Tools 2018-05-31T14:05:30+00:00

Tools: Tools for building, simulating, and analyzing WC models

  •  - DBS-pipes

    DBS-pipes is database for raw high-throughput experimental data that facilitates and enhances the reproducibility of large-scale data analysis and modeling. DBS-pipes integrates metadata about samples, genome annotations, omics data, and data analysis pipelines.

    Availability: In development
    Author: Serrano Lab, CRG

  •  - Datanator

    Datanator is a tool for discovering the data needed to build, calibrate, and validate whole-cell models. Datanator is composed of an integrated database of experimental data for whole-cell modeling and tools for identifying relevant data for modeling a specific organism and environmental condition. Datanator has a web-based graphical interface, a REST API, a Python API, and a command line interface.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage

  •  - WC-KB-Gen

    WC-KB-Gen is a Python framework for programmatically constructing knowledge bases for whole-cell models. WC-KB-Gen helps modelers retrieve data from external sources, organize this data, and record the provenance of this data. In turn, WC-KB-Gen helps modelers scalably, reproducibly, and comprehensibly discover and aggregate data for whole-cell models.

    Author: Karr Lab, Mount Sinai

  •  - WC-KB

    WC-KB is a data model for describing the experimental data needed to build, calibrate, and validate a whole-cell model. WC-KB includes a command line program and a Python API.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage
    Reference: Karr JR et al. WholeCellKB: model organism databases for whole-cell models. Nucleic Acid Res 2013.

  •  - WC-Model-Gen

    WC-Model-Gen is a Python framework for programmatically constructing whole-cell models from large datasets described with WC-KB. WC-Model-Gen helps modelers retrieve data from a WC-KB and use the data to scalably design species and reactions. In turn, WC-Model-Gen helps modelers build models scalably, reproducibly, and comprehensibly.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage

  •  - E-Cell P

    E-Cell P is a framework for automated bottom-up modeling and simulation of prokaryotes from their genomes. Starting from a genome sequence, the framework enables researchers to annotate genomes using knowledge collected from multiple databases, build agent-based models with single-nucleotide resolution, and generate genome-scale in silico omics data, all without detailed knowledge of mathematical modeling. E-Cell P also helps researchers evaluate the effect of mutations and synthetic genomes.

    Author: Takahashi Lab, RIKEN ()

  •  - WC-Lang

    WC-Lang is a data model and a file format for describing composite, multi-algorithmic whole-cell models. WC-Lang includes a command line interface and a Python API.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage

  •  - WC-Rules

    WC-Rules is a formalism for describing composite, mixed-grained, multi-algorithmic WC models. WC-Rules provides modelers a high-level, biologically-intuitive language for describing models in terms of patterns of metabolite, DNA, RNA, and protein species and rules for their interactions. Together, these species patterns and interaction rules enable modelers to describe the molecular complexity of any biochemical process including metabolism, replication, transcription, translation, and signaling. WC-Rules can also record the provenance of models including their data sources and assumptions.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage

  •  - WC-Sim

    WC-Sim is a simulator for composite, multi-algorithmic whole-cell models described with WC-Lang. WC-Sim is implemented using discrete event simulation. WC-Sim includes a command line interface and a Python API.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage
    Reference: Goldberg AP et al. Toward scalable whole-cell modeling of human cells. ACM Conf Prin Adv Discrete Simul 2016.

  •  - E-Cell

    E-Cell, started in 1996, is an open-source software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems such as cells. The latest version, version 4, enables multi-algorithmic co-simulation of compartmental, mesoscopic, lattice, and particle submodels. E-cell supports high-performance computing, rule-based modeling, and integration with several bioinformatic resources.

    Availability: Download ()
    Author: Takahashi Lab, RIKEN ()
    More info: Docs (), License (), Source ()

  •  - Scopyon

    Scopyon is a bioimaging simulation software toolkit. Scopyon supports computational simulation of total internal reflection fluorescence microscopy (TIRF), laser-scanning confocal microscopy (LSCM), and super-resolution microscopy images. Combining optical microscopy with cell simulation, Scopyon generates digital images of cells that are quantitatively comparable with real experiments and that can be used to evaluate systematic effects in measurements.

    Availability: Download ()
    Author: Takahashi Lab, RIKEN ()
    More info: License (), Source ()
    Reference: Watabe M et al, A Computational Framework for Bioimaging Simulation, PLoS One 2015 ()

  •  - WC-Analysis

    WC-Analysis is a Python framework for analyzing whole-cell knowledge bases, models, and simulation results. In particular, WC-Analysis helps models quickly and reproducibly conduct analyses for whole-cell modeling.

    Availability: Download
    Author: Karr Lab, Mount Sinai
    More info: Docs | License | Source | Test results , coverage

  •  - WC-Viz

    WC-Viz is an interactive web-based tool for visually analyzing the results of simulations of whole-cell models. WC-Viz enables modelers to design dashboards composed of time series plots and animated pathway diagrams of simulation results.

    Use online: WholeCellViz.org
    Author: Covert Lab, Stanford University 
    More info: License | Docs | Source
    Reference: Lee R et al. WholeCellViz: data visualization for whole-cell models. BMC Bioinformatics 2013.

  •  - WC-Test

    WC-Test is a Python framework for programmatically verifying whole-cell models. WC-Test helps modelers verify that their models satisfy design constraints such as mass conservation, charge conservation, self replication and quickly find errors in their models. Furthermore, WC-Test can be integrated with continuous integration systems such as CircleCI. Together, WC-Test helps modelers collaborative develop high-quality models.

    Author: Karr Lab, Mount Sinai