About Subio PlatformThe free software for the integrated analysis of various omics data.

To understand the data correctly,

To apply methods appropriately,

Grab the right tool.

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What can you do with Subio Platform?

You can overview the workflow of omics data analysis on Analysis Guide. Black rectangles represent what you can do with Subio Platform. You might think of only statistical methods though, the heart of data analysis is to understand the characteristics of data and to interpret it on the biological context. So Data Browsing is the critical part.

Appendixies: How important is it to properly view the omics data with Subio Platform?

You can analyze and store various types of omics data.

Subio Platform accepts any omics data if it is quantitative. For example, transcriptomics, proteomics, metabolomics, DNA methylation, ChIP, and so on. Measurement technologies can be anything like microarrays, high-throughput sequencing, mass spectrometry, RT-PCR, or others. You can analyze and manage such a broad range of data sets with only one free software. RNA-Seq FASTQ files are fully supported from mapping to biological interpretation. (From the next release available soon.)

Some makers of the measurement systems provide dedicated analysis software for free. You can analyze data sets of the system with such software. However, you will have to compare or integrate different types of omics data from disparate systems in a long-term vision. Subio Platform is another free software and is more advantageous because you can store and analyze data sets of various experiments. Additionally, once you become familiar with the operation, you can analyze different types of omics data without learning some other software.

R is another popular free analysis tool but is not for storing various omics data sets. Maybe you experienced exhaustively seeking or unexpectedly losing data files, especially after staff changes. If you had used the Subio Platform, you would instantly find any data sets you had analyzed before. Moreover, it can hold with the raw data files, notes, references, or presentations altogether. You can be free from such uselessness if you analyze data with the Subio Platform.

Supported File Formats

  • RNA-Seq FASTQ(from the next release available soon.)
  • Tab-delimited text
  • SOFT(Gene Expression Omnibus)
  • BED
  • GFF
  • SAM / BAM
  • BAR(Affymetrix)
  • WIG

See how to import data

Importing RNA-Seq Data (A Table of Counts or FPKMs or RPKMs) Detail
Importing Agilent Microarray Data Detail
Importing Affymetrix GeneChip Data Detail
Importing and analyzing TCGA methylation data Detail
Importing An Excel Data Detail

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High-quality viewers to approach the essence of data

You might think that the free version has significant limitations. However, the truth is that Plug-ins are not necessary for fundamental data analysis. The professional viewers of Subio Platform help your understanding about the data. You can explore deeper and extract more biological insights than using R or Excel.

Learn more on movies.

A quick and in-depth microarray data analysis. Detail

Details of each viewer.

Scatter Plot (Measurement) View Detail
Line Graph View Detail
Tree View Detail
Pathway View Detail
Genome View Detail
Scatter Plot (Samples) View Detail
Venn Diagram Detail

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The right normalization needs a visual aid, not automation

Many software boasting "user-friendly" have the automation which applies a routine of normalization and pre-processing on the data. However, the truth is that omics data are not uniform, and such automation does not work very well. The following analysis of the oddly processed data becomes terrible consequently. The processing with R/Bioconductor has the same problem. We think you should not use automation for normalization at least until it evolves smart enough.

So what should (or can) the analysis software do? We think it is to support analysts' decision makings by the visual aid. So Subio Platform presents the raw data distribution patterns, and how it shows the effect of every step on the data. Users can go through trials and errors or discuss with somebody to select the right way.

We agree that this task is hard for beginners. However, they get to learn the limitation of the data through it, and it leads their correctly interpreting analysis results. So we decided not to make software having automatic normalization, but to provide service that users can consult to experienced technical support for free. We support researchers who want to understand their data.

Learn more on movies.

Finding a proper sequence of normalization and pre-processing. Detail
How to apply the paired T-test? Detail
How to Use Fill Missing Values Block Detail

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The data management system to turn data into assets

What is interesting in omics data is you already measured genes on which you do not pay attention. Biological information or knowledge is tremendously increasing and what you can extract from the data now will not be the same in the future. You cannot thoroughly squeeze at a time. Why don't you put the data in your toolbox for future use? You cannot make full use of the omics data with R or Excel.

