Omics data is freely available from GEO, and analytical tools are also freely available from Bioconductor. Subio Platform fills missing parts, free omics data browser, repository and sharing tool. If you can use R, a full set for omics data analysis is ready.
But, still there is a bottleneck especially for biologists. So we work for them to remove obstacles.
For who can't program, we provide Plug-ins and programming service.
For who need intensive support, we provide on-line helpdesk or on-site consulting service.
For who want to make their software used by biologists. we help distribution with support facility.
We support both biologists and informaticians, and Subio Platform is supported by those people.

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Subio Inc. is a company headquartered in Tokyo, Japan.
We believe that omics is not just a trend, and will undergo enormous trials and errors for decades. So we'd like to work for mediating discussions and collaborations involving much more researchers. It will be a long long way and that's why we established a company as a self-sustainable organization.
Please see About Us.

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Subio Platform supports gene expression, miRNA, exon array, tiling array, CGH array, ChIP-chip data, or any other type of numeric table.
It doesn't support sequence or SNP data, but it can still work as a visualizer of statistics (e.g. LOD, D', p-value) with chromosomal locations.

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Subio Platform supports Affymetrix, Agilent, Illumina, NimbleGen or any type of microarray data as long as they're provided in tab-delimited text format.
For Affymetrix expression data, CEL files must be summarized into CHP files. CHP files in binary format are not acceptable. Please convert into tab-delimited text files or a pivot table.
See movie: Data Import

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Of course, you can. Please prepare both annotation table and experimental data in tab-delimited text format.

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Yes, please prepare BED or GFF format file. Also you need a gene table in BED or GFF format to create a Biological table and draw virtual chromosomes.
Learn more about BED or GFF formats.

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Yes, please download "SOFT formatted family file" of any GSE records. Subio Platform directly accepts it in "Create New Platform" or "Import Samples." Drag-and-drop a SOFT file onto those panels.

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Yes, it's absolutely free. You don't need any plug-ins to view ssa data. But, if you want to modify normalization or do additional analysis by yourself, we appreciate you consider purchasing plug-ins.

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It depends on data size (#genes x #samples.) We suggest you use a PC with 2GB RAM at minimum. If you're going to buy a PC, we recommend 64-bit system with large memory like 8GB or more.

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It depends on memory (RAM) that your PC has. A 32 bit system can manage up to 3GB RAM. Although it is very difficult to say the number exactly, the tentative limitations of one Series with 3GB RAM are as following.

• ~ 80 samples with 25,000 probes.
• ~ 40 samples with 50,000 probes.
• ~ 8 samples with 250,000 probes.

But we DON'T recommend you try such upper limitations, because system will be unstable and erroneous when it runs short of memory. If you want to analyze a large data set, please consider introducing 64 bit system with large memory like 8GB or more. "Subio Platform for 64bit" can stably handle large data sets with large memory.

Performance is another issue. For better performance, high-spec machine with faster CPU is the answer.

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There are three types of installer, ".zip" for Windows 32-bit and 64-bit, and ".dmg" for Mac. Please make sure that you've downloaded an appropriate version.
You need to save it on your local machine before you execute it. If you're Windows users, please make sure that you're not just browsing inside of the zip. Right-click on the zip file and expand (unzip, decompress) it.
On the other hand, Mac users are requested to double-click on dmg file to expand, and then double-click on "Subio Platform for Mac.pkg” to launch the installer.

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Case 1 - Failure.of Installation

For Windows Users,
Please make sure that you have saved the installer and unzipped it. If you don't see the Subio.exe icon in the Subio Platform directory, it's likely you're just browsing inside the zip file without unzipping it.
And make sure that you put Subio Platform folder in personal directories (e.g. MyDocuments or Desktop) and avoid system directories (e.g. C:\ or ProgramFiles.)
Moreover, 64-bit Windows users must avoid 2 byte characters in the absolute path of Subio Platform folder. Check your login name and folder names.

For Mac Users,
Please make sure that you've downloaded .dmg file and complete installation by double-clicking "Subio Platform for Mac.pkg” to run the installer.
For detailed instructions, please see "Getting Started."

Case 2 - Out Of Memory:

Subio Platform consumes lots of memory just because omics data is huge. If your PC has only 1GB memory or less, it's likely to get Out Of Memory error. The solution is to add more memory card, or to install into other PC with large memory.
If your PC has enough memory, we advise you restart your PC.

Case 3 - Failure on loading Series:

When you launch Subio Platform, it automatically loads the last loaded Series or imported Series. If the Series data is too large for you PC or has something wrong, Subio Platform may fail to start up. Please delete "subio.settings" file from the Subio Platform folder to avoid initial loading of Series. You can load a Series after Subio Platform opens.

Case 4 - Failure of creating Java VM:

Your OS may not allow creating Java VM especially in 32-bit Windows environment. If you get such error message, edit the -Xmx option of vmargs.txt in the Subio Platform folder. For detailed instructions, please see "Getting Started (PDF)."

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Subio Platform saves data when you create objects or finish editing. Even if Subio Platform friezes, you can see all the saved data after you restart Subio Platform.
Then, please send a tech report file to support@subio.jp. You can export it by simply selecting "Export Tech Report" under Help menu. We appreciate your cooperation.

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To backup all data, simply make a copy of entire subioplatform folder on another disk or a removal media. Please notice that it may take long time. It's also good idea to export Series Archive (ssa) files to backup particular Series within a short time.

