Motivation:

The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.



Results:

We have developed MetaboCraft, a Minecraft plugin which creates immersive visualisations of metabolic networks and pathways in a 3-D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome

Burgess, Karl

Daly, Rónán

Megalios, Anargyros

English

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Bioinformatics, YYYY, 0–0 doi: 10.1093/bioinformatics/xxxxx Advance Access Publication Date: DD Month YYYY Manuscript Category  Subject Section MetaboCraft: Building a Minecraft plugin for metabolomics Anargyros Megalios1,2, Rónán Daly2 and Karl Burgess1,2* 1Glasgow Polyomics, University of Glasgow, Glasgow Scotland., 2Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, Scotland. *To whom correspondence should be addressed. Received on XXXXX; revised on XXXXX; accepted on XXXXX  Abstract Motivation: The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our under-standing of new findings.  Results: We have developed MetaboCraft, a Minecraft plugin which creates immersive visualisations of metabolic networks and pathways in a 3-D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome. Availability: https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/ Contact: karl.burgess@glasgow.ac.uk  Supplementary information: Supplementary data are available at Bioinformatics online.   1 Introduction  Metabolomics as a field has expanded rapidly in recent years, owing both to increased interest as well as advances in instrument throughput and resolution, accordingly resulting in the accumulation of a vast metabolomic data repository (Haug et al., 2017), presenting ever-increasing challenges to scientists attempting to interpret this data. The utility of visualisations in aiding interpretation of scientific datasets is well described (Auber, 2004), however the advances in the development of visual aids for metabolomics have been slower, mostly centring on cosmetic refinements to the traditional, 2D, metabolic map paradigm.  PiMP (Gloaguen et al, 2017) is a metabolomics pipeline currently in development, which aims to streamline and standardise the process of metabolomics analysis into one tool. Exploring new and innovative approaches to data visualisation is an integral part of the development of PiMP.  At a conceptual level, metabolic maps can be interpreted as mathemati-cal graph objects, enabling the application of widely applied methods towards both their design and their interpretation (Cottret and Jourdan, 2009). MetExplore (Cottret et al., 2010) is a web service and repository of metabolic networks designed to facilitate the mapping of metabolites identified in untargeted metabolomics experiments onto genome-scale metabolic networks. To that end, it streamlines access to known metabol-ic networks in graph form, and provides this data in a machine-readable, JSON-based format.  Minecraft is an open-world, sandbox building game written in Java, similar in its conception to a virtual Lego construction set, which allows the player to construct arbitrarily large and complex structures, using a variety of visually and even functionally different building blocks. It has been extensively used in educational and scientific contexts in the past, including the illustration of physical, chemical and biological phenome-na (Short, 2012). Such applications so far have either taken advantage of “naturally” occurring game events, or necessitated one-off, quasi-manual construction of large-scale structures (Lorch and Mills, 2015). The chal-lenge presented here, given the scale of the putative dataset (i.e. the entire MetExplore database) lies therefore in devising a novel program-matic approach to dynamic, user-driven generation of structures repre-senting arbitrary metabolic networks. We anticipate the use of Metabo-craft in teaching biochemistry, at either the secondary school or under-graduate levels, providing students a unique experience of biochemical information. 2 Implementation   © The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Downloaded from https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty102/4956010by University of Glasgow useron 29 March 2018A. Megalios et al. Fig. 1.a) Selection of a particular metabolic map via the bookshelves. Maps are related via XXX algorithm, and a particular map may be selected via right clicking. Subcellular localisation of metabolic maps is also supported. Clicking on a labelled pumpkin (not shown) creates a subset of bookshelves corresponding on only those maps in a particular subcellular compartment. b) the citric acid cycle displayed in Minecraft. Glowstones (yellow) represent enzymes, red blocks are decreased metab-olites, black blocks are non-detected, and blue blocks are upregulated. Small white blocks are side metabolites, such as H2O.  The MetaboCraft server stack is comprised of three components: a Spig-ot server, a Shiny server and a plumber server. The Spigot server runs JavaScript code, while the Shiny and plumber servers run R code.  