You know that new technologies are rising rapidly. One type of omics data tells you only one aspect of the super-complicated living system. So you will need to combine the old and new omics data to guess what is happening in the living system. Subio Platform is technology-neutral, and it can handle any quantitative data conveying biological information. You can store various types of omics data generated over time and integratively analyze them with Subio Platform.

By the way, tons of omics datasets are available via the internet. Subio Platform supports semi-automatic import data from two popular large-scale databases, Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Someone analyzed the data already though; nobody has extracted all knowledge from the data yet. If you keep such data in your Subio Platform as the reference, your toolbox becomes more powerful.

Data import; Experimental data files

Importing An Excel Data Detail
Importing RNA-Seq Data (A Table of Counts or FPKMs or RPKMs) Detail
Importing Agilent Microarray Data Detail
Importing Affymetrix GeneChip Data Detail

Data import: Public datasets

Importing and analyzing public expression data sets from GEO. Detail
Importing TCGA RNA-Seq data Detail
A demonstration of analyzing TCGA-LAML miRNA-Seq data. Detail
Importing and analyzing TCGA methylation data Detail

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Sharing, co-working, discussing as a strategic education

Let's think you ask somebody to analyze data. You know that the real biological experiment is far from the perfect. So you, who know very well about the experimental design and assumptions, are needed to be involved in the decision makings during the data analysis. However, you are not often invited to the discussion and receive Excel and PDF files as a result. The reality is that analysis workflow is a black box, and you don't know how they made decisions and if they are right.

Even if you have raw data, it is not likely to happen that other analysts analyze the data to generate second opinions. If so, it never works as a quality-assurance of the data analysis.

So we developed implemented a new data sharing format named SSA containing all information about the dataset such as raw data files, gene annotation and other biological information, parameters and experimental information, final and intermediate results, data of associated experiments, reference papers. You can easily import the SSA file into Subio Platform by drag & drop. It allows you and other researchers checking the quality of data itself and analysis steps.

Additionally, you and collaborators can take over the analysis with Subio Platform of their own. Many people's eyes with different knowledge, skills or backgrounds drastically increase the chance of discovery than an individual perspective. Letting all members be involved in analyzing and discussing is the best education in the omics. It will nurture the significant strength of the team in the future. The active data sharing is the long-term strategy.

Learn more on movies.

The deep sharing of omics data by SSA file. Detail

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Plug-ins are not only analysis tools. What will they bring?

You cannot launch or log in to commercial data analysis software like GeneSpring after a license expires. You have to keep paying to access to your own data. It can be an obstacle for turning data to long-term assets, sharing data and fueling open discussions.

We sell plug-in licenses, and you can buy them for specific computers and periods. The big difference from other commercial tools is you still can see all the data even after a license expires, including analysis results created with plug-in tools. Moreover, we show above that you can continue intrinsically analyzing data without plug-ins. So do members who are received SSA files. Not all members must buy plug-in licenses. Most of them can join the analysis and discussions without plug-ins.

It will bring significant changes to your team.

  1. Biologists do not leave the data analysis tasks to bioinformaticians but work with them.
  2. Bioinformaticians do not use jargons or formula but try to explain visually.
  3. Many people join the discussion, and new ideas continuously emerge.

We think such an in-depth co-working environment is the fundament of new life science which is one of the most challenging frontiers for human beings.

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Learn more on movies.

Go to Plug-ins page.

Weak points of Subio Platform

Not Famous.

Almost no researchers know Subio Platform, comparing to Excel, R, and GeneSpring. You might worry about using such unknown software.

Subio set the policy that we do not spend money on sales or marketing, but on the development and user support. We do not hire salespersons, appear at trade shows or on media.

By avoiding spending our time and money on such things, we have been focusing on the development and improvement of Subio Platform. We have listened to users' feedbacks and implemented suggested idea. We are proud of the achievement of excellent usability as a result.

Even though Subio Platform is not very popular, you can use the output for publications. If you get comments from referees, our technical support helps your reasonable justifying or logical modifications. Many users use it for ten years, and there are a good number of publications citing our software.

