- Is Subio Platform really free? Why?
- Who are Subio?
- What kind of omics does Subio Platform support?
- Can I import my microarray (e.g. Affymetrix, Agilent, Illumina, NimbleGen, etc.) data into Subio Platform?
- Can I import custom array data?
- Can I import tag count data from deep sequencing (ChIP-seq or RNA-seq)?
- Can I reanalyze GEO data sets on local PC?
- A co-worker gave me .ssa file(s). Can I see the data without paying?
- How much memory does my PC need?
- How many sample can it analyze at a same time?
- The Installer of Subio Platform doesn't work. How can I solve?
- Subio Platform fails to launch. How can I solve?
- Subio Platform shuts down suddenly and unexpectedly. Can I recover my work in the session?
- How can I backup my data in Subio Platform?
- Can I get demo version of Subio Platform?
- I don't see anything on the genome view of Subio Platform. Why?
- There are something I can't do with Subio Platform nor Plug-ins. What can you do for me?
- What is Activation? What is Serial Number?
- I couldn't activate a Plug-in with my Serial Number. How do you help me?
- Can I change a PC from which I'm currently using my Plug-in to new one? Can I use my Plug-in license from another PC?
- When will my Plug-ins expire?
- What organisms does Genpac Plug-in support?
- My Genpac Plug-in doesn't work. How can I solve?
Order and Payment
- Can I get a support of Subio Platform, even if I don't buy any Plug-ins?
- Can I ask general questions about omics data analysis, actually not about Subio Platform or Plug-ins?
- How can I post a topic/comment to Forum?
- What do I need to get a support via internet conference?
- Do you provide a toll-free number?
- Do you have training programs of data analysis using Subio Platform?
Thousands of omics data are now freely available from GEO, and analytical tools are also freely available from Bioconductor. Subio Platform fills the missing part, free data management system with rich browser and data sharing functionality.
But, still there is a bottleneck of using statistical tools which requires programming skills, especially for wet researchers. So we work for them to remove the obstacles.
- - For those who can't program, we provide Plug-ins and programming service.
- - For those who need intensive support, we provide on-line helpdesk or on-site consulting service.
- - For those who want to make their software used by many biologists. we help distribution with user support capability.
Subio Inc. is a company headquartered in Tokyo, Japan.
We believe that omics is not just a trend, and will be undergoing enormous trials and errors for decades. So we'd like to work for mediating discussions and collaborations involving much more researchers of the new life science. It must be a long long way and that's why we established a company as a self-sustainable organization, not a government-sponsored project.
Please see About Us.
Subio Platform supports any types of microarray derived gene expression, miRNA, exon, tiling, CGH, ChIP-chip data. Also it supports NGS derived RNA-seq or ChIP-seq data and MS derived proteomics or metabolomics data. It can be said that it accepts any other type of numerical data which you have in Excel format.
Can I import my microarray (e.g. Affymetrix, Agilent, Illumina, NimbleGen, etc.) data into Subio Platform?
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 transformed into CHP (txt) files or a pivot table. CHP files in binary format are not acceptable.
See movies of data import: Data Import
Of course, you can. Please prepare both annotation table and experimental data in tab-delimited text format.
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.
See a movie: Import ChIP-Seq Data
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.
See a movie: Import GEO data
Yes, Subio Platform is a free viewer and you can browse ssa data for absolutely free. You don't need any plug-ins to view ssa data. But, if you want to modify normalization or run additional analyses by yourself, we appreciate you consider purchasing plug-ins.
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.
It depends on memory (RAM) installed in your PC has. A 32 bit system can manage up to 2 - 4 GB RAM. Although it is very difficult to say an exact number, 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 limits, because system will be unstable and erroneous when it's running short of memory. If you want to analyze a large data set, please consider introducing 64 bit system with large memory like 8 - 32 GB. "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 and storage is the solution.
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 to select the option to unzip the file.
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.
Case 1 - Failure of Installation:
Installer files can be deficient. Check the file size.
Please install as following the instruction on the Getting Started Guide (PDF).
For Windows Users,
Make sure to unzip the download file. If you don't see the Subio.exe icon in the extracted folder, it's likely you're only previewing without unzipping.
The extracted folder should be placed under personal directories (e.g. My Documents or Desktop) rather than system directories (e.g. C:\ or Program Files.)
Case 2 - Failure of writing in the install directory:
Subio Platform fails to launch if your account doesn't have write permission to the install directory and its sub directories. If you don't see any error log files in the install directory, it’s likely to be this case. Give write permissions to your account, or place the install folder under your user directories and then change the access right.
Case 3 - Out of memory error:
Subio Platform requires memory according to data size. If your PC/Mac has only 1GB memory or less, it's easy to cause out of memory errors. The solution is to add memory cards, or to use Subio Platform on a PC/Mac with large RAM.
If you see memory errors with a PC/Mac with large memory, we advise restart the box.
Case 4 - Failure of creating Java VM:
32-bit Windows causes an error of not creating Java VM, if you set too big java heap size. You have to edit vmargs.txt to reduce –Xmx size.