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You can use full functions of Subio Platform for absolutely free of charge.
On the other hand, you need to buy a license to use a Plug-in. We're sorry but we don't provide free demo. Please see movies to know learn what you can do with Plug-ins, or contact to helpdesk. We'll show you what you can do, or can't do, with Subio Platform via web meeting.
See Basic Plug-in Movies and Genpac Plug-in Movies.

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First, you have to load a Biological Table to make Genome View activated. After you load one, you can see virtual chromosomes in the chromosomes tab.
Still you don't see anything on Genome View, please make sure that the current Platform has location information (minimum requirements are chrom, chromStart and chromEnd columns), and chromosome names of Platform and Biological Table are exactly same.
Then you have to drag a rectangle to specify a proper region, where Genome View displays, in the chromosomes tab.

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There are several options. First, you can work with R to achieve a task-specific or statistically advanced analysis. Second, we will create scripts or programs for you. Although we charge you for services, it won't be very expensive. Please consult our Helpdesk. Third, if you don't hurry, you can request features for future versions. Please post on the User Forum with "feedback" tag, or let us know from Contact Us.

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Activation is to authorize one nodelock computer from which you use Plug-ins. You need to purchase a Serial Number from this web site, and then exercise it on the PC to activate the Plug-in.
For instruction of activation, please see "Data Import And Analysis Guide (PDF)." There is a section titled "Serial Number and Activation."

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To exercise your Serial Number to activate Plug-ins on your PC, Subio Platform on the PC needs to access to the license server via Internet. If your PC is not connected or your network doesn't allow such connection, activation fails.
In such cases, please save a error log file and send it to our helpdesk. We'll create a license file for you and send it back to you.

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No. you can't change PC once you've activated a Plug-in, because activation authorizes one PC which you use the Plug-in. Please consider purchasing additional Serial Number if you want to use a same Plug-in from another PC.
Or you can export Series Archive (ssa) file including analysis result, and import it on another PC. You don't need Plug-in to view it.

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Please select "Plug-in Manager" under the Plug-in menu. You can see the expiry date on the panel.

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Genpac database supports the following 11 organisms.
H.sapiens, M.musculus, R.norvegicus, D.rerio, D.melanogaster, C.elegans, A.thaliana, S.cerevisiae, S.pombe, B.subtilis, E.coli.

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After you exercise your Genpac Plug-in Serial Number, still there is something you have to do in the Preference panel.
Open "Plug-in Manager" and then open Preferences [Genpac Plug-in] panel. In this panel, you have to complete "Sign-up for Genpac" with your Genpac Registration Password which is sent you with the Serial Number.
Finally, open Data Manager and click "Select Symbol Column" button, and select a column containing Gene Symbol or Entrez Gene ID.
For detailed instructions, please see "Data Import and Analysis Guide (PDF)."

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All Plug-ins are already included in Subio Platform, so we don't send any additional software. Only you need to use is to activate by exercising a Serial Number. Please purchase a Serial Number from this web site. Click on "Add to Cart" button, and specify number of licenses. You can checkout by a credit card or PayPal. After you complete transaction, you'll recieve an emal containing Serial Numbers.

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Yes. After you click on the "Proceed to Checkout" button of shopping cart, please find a description like
"Don't have a PayPal account?
Use your credit card or bank account (where available). Continue"
Then click "Continue" to complete your order by a credit card.

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Your Serial Number will be sent by email which you input on the checkout page. Please see your email box and find a message titled "Subio Plug-in Serial Number" from payment@subio.jp. If you don't see it, please check if your spam filter wrongly move or delete the message.

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Serial Number itself won't be expiring. Once you exercise it, your license will expire after one year.

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Starter Package includes one Basic Plug-in and 5 hour service. This is suitable for who has no experience of omics data analysis and needs analysis result right away. We support the fastest and stress-free introduction for you. Only you need to do is to send us an annotation table and microarray data files in tab delimited text file.

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If you purchase multiple Serial Numbers of one type of Plug-in, we'll refund to your credit card as following the discount rate bellow. Serial Number won't be expiring, so you can use this discount program for multi-year discount.

• No discount for 1st and 2nd.
• 5% off for 3rd to 9th.
• 7% off for 10th to 29th.
• 10% off for over 30th.

For example, when you buy five, you get 5% off for 3 Serial Numbers.

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Of course, we're willing to help you. It's absolutely free for trouble shooting and instructions within 30 min. It's done within 30 min in most cases.
If we think it will take longer, we'll offer you to buy helpdesk tickets. As helpdesk services, we advise how to operate Subio Platform and Plug-ins or related things.

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Yes, we'll help you as a Professional Service at 10,000 JPY (about 100 USD) per hour. For example,
- second opinion for your (or other's) analysis.
- about web tools and format/ID exchange.
- about programming or system development.

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Any sign-up user can post a topic or comment to Forum. If not yet, please go to Sign-up.
Then click "Post a New Topic" at upper-right, or click "Add comment for this topic" in each topic page.

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Only you need is a PC connected to Internet and a headset. For more information, please see https://www2.gotomeeting.com/en_US/pre/support.tmpl.

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No, we don't have toll free number. If you dial to the number on the Helpdesk page, you'll be charged a regular international call rate. You can call via Skype for free.

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We're sorry but we plan only Japanese seminars in 2010. But we will provide an webinar in English for you at 3,000 JPY (about 30 USD) per hour, if you request. For Subio Platform operations, it will take 1 - 2 hours. If Plug-ins work flow is included, it will take 5 - 6 hours in total. You need a headset to talk over Internet. Please Contact Us for more information.

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