University College Cork, Lab Researcher
Dr. John Mac Sharry
It is an excellent user interface and the tutorials are brilliant.
You got lost in an unfamiliar town and met a man who kindly showed the way.
You said "Thank you!" and followed the direction, but you couldn't find it.
You might wonder if he really knew it.
This is what is happening in the omics. Textbooks describe the steps in detail though; actually, nobody knows how to handle the omics data.
If you are looking for software for the following purposes, you can choose any software such as GeneSpring, Partek, Qlucore, R/Bioconductor. You can do it somehow.
However, if you think like below, Subio Platform is the solution.
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.
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.
|What you can do on Subio Platform without plug-ins||Detail|
|Scatter Plot (Measurement) View||Detail|
|Line Graph View||Detail|
|Scatter Plot (Samples) View||Detail|
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.
|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|
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 GEO or GDC databases. 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.
|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|
|Importing and analyzing public expression data sets from GEO.||Detail|
|Importing TCGA RNA-Seq data||Detail|
|Importing TCGA miRNA-Seq data||Detail|
|Importing and analyzing TCGA methylation data||Detail|
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.
|The deep sharing of omics data by SSA file.||Detail|
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.
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.
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.
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.
|Working with R/Bioconductor for further statistical analysis.||Detail|
If you compare analysis software, you may focus on statistical features. However, they are not everything to make your work easy and efficient. Please consider the following points.
|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 sharing, co-working|
|Cost of using by team|
|Technical support, training|
|Extensibility (functions, data size,
number of participants)
To download Subio Platform, enter your information below, agree to the terms and conditions, and click the download button.
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.
University College Cork, Lab Researcher
It is an excellent user interface and the tutorials are brilliant.
Univ. of Copenhagen, Professor/Manager
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...
Very flexible and powerful solution. Great technical support. VERY good advisory support!