Collaboration Between Shimadzu, The Systems Biology Institute, and Osaka University
Starting the Provision of an Open Platform Multi-omics Data Analysis Pack
On June 6, Shimadzu Corporation starts to provide, at no cost, the Shimadzu Multi-omics Data Analysis Pack. Intended for metabolic engineering, this gadget pack automatically visualizes large-volume of data sets from proteomics*1, metabolomics*2, and flux analysis*3, obtained using Shimadzu gas chromatograph mass spectrometers and liquid chromatograph mass spectrometers, on metabolic maps and perform a variety of data analyses. Multi-omics is a cutting-edge research area in the field of life sciences. It involves the integrated analysis of changes in genes, proteins, metabolites and other substances, towards a holistic elucidation of biological activities at cellular level. Multi-omics is expected to be useful in a variety of fields such as drug discovery, diagnostics, and biofuel research.
Mass spectrometers, a specialty of Shimadzu, are indispensable for multi-omics research. In recent years, with the emergence of ultra-fast mass spectrometers, the amount of data that can be obtained has grown enormously. As a result, the data analysis process has become a research bottleneck. Creating charts from quantitative trend data on each metabolites and proteins and rendering the results visible on a metabolic map, takes over ten hours even for experienced analysts. Using this pack, the work can be reduced to a few minutes. The pack frees researchers from tedious manual data analysis and visualization, allowing them to focus on the discovery of new ideas and generation of novel hypotheses.
Overview of This Pack
Research for creating substances with advanced functions utilizing microorganisms and cells, rather than chemical synthesis, has expanded in recent years in a variety of fields, including biofuels, pharmaceuticals, and food products for example. Advancement in gene editing techniques is further creating new avenues of research. In this direction of research, the effect of incorporating genes into microorganisms and cells is measured as changes in the concentrations of metabolites and metabolic enzymes. This pack significantly increases the efficiency of data analysis for these measurements.
This pack is available on the, Garuda Platform, an open, community-driven, connectivity and automation platform to connect, discover and navigate through various analytics tools, services and database (called gadgets on Garuda). The community version of the platform is available on the Garuda Alliance, and has been in operation since 2010, led by the Systems Biology Institute (SBI), a non-profit private research institution based in Tokyo. It provides an open platform to enable researchers to create a user defined workflow (called Garuda recipes), from data acquisition to data analysis, powered by an ever-increasing suite of inter-operable gadgets. Currently, the community version of the platform is in beta with more than 50 tools (gadgets) available freely, developed by the world's leading research agencies, along with customized gadgets available in commercial versions for specific businesses and organizations.
The Shimadzu multi-omics data analysis pack presents a collection of multiple gadgets that can be interfaced with existing gadgets on the community version, creating a seamless user experience for complex data analysis and visualization workflows. This pack can be downloaded free of charge from a dedicated site on Garuda Alliance website (link available in later section). In the words of Dr. Hiroaki Kitano, President of SBI, "Connecting mass spectrometers directly with a variety of data analysis software programs developed by the world's top research agencies in the life science field is groundbreaking. This offers the possibility of stimulating a new research cycle."
This pack is one of the outcomes of collaborative research being pursued by Shimadzu with SBI and Osaka University, utilizing the Osaka University and Shimadzu Analytical Innovation Research Laboratory, an open innovation laboratory established by Shimadzu at Osaka University in December 2014. Fumio Matsuda, an associate professor with the Osaka University Graduate School of Information Science and Technology, developed an optimal workflow for research by combining multiple gadgets with this pack. In his words, "This pack simplified the visualization of metabolic measurement data, a conventionally tedious and time consuming process. This improves the datability*4 of extracting useful information and knowledge from big data sets obtained from mass spectrometers. Increasing the productivity of research sites enables researchers to focus on interpreting the analysis results, leading to new valuables discoveries and creations."
In the words of Shuzo Maruyama, General Manager of the Analytical & Measuring Instruments Division at Shimadzu, "Development of life science research is progressing at rapid pace. We are no longer in an era when a single company can assess cutting edge needs and provide the solutions. We will work continuously with global research agencies in order to keep providing solutions to respond to potential user needs."
The results to date will be announced at the annual conference of the American Society for Mass Spectrometry (Indianapolis, USA, June 4 to 8, 2017). This pack can be downloaded free of charge from http://www.garuda-alliance.org/gadgetpack/shimadzu starting on June 6. Utilizing feedback from users, a more sophisticated commercial edition is scheduled for release within the year.
The Garuda platform has deep integration with Garuda's proprietary artificial intelligence (AI) function, and provides interface to connect with other AI platforms. AI-based data analysis will also be possible in future extensions of this pack. Commercialization of a pack incorporating AI-based data analysis is scheduled during 2018.
*1: Research to comprehensively assess the structure and functions of proteins
*2: Research to comprehensively assess the metabolites produced by cellular activity
*3: A method of accurately tracking the amount of a single metabolite based on the difference between two values: the amount produced and the amount consumed
*4: This word was coined by combining "data" and "ability". It refers to the activity of extracting useful information and knowledge from ultra large amounts of data and utilizing it. It is a core concept in the data sciences.