Fewer Statistical Functions

The design policy of Subio Platform is that wet biologists can use it easily. So we select statistical functions very carefully.

Although "Highly sophisticated" statistical methods have strict restrictions on applicable conditions or assumptions, users tend to ignore them and wrongly use them. You know how much p-values are abused in the biological society. So we selected only general methods which can relatively widely be applicable.

We also eliminated methods which became nonsense in the history of the microarray data analysis. For example, z-score normalization used to be necessary due to the terrible quality of spotted dual-channel microarrays. However, it lost the value as microarray technologies mature. It became rather harmful because it cancels the difference of variance which is one of the relevant biological information.

Any methods have advantages and disadvantages, and the balance changes according to data characteristics. So it is dangerous to mimic a way of a textbook or paper. What we think most important is that users can choose the right methods to the data case by case. So we carefully eliminated means even if they often use in papers or textbook, rather than putting methods as many as possible.

However, we know sometimes you need those functions which we eliminated from Subio Platform. So you can work with both Subio Platform and R/Bioconductor together. Subio Platform with interactive viewers and R with a comprehensive collection of statistical methods are the most potent combination. If you cannot make R scripts, please consider our Software Development Service.

By the way, you might use commercial data analysis software having tools which Subio Platform does not have. And you might think you cannot move to Subio Platform because you need the tools. If so, please consider our Software Development Service. Although we charge on the development, it can be reasonable if you take into account license fees of the following years.

Learn more on movies.

Working with R/Bioconductor for further statistical analysis. Detail

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If you compare analysis software, you may focus on statistical features. However, they are not everything to make your work easy and efficient.

Items Subio Platform GeneSpring or
other commercial software
R + Bioconductor Excel + PDF
Visual aid with interactive operations
Statistical analysis tools, automation
To allow trials and errors,
or exploratory data mining
Data management
Data sharing, co-working
Cost of using by team
Technical support, training
Publicity, familiarity
Extensibility (functions, data size,
number of participants)

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System Requirements

  • Windows 10 (64-bit) / macOS 10.14 Mojave or later
  • 2 GHz or faster processor
  • 4 GB or more of RAM
  • 5 GB or more of available hard-disk space
  • 1024 x 768 display

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License Agreement and Privacy Policy

Subio Platform End User License Agreement version 1.4

This Agreement, and any new versions, between Subio and You, covers all Your use of Subio Platform and Plug-ins from any terminals. Unless You have another agreement directly with Subio that controls and alters your use or distribution of Subio Platform, the conditions of the applicable license agreements below apply to you.

1. Definitions.

this End User License Agreement, as may be renewed and/or amended from time to time.
You (or Your)
an individual or a legal entity exercising rights under, and complying with all of the terms and conditions of, this License or a future version of this License issued under Section2.8.
Subio Inc., headquartered in Amami island, Japan.
Plug-in Partner
an individual or a legal entity who develops and provides Plug-ins, which are distributed together with Subio Platform.
Subio Platform
Subio Platform, which Subio creates, owns and distributes exclusively. All Plug-ins depend on Subio Platform and they don't work alone nor even start without Subio Platform.
a software created by Subio or Plug-in Partners that works with, adds a variety of functionalities to and distributed together with Subio Platform. You will Activate a Plug-in to use it from a computer installing Subio Platform.
Activate (or Activation)
to authorize one computer to use a Plug-in for one year, by exercising a Serial Number.
Activation Key
a file created as a result of Activation, and it is necessary for Subio Platform to access to the Activated Plug-in.
Serial Number
Plug-in customers will purchase Serial Numbers from Subio or a reseller. Serial Number can be exercised only one time from a computer which is connected to the internet.

2. License and Restrictions

2.1 License of Subio Platform

Subject to the terms and conditions of this Agreement, Subio hereby grants You a limited, personal, non-commercial, non-exclusive, non-sublicensable, free of charge license to download, install and use Subio Platform on Your computer. You may use Subio Platform and Plug-ins anywhere like universities, research institutions, home or at work.

2.2 No Granting of Rights to Third Parties

You will not sell, assign, rent, lease, distribute, export, import, act as an intermediary or provider, or otherwise grant rights to third parties with regard to Subio Platform, Plug-ins or any part thereof.

