Subio Platform

Subio Platform is a data analysis software for RNA-Seq, microarray data. And it works fine for the integrative analysis of multi-omics data sets regardless of the type or manufacturer of the measurement system.

What to learn;

Command Operation?

Or Data Analysis?

  • Subio Platform downloads: > 12,000
  • Plug-ins installations: > 3,000
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FREE Download

To download Subio Platform, enter your information below, agree to the terms and conditions, and click the download button.

System Requirements

  • Windows 10 or 11 (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

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 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

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 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.

What you can do with Subio Platform

As you know, R (Bioconductor) and Python are powerful statistical tools widely used in this field. But researchers also need a set of various utilities to challenge the complexity of life science. Subio Platform offers the whole without a pricy license fee like GeneSpring. Plug-ins are not free but reasonable compared to free bioinformatics tools because you must pay the high implicit learning- and maintenance-cost. Moreover, you might be surprised that you can accomplish almost all analyses without plug-ins for preliminary analysis.

We provide lots of free information about usage, tutorials, troubleshootings, and case studies from this website so that you can learn by yourself. We also offer charged services of online training and outsourcing data analysis services.

Now please let us introduce you Subio Platform software.

Graphical Operation

The intuitive interactive data browser is essential for understanding.

If you drag on a chart, you'll instantly know what those genes are. Likewise, if you reversely search for gene names or keywords, you'll immediately see how those genes behave on the graph. In such ways, it is much easier to understand the data than to operate with commands. And all views are associated so that you can grab the data from multi-angles.

The omics data is so complex that you must fully use such sophisticated graphical aids because understanding data is fundamental. Unfortunately, many training programs about omics data analysis tend to underestimate viewing data while focusing too much on statistical commanding. However, you have to understand the data adequately first of all.

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

Details of Normalization and Pre-processing;

How do you find a proper sequence of normalization and pre-processing? Detail
Details of normalization and pre-processiong for RNA-Seq dasta; Detail
Why do you turn signals into log ratios? Detail
Why do you better avoid "sophisticated" normalizations? - A lesson from RMA. Detail
Why shouldn't you use Z-score normalization? Detail

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Supporting Various Types of Omics Data

Undoubtedly, it would be a great help if you have a database of your own experimental data with massive omics data sets available from the web like GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas). Indeed, nobody can thoroughly extract biological knowledge from omics data. So the legacy data sets are still juicy.

However, handling data sets in various formats generated by multiple systems might take time, and of course, it requires experience and skills. If it's hard, we can offer Data Analysis Service.

Supporting file formats;

  • tab-delimited text files (RNA-Seq count/TPM/FPKM, Microarray signals, DNA methylation ratio, proteomics abundances, etc.)
  • RNA-Seq FASTQ files
  • BED/WIG/Bigwig files (ChIP-Seq, ATA-Seq, etc.)
  • And more.

Details of importing data files;

Importing RNA-Seq FASTQ files Detail
Importing text file(s) of RNA-Seq count/TPM/FPKM Detail
Importing Agilent Technologies' microarray data files Detail
Importing Thermo Fisher's (ex. Affymetrix) GeneChip data files Detail
Importing legacy data in Exel worksheets Detail
Importing Bigwig files Detail

Details of importing data sets from the web;

Importing microarray data sets from GEO Detail
Importing TCGA RNA-Seq data sets Detail
Importing TCGA miRNA-Seq data sets Detail
Importing TCGA DNA methylation array data sets Detail

If you are still looking for the file type you want to analyze, or if you face errors in importing files, please find solutions on the web or consider charged online training.

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Instant And Deep Sharing of Omics Data

Human beings have yet to learn how to interpret omics data. So we absolutely need much more discussion involving biologists, not only bioinformaticians. However, it takes work for them to participate due to the unfriendliness of bioinformatics tools.

If you export the SSA file from Subio Platform, you can hand the raw data with final and intermediate results in a single file. Your collaborators rebuild the analysis environment only by importing the SSA file, and they can instantly start examining analysis results and re-analyzing from their perspectives. It enables deeper discussion and collaboration than PDF- and Excel-based handovers.

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Small License Fee Enables Sustainability

Although open-source and free software have supported bioinformatics, the problems of such tools also become apparent. For example, operating systems and middleware must keep updated to counter various threats. On the other hand, bioinformaticians abandoned their tools without maintenance, and it caused problems that researchers couldn't use the same software in their long-running studies. This problem happened because bioinformaticians' evaluations are biased toward developing new tools, and there is little incentive to maintain existing tools.

To solve this problem, we established Subio as an autonomously sustainable operating entity that receives a small license fee from plug-in users. Since the advent of microarrays, various measurement devices and analysis software have appeared and disappeared, but Subio has kept running without wavering from its original purpose. As a result, it becomes the only stable software platform to accumulate and integrate new and legacy omics data for analysis.

Subio also proposes to bioinformaticians an alternative distribution of their tools to keep them maintained.

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Integrate with Bioinformatics Tools in R or Python

Subio Platform offers valuable utilities and interactive GUI that R or Python don't provide, but conversely, it doesn't offer advanced statistical features. However, you can easily output data from Subio Platform and let R or Python tools take over the statistical tasks.

Subio Platform and bioinformatics tools written in R or Python complement each other rather than compete. By combining them, you can build a comprehensive analysis system at a very reasonable cost.

See the last part of this movie.

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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!

Read more customers' comments.

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