See Getting Started Guide (PDF) for more information.
Case 5 - Failure on loading Series:
Subio Platform automatically loads a Series as launching. If the Series data is too large for your PC/Mac or has something wrong, Subio Platform fails to start. Please delete "subio.settings" file in the install directory and then launch it.
It is likely to cause a critical error if you try to load the Series data. Please export the Series into an SSA file and send to us. We might be able to fix the problem and return it.
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 our helpdesk. You can export it by simply selecting "Export Tech Report" under Help menu. We appreciate your cooperation.
To backup all data, simply make a copy of the 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.
Subio Platform for absolutely free. If you want to use Plug-ins, you need to buy serial numbers. And 10 days free trials of Plug-ins are available.
Free Trial of Plug-ins: https://www.subio.jp/products/trial
Firstly, you have to load a Biological Table to make the genome view active and virtual chromosomes created in the chromosomes tab.
Still you don't see anything on the 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 matches exactly.
Then you have to drag a rectangle to specify a proper region, where the genome view displays, in the chromosomes tab.
Please don't hesitate to contact our helpdesk, if you can't solve a problem.
There are several options. First, you work with R to run highly-complicated statistical analysis. Second, we create R scripts or programs for you as a chargeable service. Please consult our helpdesk. Third, if you don't hurry, you can send the features request to our helpdesk. Posting it on the user forum with "feedback" tag is a good idea, because it is likely to be prioritized if it gets positive comments from other users. Of course you can privately send a message from Contact Us.
Activation is to authorize one computer to use Plug-ins. Please buy a Serial Number from this web site, and then exercise it on the PC or Mac to activate.
For instruction of activation, please see "Data Import And Analysis Guide (PDF)." There is a section titled "Serial Number and Activation."
To exercise your Serial Number to activate Plug-ins, Subio Platform accesses to the license server through the internet. If the PC is not connected to the internet or network administrator doesn't allow connecting, the activation must fail.
In such cases, please save the error log file and send it to our helpdesk. We'll create a license file and send it back to you.
Can I change a PC from which I'm currently using my Plug-in to new one? Can I use my Plug-in license from another PC?
No. you can't change PC once you've activated, because it creates a license file being valid for one year.
Only we can do is issuing another Serial Number at a certain handling fee. We charge 1/10 of price per month after the purchase to set off. For example, you buy a Basic Plug-in on 20th January and your PC breaks 10th March, we will reissue a new Serial Number at a cost of 50,000 *3/10 = 15,000 JPY. When you get the reissued Serial Number, you must not use the old license.
Please contact to helpdesk for an estimate.
*Please be noticed that we can't reissue Genpac Plug-in's Serial Number, because it's not our asset but Nalapro Technologies Inc.'s.
Please select "Plug-in Manager" under the Plug-in menu. You can see the expiry date on it.
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.
After you exercise your Genpac Plug-in Serial Number, still there is something you have to do in the Preference panel.
Select "Preferences" under the "Plug-in" menu, and open the "Genpac Plug-in" tab. You have to complete "Sign-up for Genpac" with your Genpac Registration Password which is sent you with the Serial Number by an email.
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)."
All Plug-ins are already included in Subio Platform, so we don't send any additional software. If you want to use a Plug-in, please purchase a Serial Number, and activate the Plug-in by exercising the Serial Number. To purchase Serial Numbers of a Plug-in, click on the "Add to Cart" button and set number of licenses in a shopping cart, and then check out with your credit card or PayPal account. After you complete the transaction, you'll receive an email containing Serial Numbers.
Yes. After you click on the "Proceed to Checkout" button of shopping cart, please find a message saying
"Don't have a PayPal account?
Use your credit card or bank account (where available). Continue"
Then click "Continue" to check out with your credit card.
Yes, we can send the invoice in the following currencies from PayPal.
USD, EUR, GBR, AUD, BRL, CAD, CZK, DKK, HKD, HUF, ILS, MXN, TWD, NZD, NOK, PHP, PLN, SGD, SEK, CHF and THB.
You can pay by PayPal or credit cards. The prices in foreign currencies vary according to the exchange rate.
Please send a message from Contact Us.
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". If you don't see it, please check if your spam filter wrongly moves or deletes the message. Still you can't find it, please contact to our helpdesk.
Serial Number itself won't be expiring. Once you exercise it, your license will expire after one year.
Yes, we're willing to help all Subio Platform users. It's absolutely free for trouble shooting and training of Subio Platform.
Can I ask general questions about omics data analysis, actually not about Subio Platform or Plug-ins?
Any sign-up user can post a topic or comment to the User Forum. If you have not done yet, please go to Sign-up page.
Then click "Post a New Topic" at upper-right, or click "Add comment for this topic" in each topic page.
What you need is a PC, which is connected to the internet and Subio Platform is installed, with an audio device like a headset or a mic & speaker. If you can talk over Skype, your environment must be perfect.
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. But you can call via Skype for free.