About Subrium

Subrium is a web-based repository for multi-omics data sets. It's not only storage, but a visualization tool so that you can browse the landscape of the lots of and a variety of omics data sets from different technologies like gene expression arrays, CGH arrays, ChIP-chip, methylation arrays, RNA-Seq, ChIP-Seq, Methyl-Seq and more.

Because nobody knows how to mine the biological knowledge from data, the omics data is still juicy even after someone applied an approach on it. Omics data shouldn't be disposable. It can be your long-term asset.

If you have the data as Excel file or other ways you can't instantly access to it, you might be missing opportunities. Don't treat data like frozen cells in refrigerators. One of clear advantages of omics data is you have already measured the gene, which you didn't focus on it before. At the moment you need the data, get it instantly from the repository before you spoil the idea. Subrium provides a hot access to your data via a web browser.

Subio's Products and Services Data Analysis Service(for assessment) Premium Analysis Service FASTQ File Processing Service Data Analysis Service Plug-ins Subio Platform Subrium Balloons are designed by Freepik.

Simple 3 Steps

Step1: Extract data sets.

Search data sets in which you're interested, by keywords or tags.

Step2: Select genes.

Search genes by symbol or keywords. You can browse up to 5 genes at the same time.

Step3: View charts.

The selected data sets are listed, and you can browse patterns of the genes in line charts or gene views, which is organized by relative locations from TSS per gene.

Click on a title on black ribbons to display details of the data set. You may find download links of the SSA files so that you reanalyze them with Subio Platform on your computer by yourself.

Try Subrium

Overviewing A Lot of Multi-Omic Data Sets on Subrium

Subrium is a web system to build a repository for massive multi-omics data sets. Also it allows you to overviewing patterns of gene/miRNA expression, protein binding or epigenetic status or copy numer variations of the selected genes.

Case Study

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Technical Information

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Why Subrium?

For sharing omics data without making black-boxes.

We think it doesn't make sense to keep log ratios or p-values even at the first level of accessing your omics data. It's very important to keep raw data to enables reanalysis in the future, but it may not be practical as data sizes are enormously growing. So we think it's realistic to have a repository of quasi-raw data with instant visualization, and keep a link to the raw data.

The other point is providing SSA files so that members can download and reanalyze on their computer by themselves. But it can generate many versions of SSA files. That's why Subrium is needed as a central source of the official SSA files for teams.

For turning omics data into your assets.

Normalization or standardization has been a problem to integrate or compare among data sets in one repository. Different technologies, protocols, sources and technicians generate different characteristics of raw data, and no statistical method can cancel such differences. New technologies keep emerging and different types of data will be added in the future.

Our solution is simple. (Quasi-)raw data are comparable inside datasets, but independent among data sets. Human brain can bridge as watching patterns in multiple charts. For example, you can understand a relationship between methylation and gene expression patterns of a gene in respective charts. You don't need to merge them into one as oddly normalizing such different types of data. In this way, you can store your expression microarray data in the past and up-coming Methyl-Seq or proteomics data in the future, and overview them to grasp the landscape.

The other point is you have limited knowledge about mechanism of biological phenomena, and new information will be added continuously. So it's just impossible to focus on all interesting points right now. All you can do is preparing data as searchable and visible for the time comes. You can access to your legacy data anytime via web browser. Don't put it in the refrigerator. Having such a database was very expensive, though. The cost of Subrium is pretty reasonable to do it.

For strengthening your hypotheses.

The demonstration movie above tells you it's only by chance if you have clearly differentially expressed patterns or not. Even if your data set doesn't show clear difference at statistically significant level, maybe similar data sets from publicly available data sets support your hypothesis. Or maybe you shouldn't conclude only on your data, because it may specific to the data set. Confirming with other data sets may save your time and money to confirm by eliminating false positives. It's like more promising way than statistical approach. But having all public data sets is just annoying. You should have only related data sets and annotate them on the context of your study. We think it's worth having such a custom-made test tool, not a whole GEO data sets.

4 Plans of Subrium

Shared Plan Cloud Limited Plan Cloud Plan In-House Plan
Server *1 Shared Cloud
Dedicated Cloud
In-House Server
User Account *2 Administrator
Administrator (Limited)
Curator
Member
Guest
Security

*1 Server

Shared Cloud
A shared server on cloud which is accessible to everyone. But we can add password-protected private series on it, too.
Dedicated Cloud
We setup a dedicated instance on Amazon Web Services.
In-House Server
We setup an instance on a server at your site.

*2 User Account

Administrator
The administrator can add public data sets, and can create groups by inviting curators.
Administrator (Limited)
The administrator can add public data sets, but cannot create groups.
Curator
Curators can add group-private data sets and invite members to their own groups.
Member
Invited members can browse group-private data sets.
Guest
All visitors can browse public data sets without sign-in.