2.3 No Modifications

You will not undertake, permit or authorize the modification, creation of derivative works, translation, reverse engineering, decompiling, disassembling or hacking of Subio Platform or any part thereof except to the extent permitted by law. Only one exception is that You are allowed reverse engineering of Subio.jar, Subio64.exe and jp.subio.plugins.b.jar.

2.4 Third Parties

Subio Platform incorporates and distributed together with software which are owned and controlled by third parties. Any such third party software falls under the scope of this Agreement. Any and all other third party software that may be distributed together with Subio Platform will be subject to You explicitly accepting a license agreement with that third party. You acknowledge and agree that You will not enter into a contractual relationship with Subio regarding such third party software and You will look solely to the applicable third party and not to Subio to enforce any of Your rights.

2.5 Use of Plug-ins

Subio Platform incorporates and distributed together with Plug-ins which are owned and controlled by Subio or Plug-in Partners. To use Plug-ins, You must purchase Serial Number for each Plug-in from Subio or resellers. If You buy them in Japan, You are also responsible for paying consumption tax. You will explicitly acknowledge the End User License Agreement of the Plug-in by its Activation. Once You have Activated a Plug-in, You may not change the expiration date and the authorized computer. You are not allowed to try, do nor inform any ways of Activation other than the instruction provided by Subio.

2.6 Prohibition of Plug-in Development

You are not allowed to create and distribute Plug-ins, unless You explicitly sign the Subio Plug-in Partner Agreement or an alternative agreement and comply with the terms and conditions thereof.

2.7 Exclusive Ownership

Any and all IP Rights in Subio Platform, contents of Subio website, all materials and documents which are created by Subio are and shall remain the exclusive property of Subio and/or its licensors. Nothing in this Agreement intends to transfer any such IP Rights to You.

2.8 New Versions of Subio Platform and Plug-ins

Subio, in its sole discretion, reserves the right to add additional features or functions, or to provide programming fixes, updates and upgrades, to Subio Platform and Plug-ins. Subio has no obligation to make available to You any subsequent versions of Subio Platform and Plug-ins. You may have to enter into a renewed version of this Agreement, in the event You want to download, install a new version of Subio Platform.

2.9 Suspension

Subio may, in its sole discretion and to the maximum extent permitted within Your jurisdiction, modify or discontinue or suspend Your ability to use any version of Subio Platform and Plug-ins, and/or disable any Subio Platform You may already have accessed or installed without any notice to You, for the repair, improvement, and/or upgrade of the underlying technology or for any other justifiable reason, including but not limited to, circumstances where You, at Subio's discretion, are in breach of this license, creating problems, possible legal liabilities, or engaging in fraudulent, immoral or illegal activities, or for other similar reasons.

3. Disclaimer of Warranties and Limitation of Liability

3.1 No Warranties

Installing Subio Platform enables You to manage, visualize and analyze Omics data. Subio cannot guarantee that You will always be able to get correct calculations and visualizations, nor can Subio guarantee that You can store data entirely and perfectly without inadequate modifications or losing integrity of the data. Subio Platform and Plug-ins are provided “as is” with no warranties whatsoever; Subio does not, either expressed, implied or statutory, make any warranties, claims or representations with respect to Subio Platform and Plug-ins, including, without limitation, warranties or conditions of quality, performance, non-infringement, merchantability, or fitness for use for a particular purpose. Subio further does not represent or warrant that Subio Platform and Plug-ins will always be available, accessible, uninterrupted, timely, secure, accurate, complete and error-free, nor does Subio warrant any quality of analysis with the Subio Platform and Plug-ins.

3.2 Your own Risk

Maintenance of Your computer and backup of Your data is entirely responsibility of You. You may be exposed to information security risks by using Subio Platform and Plug-ins with on-line resources. You further acknowledge and agree that the entire risk arising out of the use or inability to use Subio Platform and Plug-ins remains with You, to the maximum extent permitted by law. You understand, therefore, that You use Subio Platform and Plug-ins at Your own risk.

