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Archived Comments for: FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

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  1. Highly Customizable Visualization with Omix

    Katharina Noeh, Research Centre Juelich

    10 September 2012

    The authors compare different visualization solutions and assess them with respect to their functionalities. One of the software tools is our visualization tool Omix. The authors claim that "the import of external flux data" in Omix is "an absent or inadequately supported feature" (cf. Table 1).

    In fact, one of the central features of Omix is the ability to annotate each graphical property of a network drawing, e.g. reaction and metabolite nodes, with "external" data. Here, the mapping of data sets to the graphical components is done by writing a few lines of scripting code. By this scripting language, any type of data can be easily mapped to any of the network components. Actually, making visualization as easy and customizable as programming in MATLABTM, is the distinguished key innovative feature of Omix. Therewith, our solution is much more general than the aspects addressed by the FluxMap publication.

    Typical Omix visualization examples can be downloaded here.

    Further information about Omix:

    [1] Droste P, von Lieres E, Wiechert et al. 2010: Customizable Visualization on Demand for Hierarchically Organized Information in Biochemical Networks. Lecture Notes in Computer Science, 2010, 6026/2010, 163-174, DOI: 10.1007/978-3-642-12712-0_15.

    [2] Dalman T, Droste P, Weitzel M, Wiechert W, Noeh K. Workflows for Metabolic Flux Analysis: Data Integration and Human Interaction. Lecture Notes in Computer Science, 2010, 6415/2010, 261-275, DOI: 10.1007/978-3-642-16558-0_23.

    [3] Droste P, Miebach S, Niedenfuehr S, Wiechert W, Noeh K. Visualizing Multi-Omics Data in Metabolic Networks with the Software Omix - A Case Study. BioSystems, 2011, 105:154-161,
    DOI: 10.1016/j.biosystems.2011.04.003.

    Competing interests

    No any competing interest

  2. "...but what is available for biological researchers?"

    Hendrik Rohn, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

    4 October 2012

    "Dr. Noeh compares OMIX with FluxMap and, indeed, we are impressed by the visual capabilities and the flexible scripting interface of OMIX. On the other hand, even if the tool may potentially provide a more general solution, it does not at the moment. The feature "import of external flux data" indicates not just an import of data and mapping to visual attributes, but that the tool has to respect the unique properties of flux data during import. This feature demands that an easy and intuitive way of importing this special kind of data is provided, together with all its prerequisites regarding a simple data template, splitting the reaction formula, respecting substance weights and stoichiometric constants etc. It is true, that OMIX is powerful enough to rebuild most of FluxMap's functionality, but still one has to program it. We are sure that this needs considerable knowledge of programming and of the OMIX framework, as well as more than a "few lines of code". She states that "writing a few lines of scripting code" makes "visualization as easy and customizable as programming in MATLAB". Most biologists simply don't have the ability to write code. Computer scientists/bioinformaticians can't expect programming skills from biological researchers, but have to provide appropriate tools which enable to analyze data without the need for diving to deep into technical details. In our experience biologists were instantly able to visually analyze flux data using FluxMap without the need for detailed instructions. Finally, OMIX is free for non-commercial use only and the source code is not available, in comparison to the open source tool FluxMap."

    Competing interests

    None declared