Systems Biology Tool Kit

Tools and resources for researchers interested in plant systems biology.

3D Cell Atlas

Digital Single Cell Analysis

3DCellAtlas is a computational approach to perform digital single cell analyses in 3D plant organs.

This approach identifies both cell types and cell position within 3D cellular reconstructions of plant organs, enabling equivalent cells in different images to be identified. Both the geometric properties and the abundance of reporter constructs within individual cells can be quantified and compared across different organs at single cell resolution

AGRIS- The Arabidopsis Gene Regulatory Information Server

Arabidopsis Gene Regulatory Information Server. An information resource of Arabidopsis cis regulatory elements and transcription factors.

From the abstract: Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively. Tools recently incorporated into AGRIS include the integration of AtRegNet with visualization tools, such as the recently developed ReIN application. All the information in AGRIS is publicly available and downloadable upon registration.


AraCyc is a metabolic pathway database for Arabidopsis thaliana that contains information about both predicted and experimentally determined pathways, reactions, compounds, genes and enzymes. The Omics viewer is a software for displaying large scale data such as microarray gene expression results or proteomic data in the context of biochemical pathways.

At RegNet, Arabidopsis Regulatory Network

Web-based tools to help researchers visualize the complex networks of transcription factor interactions. Simply enter AGI locus and get back target genes nodes and edges of interactions.


AthaMap provides a genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana. The database was updated to the TAIR8 genome release. 

From the abstract: The AthaMap database generates a map of potential transcription factor binding sites (TFBS) and small RNA target sites in the Arabidopsis thaliana genome.

BAR Expressolog Tree

Explores "expressologs" (orthologs that exhibit the highest expression profile ranking) in 6 plant species with an intuitive interface for visualizing both sequence and expression pattern similarity.

BRENDA The Comprehensive Enzyme Information System

Comprehensive enzyme information edited from the scientific literature for many proteins across a range of organisms including Arabidopsis.

From the abstract: The BRENDA (BRaunschweig ENzyme Database) enzyme information system is the main collection of enzyme functional and property data for the scientific community. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. The number of manually annotated references is more than 100,000, the number of ligand structures almost 100,000. BRENDA now provides new viewing options such as the display of the statistics of functional parameters and the 3D view of protein sequence and structure features. Furthermore a ligand summary shows comprehensive information on the BRENDA ligands. The enzymes are linked to their respective pathways and can be viewed in pathway maps. It is possible to submit new, not yet classified enzymes to BRENDA, which then are reviewed and classified by the International Union of Biochemistry and Molecular Biology.

Comprehensive Systems Biology Database

The Comprehensive Systems-Biology Database (CSB.DB) provides a useful portal into systems biology by allowing statistical analysis of gene expression data. CSB.DB maintains databases of various model organisms, namely Escherichia coli, Saccharomyces cerevisiae and Arabidopsis thaliana (this include NASC affymextric data). Comprehensive analyses of these data sets can be achieved via various tools provided by CSB.DB allowing parallel evaluation of a compendium of data.


Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. This tool presents a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse.


Software for analysing and visualizing biological network data and integrating these with any type of attribute data. 

Gene Ontology Consortium

From the website: The Gene Ontology project provides an ontology of defined terms representing gene product properties. The ontology covers three domains: cellular component, the parts of a cell or its extracellular environment; molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; and biological process, operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.


GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest, developed by the Gutiérrez Lab.

GoldenBraid 3.0

GoldenBraid version 3.0 is a tool for modular construction of multigenic DNA structures in Synthetic Biology applications. This webpage provides support for GB3.0 users, including searchable databases of GB elements and experiments and a number of software tools for in silico simulation of DNA assembly reactions.

The GB3.0 version introduces a number new features. The most relevant one is the possibility to incorporate experiments to the GB database. This option was introduced to enable the association of functional specifications to the description of GB3.0 elements. Other important novelties are the improvement of domestication tools, the design of descriptive datasheets, or the inclusion of a special section dedicated to genome engineering, among others.