3.3 No Liability

The Subio Platform is being provided to You free of charge. You acknowledge and agree that Subio and its licensors and Subio staff will have no liability in connection with or arising from your use of Subio Platform and Plug-ins. Your only right or remedy with respect to any problems or dessatisfaction with Subio Platform and Plug-ins is to immediately uninstall and cease use of such Subio Platform and Plug-ins. Any indirect, incidental, special or consequential damages (including without limitation any loss of or corruption to data, interruption, computer failure or pecuniary loss) arising out of the use or inability to use Subio Platform and Plug-ins; and any loss of income, business or profits (whether direct or indirect) arising out of the use or inability to use Subio Platform and Plug-ins; any loss or damage which may be incurred by You as a result of;

  1. Any errors or incorrect calculations when using Subio Platform and Plug-ins;
  2. Any interruption or inability to use Subio Platform and Plug-ins or their functionalities due to network error or inaccessibility and unavailability of server;
  3. The suspension or termination of this agreement by You or by Subio for any reason; and
  4. The release or the decision not to release new versions of the Subio Platform and Plug-ins to you.

The limitations on Subio's liability to You described above shall apply whether or not Subio or the Subio staff has been advised of the possibility of such losses or damages arising.

3.4 Jurisdiction's Limitations

As some jurisdictions do not allow some of the exclusions or limitations as set forth above, some of these exclusions or limitations may not apply to You. In such event the liability will be limited to the maximum extent possible within the applicable legislation.

4. Miscellaneous

4.1 Entire Agreement

The terms and conditions of this Agreement constitute the entire agreement between You and Subio with respect to the subject matter hereof and will supersede and replace all prior understandings and agreements, in whatever form, regarding the subject matter. Nothing in this clause shall exclude or restrict the liability of either You or Subio arising out of fraud or fraudulent misrepresentation.

4.2 Partial Invalidity

If any provision, or any part of a provision, is found by any court or administrative body of competent jurisdiction to be illegal, invalid or unenforceable, and the provision (or part-provision) in question is not of a fundamental nature, the legality, validity or enforceability of the remainder of the terms and conditions of this Agreement (including the remainder of the term which contains the relevant provision) shall not be affected.

4.3 No Waiver

The failure to exercise, or delay in exercising, a right, power or remedy provided by this Agreement or by law shall not constitute a waiver of that right, power or remedy. If Subio waives a breach of any provision of the terms and conditions of this Agreement shall not operate as a waiver of a subsequent breach of that provision, or as a waiver of a breach of any other provision.

4.4 No Assignment

You are not allowed to assign the terms and conditions or any rights hereunder. Subio is allowed at its sole discretion to assign the terms and conditions or any rights hereunder to any third party, without giving prior notice.

4.5 Applicable Law and Competent Court

The terms and conditions of this Agreement shall be governed by and interpreted in accordance with the laws of Japan and shall be subject to the jurisdiction of the courts of the district of Kagoshima.

4.6 Language

The original English version of this Agreement may have been translated into other languages. In the event of inconsistency or discrepancy between the English version and any other language version, the English language version shall prevail.

You expressly acknowledge that you have read this agreement and understand the rights, obligations, terms and conditions set forth herein. By installing Subio Platform, You expressly consent to be bound by its terms and conditions and grant to Subio the rights set forth herein.

Your current operating system may not to be supported. Choose one from the below.

Request a Demonstration

We're happy to show you a demonstration of Subio Platform and Plug-ins via web meeting. Many are impressed by realizing the importance of watching data from multiple angles while many textbooks ignore this point. Please send a request with a convenient time and date for you.

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Customers' Opinion

Dr. John Mac Sharry

University College Cork, Lab Researcher

Dr. John Mac Sharry

It is an excellent user interface and the tutorials are brilliant.

Dr. Reidar Albrechtsen

Univ. of Copenhagen, Professor/Manager

Dr. Reidar Albrechtsen

This subio software platform is very easy to handle, even you include several hundred patients. The response is extremely fast compare with other similar softwares. Al...

Dr. Oleg Gusev

RIKEN, professor/manager

Dr. Oleg Gusev

Very flexible and powerful solution. Great technical support. VERY good advisory support!

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