Page 25 - Shimadzu Journal vol.5 Issue1

Topics

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

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