Software for systems biology: from tools to integrated platforms

@article{Ghosh2011SoftwareFS,
  title={Software for systems biology: from tools to integrated platforms},
  author={Samik Ghosh and Yukiko Matsuoka and Yoshiyuki Asai and Kun-Yi Hsin and Hiroaki Kitano},
  journal={Nature Reviews Genetics},
  year={2011},
  volume={12},
  pages={821-832}
}
Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review… 
Accelerating in silico research with workflows: A lesson in Simplicity
Computational Tools and Resources for Integrative Modeling in Systems Biology
TLDR
Several resources and computational tools which support the investigation of biological networks are reviewed and several resources and methods for integrative modeling are described.
Computational Systems Biology
Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering
TLDR
Challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering are discussed.
GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis
TLDR
GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases and provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use.
Integrating -Omics: Systems Biology as Explored Through C. elegans Research.
ssbio: A Python Framework for Structural Systems Biology
TLDR
The ssbio package provides an automated pipeline to construct high quality genome-scale models with protein structures (GEM-PROs), intuitively linking 3D structural data with established systems workflows.
Computational Infrastructures for Data and Knowledge Management in Systems Biology
TLDR
This chapter describes some of the challenges for computational analysis infrastructure, including bottlenecks and most pressing needs that have to be addressed to effectively support the development of systems biology and its application in medicine.
ssbio: a Python framework for structural systems biology
TLDR
The ssbio package provides an automated pipeline to construct high quality genome‐scale models with protein structures (GEM‐PROs), wrappers to popular third‐party programs to compute associated protein properties, and methods to visualize and annotate structures directly in Jupyter notebooks, thus lowering the barrier of linking 3D structural data with established systems workflows.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 120 REFERENCES
PANTHER pathway: an ontology-based pathway database coupled with data analysis tools.
  • H. Mi, P. Thomas
  • Biology, Computer Science
    Methods in molecular biology
  • 2009
TLDR
This chapter first discusses how biological knowledge is represented, particularly the importance of ontologies or standards in systems biology research, and uses PANTHER Pathway as an example to illustrate how ontologies and standards play a role in data modeling, data entry, and data display.
Computational Systems Biology
TLDR
This survey of the bioinformatics analysis of NGS data can help researchers to choose appropriate tools when dealing with the sequencing data and introduce popular methods in quantitating the semantic similarity between ontology terms and their software implementations.
Resources, standards and tools for systems biology.
TLDR
Different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology are described.
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
TLDR
This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Beyond standardization: dynamic software infrastructures for systems biology
TLDR
It is argued that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.
Pathway databases and tools for their exploitation: benefits, current limitations and challenges
In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
TLDR
The SBW architecture, a selection of current modules, including Jarnac, JDesigner, and SBWMeta-tool, and the close integration of SBW into BioSPICE, which enables both frameworks to share tools and compliment and strengthen each others capabilities are described.
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
TLDR
Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Taverna: a tool for the composition and enactment of bioinformatics workflows
TLDR
The Taverna project has developed a tool for the composition and enactment of bioinformatics workflows for the life sciences community that is written in a new language called Scufl, where by each step within a workflow represents one atomic task.
Presenting and exploring biological pathways with PathVisio
TLDR
This work presents PathVisio, a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects.
...
1
2
3
4
5
...