KEGG, Kyoto Encyclopedia of Genes and Genomes

Collection of databases and software for understanding higher order networks and functions in cell/organisms from existing genome data.


From the abstract: MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. It can group genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes; group hundreds of metabolites into pathways or groups of structurally related compounds; and use these groupings to organise and display experimental data sets onto diagrams of the users' choice.


ONDEX is a free, open-source software that enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques.


OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.

Plant Ontology Consortium

From the website: The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomy and morphology and stages of development for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics and genetics experiments.

Plant Regulome

Plant regulome aims to:

  • Produce nucleotide-resolution maps of cis-regulatory DNA in major developmental stages, tissues and cell types in the reference strain Col-0.
  • Define the chromatin structural and cis-regulatory DNA response programs of Col-0 tissues to major hormonal, biotic and abiotic cues.
  • Determine the divergence and conservation of cis-regulatory DNA in closely related Arabidopsis ecotypes
  • Integrate cis-regulatory DNA programs into gene regulatory networks and to and disseminate high-quality cis-regulatory annotations as well as primary data to the public


The Plant GeneSet Enrichment Analysis Toolkit (PlantGSEA) is an online websever for gene set enrichment analysis of plant organisms developed by Zhen Su Lab in China Agricultural Unversity. We developed this to meet the increasing demands of unearthing the biological meaning from large amounts of data.

The PlantGSEA was designed to serve researchers from plant community with a user-friendly interface as well as performance-efficient frame. It has several features when comparing with other similar tools:

System Biology Workbench (SBW)

Designed by the Sauro Lab, SBW is a free download which provides a framework for application intercommunications. It supports many languages and runs on different platforms. The package includes Jarnac, a biochemical network simulation tool; JDesigner, which designs biochemical networks; and a MatLab Interface.

From the abstract: In this paper, we describe the Systems Biology Workbench (SBW), a software framework that allows heterogeneous application components--written in diverse programming languages and running on different platforms--to communicate and use each others' capabilities via a fast binary encoded-message system. Our goal was to create a simple, high performance, opensource software infrastructure which is easy to implement and understand. SBW enables applications (potentially running on separate, distributed computers) to communicate via a simple network protocol.

Systematic analysis of Arabidopsis promoters

Tools for the systematic analysis of Arabidopsis cis-regulatory elements and the associated proteins that control gene transcription. 

From the abstract: We have assembled approximately 20 000 Arabidopsis thaliana promoter regions, compatible with functional studies that require cloning and with microarray applications. The promoter fragments can be captured as modular entry clones (MultiSite Gateway format) via site-specific recombinational cloning, and transferred into vectors of choice to investigate transcriptional networks. The fragments can also be amplified by PCR and printed on glass arrays.

Systems Biology

Japanese portal site for systems biology, including news and new resources in the field. 

The Systems Biology Researcher Database

An information and knowledge exchange platform for all systems biology researchers worldwide.

The Virtual Seed Web Resource

Web-based tools for analysis of gene expression occurring during seed maturation, dormancy and germination.

Virtual Plant

Integrates genomic data and provides visualization and analysis tools for rapid and efficient exploration of Arabidopsis genome wide data.

From the abstract: VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology

WikiPathways for Plants

In the interest of plant research and to facilitate community-based annotation of biological pathways (metabolic/biochemical, signaling, genetic and gene-interactions) in plants, WikiPathways, the Jaiswal Lab at Oregon State University, and the Gramene database present to you a freely-available platform which allows you to add, edit and download known and novel published pathways from plants.

Citation: Hanumappa et al. WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice 2013, 6:14 doi:10.1186/1939-8433-6-14. (View Citation)


From the website: xCellerator is a Mathematica package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and their subsequent solution via numerical integration.

YieldBooster: Systems Biology of Yield

It is our ambition to decipher the molecular networks underpinning yield and organ growth, both under standard as well as mild drought stress conditions, in Arabidopsis and the C4 crop maize. Systems biology will ultimately provide a holistic view enabling the optimalization of plant productivity, either by advanced plant breeding or genetic engineering.