Price List

USD EUR JPY

Shared Plan

Upload A Data Set to The Subrium Shared Server:

To visualize your own or public data set on Subrium, please order this service to have us import it as a private series or a public one. Private series aren't visible to other users or guests and you need to sign-in to browse them. Public series are visible to everyone without sign-in.

We accept SSA file or SOFT file for this service. If you have raw data or any other format files, we convert them into SSA/SOFT file as Data Analysis Service.

Price
Uploading Private Series 100 USD / Series
Uploading Public Series 50 USD / Series

Cloud Limited Plan

We setup a dedicated instance of Subrium on the cloud. A part of administration function is restricted, and you cannot create user groups.

1st year Following year
License 1,000 USD 900 USD
Initial fee 500 USD 0
Hosting fee 500 USD 500 USD
Total 2,000 USD 1,400 USD

Cloud Plan

We setup a dedicated instance of Subrium on the cloud.

1st year Following years
License 2,000 USD 1,800 USD
Initial fee 500 USD 0
Hosting fee 500 USD 500 USD
Total 3,000 USD 2,300 USD

In-House Plan

We setup an instance of Subrium on a server at your site. It is possible to use without connecting to the internet.

1st year Following years
License 6,000 USD 5,400 USD
Initial fee 5,000 USD 0
Hardware Install by Yourself 0
On-site support Travel Expense *3 Travel Expense
Total 11,000 USD 5,400 USD
  • *3 Travel expenses will be determined on the contract.

Shared Plan

Upload A Data Set to The Subrium Shared Server:

To visualize your own or public data set on Subrium, please order this service to have us import it as a private series or a public one. Private series aren't visible to other users or guests and you need to sign-in to browse them. Public series are visible to everyone without sign-in.

We accept SSA file or SOFT file for this service. If you have raw data or any other format files, we convert them into SSA/SOFT file as Data Analysis Service.

Price
Uploading Private Series 100 EUR / Series
Uploading Public Series 50 EUR / Series

Cloud Limited Plan

We setup a dedicated instance of Subrium on the cloud. A part of administration function is restricted, and you cannot create user groups.

1st year Following year
License 1,000 EUR 900 EUR
Initial fee 500 EUR 0
Hosting fee 500 EUR 500 EUR
Total 2,000 EUR 1,400 EUR

Cloud Plan

We setup a dedicated instance of Subrium on the cloud.

1st year Following years
License 2,000 EUR 1,800 EUR
Initial fee 500 EUR 0
Hosting fee 500 EUR 500 EUR
Total 3,000 EUR 2,300 EUR

In-House Plan

We setup an instance of Subrium on a server at your site. It is possible to use without connecting to the internet.

1st year Following years
License 6,000 EUR 5,400 EUR
Initial fee 5,000 EUR 0
Hardware Install by Yourself 0
On-site support Travel Expense *3 Travel Expense
Total 11,000 EUR 5,400 EUR
  • *3 Travel expenses will be determined on the contract.

Shared Plan

Upload A Data Set to The Subrium Shared Server:

To visualize your own or public data set on Subrium, please order this service to have us import it as a private series or a public one. Private series aren't visible to other users or guests and you need to sign-in to browse them. Public series are visible to everyone without sign-in.

We accept SSA file or SOFT file for this service. If you have raw data or any other format files, we convert them into SSA/SOFT file as Data Analysis Service.

Price
Uploading Private Series 10,000 JPY / Series
Uploading Public Series 5,000 JPY / Series

Cloud Limited Plan

We setup a dedicated instance of Subrium on the cloud. A part of administration function is restricted, and you cannot create user groups.

1st year Following year
License 100,000 JPY 90,000 JPY
Initial fee 50,000 JPY 0
Hosting fee 50,000 JPY 50,000 JPY
Total 200,000 JPY 140,000 JPY

Cloud Plan

We setup a dedicated instance of Subrium on the cloud.

1st year Following years
License 200,000 JPY 180,000 JPY
Initial fee 50,000 JPY 0
Hosting fee 50,000 JPY 50,000 JPY
Total 300,000 JPY 230,000 JPY

In-House Plan

We setup an instance of Subrium on a server at your site. It is possible to use without connecting to the internet.

1st year Following years
License 600,000 JPY 540,000 JPY
Initial fee 500,000 JPY 0
Hardware Install by Yourself 0
On-site support Travel Expense *3 Travel Expense
Total 1,100,000 JPY 540,000 JPY
  • *3 Travel expenses will be determined on the contract.

Prices in USD or EUR will change according to exchange rate without previous announcement.

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