - 2007
ER  -