A series of shell scripts are provided for installing, running, and mainte-nance. The installer automates the downloading and compilation of Spigot, the downloading and installation of the relevant plugins and finally the JavaScript component of MetaboCraft, on top of Spigot. It initialises the configuration of the Minecraft world with a variety of settings appropriate for the desired functionality. It also attempts to au-tomate the installation of the necessary R packages, which due to varia-tions in R setups is not always achievable. The script attempts to antici-pate such cases and prompt the user to manually install the missing packages, if necessary. As well as being able to install the components by hand, a Docker image is available that provides a one-click installa-tion option for quick and easy setup.  By default, MetaboCraft displays data from MetExplore BioSource 4324, derived from the Recon 2 reconstruction of the human metabo-lome (Thiele et al., 2013). Support for other data sources is currently experimental. An example dataset (Stipetic et al., 2016) is provided with the MetaboCraft distribution for demonstration of the uploading feature. 3 Results The Shiny web application can be accessed on port 38909 on the local machine. After optionally uploading their files, on logging into the server using Minecraft, the user is presented with a welcome message inform-ing them of the default viewing parameters and the data files uploaded under their name and available to them. They are presented with a pano-ramic view of the full default metabolic network map, along with a series of control blocks presenting the choice of cellular compartments. Choos-ing a compartment presents the user with a view of the network map of that specific compartment, while choosing a pathway from the map presents the 3D graph of that pathway, along with an option to go back to the map view. The various entities represented in a metabolic pathway graph are colour-coded for legibility.  Several commands are also implemented for the user to input into the Minecraft console, allowing direct access to these features, as well as additional control over the behaviour of MetaboCraft, such as switching between uploaded files and changing the pathway network map layout.   MetaboCraft joins an already crowded field of visualisation frameworks for metabolic networks, such as MetExploreViz, (Cottret et al, 2010), CytoScape (Shannon et al. 2003) and TULIP (Auber et al. 2004). Alt-hough it currently lacks the maturity and flexibility of such solutions, it is unique in immersiveness and approachability. Basing the program on a widely recognised 3D modelling platform significantly lowers the barrier to entry for new users with little previous experience of metabolomics, while the Minecraft environment presents a host of as yet untapped fea-tures, paving the way for adding elements of real-time interactivity to visualisations in the future. Funding This work was supported by the Wellcome Trust [105614/Z/14/Z].  Conflict of Interest: none declared. References Auber,D. (2004) Tulip : A huge graph visualisation framework. In, Mutzel,P. and Junger,M. (eds), Graph Drawing Software, Mathematics and Visualization. Springer Berlin Heidelberg, pp. 105–126. Cottret,L. et al. (2010) MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res, 38, W132–W137. Cottret,L. and Jourdan,F. (2010) Graph methods for the investigation of metabolic networks in parasitology. Parasitology, 137, 1393–1407. Gloaguen, Yoann, et al. PiMP my metabolome: An integrated, web-based tool for LC-MS metabolomics data. Bioinformatics (2017). Haug,K. et al. (2017) Global open data management in metabolomics. Curr Opin Chem Biol, 36, 58–63. Heller,S. et al. (2013) InChI - the worldwide chemical structure identifier standard. J Cheminform, 5, 7. Mills,J. and Lorch,M. How Minecraft could help teach chemistry’s building blocks of life. The Conversation. Shannon, Paul, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13.11: 2498-2504. Short,D. (2012) Teaching scientific concepts using a virtual world—Minecraft. Teaching Science-the Journal of the Australian Science Teachers Association, 58, 55.  Stipetic et al. (2016) A novel metabolomic approach used for the comparison of Staphylococcus aureus planktonic cells and biofilm samples.Metabolomics, 12.4 75 Thiele,I. et al. (2013) A community-driven global reconstruction of human metabo-lism. Nat. Biotechnol., 31, 419–425. Downloaded from https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty102/4956010by University of Glasgow useron 29 March 2018

MetaboCraft: building a Minecraft plugin for metabolomics

Abstract
               
                  Motivation
                  The rapid advances in metabolomics pose a significant challenge in presentation and interpretation of results. Development of new, engaging visual aids is crucial to advancing our understanding of new findings.
               
               
                  Results
                  We have developed MetaboCraft, a Minecraft plugin which creates immersive visualizations of metabolic networks and pathways in a 3D environment and allows the results of user experiments to be viewed in this context, presenting a novel approach to exploring the metabolome.
               
               
                  Availability and implementation
                  https://github.com/argymeg/MetaboCraft/; https://hub.docker.com/r/ronandaly/metabocraft/
               
               
                  Supplementary information
                  Supplementary data are available at Bioinformatics online.
               </jats:sec

MetaboCraft: building a Minecraft plugin for metabolomics

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