12 Ways Omicsoft Can Improve Your Handling of Genetic and Genomic Data

SPEED

Omicsoft specializes in speeding up your everyday tasks when it comes to genomic and genetic data.  With other solutions, you can expect queries to take minutes, if not hours.  For most analyses and queries, Omicsoft’s products take seconds to complete.  We have implemented a number of proprietary techniques that allow analyzing your data and then accessing that data to occur at the fastest speeds.  Do you have thousands of samples and millions of rows in your data?  This is never a problem with Array Studio and Array Server.  Most functions can even be performed with a regular laptop (1GB RAM recommended).

Statistics

Omicsoft’s products have been designed and optimized by statisticians.  For expression data, the General Linear Model provides the framework for most analysis on the market. All major analysis is benchmarked with either SAS® or R, including the automatic generation of equivalent SAS code for comparison purposes. For genotyping data, Array Studio comes with the most complete statistical package on the market (including support for imputed data, dose data, quantitative traits, categorical traits, survival traits, repeated measure traits, and more).  For any genotype analysis that cannot be performed within Array Studio, this information can be easily imported (including direct importing from PLINK).  Array Studio also includes modules for analyzing copy number data, CGH data, methylation data, ChIP on ChiP data, and more.  It also includes numerous modules for clustering, segmentation, and classification for a variety of data types.

Array Server provides the power to easily do a list analysis (compare the results of a single project across thousands of other public and private projects) and return results showing overrepresentation, perform a meta analysis (find overlapping regions or genes of significance between projects), and CNV Region Analysis (find overlapping regions of copy number variation across projects).

Visualizations

Omicsoft’s visualizations are advanced and have been compared positively to products such as Spotfire®.  With over 50 unique views designed for genetic and genomic data, Array Studio and Array Server offer the widest range and most customizations of visualizations on the market.  Omicsoft boasts an industry leading interactive genome browser that is used with nearly all data types.  Simple one-click export to PowerPoint and the ability to save all views as PDF, JPG, BMP, TIFF, and more make it the easiest program in the market for exporting your visualizations to a format suitable for presentations and publications.

Interactivity

All of Omicsoft’s modules and visualizations are completely interactive.  While static charts are nice for presentations and publication, the ability to interact with your data is essential for data exploration.  Omicsoft’s “L-Shaped Design concept”, which allows interaction of the Sample Design, Variable Annotation (i.e. gene annotation, SNP annotation, et..) and the data (i.e. expression value, genotype call, log2 ratio, etc..) allows each view to integrate each part, allowing for easy customizations of the charts, filtering, and more.

Annotation

Omicsoft provides advanced integration of annotation (gene annotation, SNP annotation, etc.).  When importing data, annotation is attached automatically and integrated with the L-shaped design.  Omicsoft’s proprietary techniques allow the attaching of annotation to a dataset without the common memory and slow-down problems normally observed with this type of data.  The annotation is used throughout Omicsoft’s products, including our industry leading Genome Browser.

Data Types

Omicsoft supports more data types than anyone else in the market.  This includes both its enterprise product (Array Server) and its standalone analysis software, Array Studio.  Easily analyze Expression, CGH, Copy Number, SNP, Genotyping, Imputed SNP/Genotype, Methylation, ChIP on ChiP, RT-PCR (Taqman), and more.  Any of these data types can also be stored on the server, allowing for quick retrieval and further cross platform/cross-project integration.  For data not fitting any one of those exact categories, Omicsoft products include support for any data in the “High dimensional data format”—data that includes a sample design, a value, and annotation information. 

Project/Data Management

Omicsoft’s products include a streamlined project interface. Everything, including all generated views, filters, etc. are stored within a project (and subsequently published to the server).  Omicsoft’s intuitive use of the “List” concept eliminates the need to constantly subset, transpose and transform your data.  All of this is done by the programs on-the-fly.  Advanced manipulations (transform, transpose, subset, split, etc.) are available when absolutely necessary.  Omicsoft’s Solution Explorer easily allows working with multiple projects simultaneously, and combined with the server, thousands of projects can be easily searched and information returned in seconds.

Cross-project/platform Integration

Omicsoft’s products offer a variety of cross-platform and cross-species integration, from performing a meta analysis (finding overlapping regions of interest between projects), list analysis (find overrepresented projects given a list of genes, variables, etc.), and more, Omicsoft offers the most complete integration solution on the market.  Easily query a gene or genes of interest in one platform, and get the results for all projects matching that query (whether it is in another platform or potentially another species) in a matter of seconds.  Have a set of ratios (called estimates in Omicsoft products) that you want to query against?  Query thousands of ratios in seconds, and cluster the results all with a few clicks.  Easily “Broadcast” the results of one view into that of any other opened views with a click of the button.

Omicsoft’s duplex dataset concept allows easy integration of Copy Number and Expression data, CGH/Expression, Methylation/Expression, and Expression/Expression (e.g. RT-PCR vs. Expression), and more.  Perform correlation analysis on this data to look for trends.  Easily answer questions like “Does the increase in copy number in region x have a direct impact on expression for that gene?”

Access to Public Data

Omicsoft has analyzed over 5000 GEO and ArrayExpress public datasets, mainly so that you do not have to do so yourself.  We know it is painful to work through and parse the correct designs for some of the public projects available, so we have done this for you. Our statisticians have gone through and parsed the correct designs and statistical tests needed to analyze these projects.  This data is all stored on your server, alongside your own data, and can be easily queried. Easily access datasets like GSE2109 (contains over 2100 oncology samples) and query your own gene list against it.  Or, take your gene list of interest and find any projects that show overrepresentation (querying against 5000+ public projects).  Want a more detailed analysis?  Just download the project to your local machine and add to the already generated and QC’d analysis.  As new projects become available in the public domain, your support subscription guarantees you always have the latest data.

Computing

Using a combination of Array Server and Array Studio, computing is spread out between the client side and the server side.  For speed purposes, most calculations are done on the client side, allowing for the unprecedented speed in our analysis modules.   In contrast, storage of raw and analyzed data occurs on the server side, allowing for using the power of the server for querying of analyzed results.  Using the client/server implementation also allows the user to retain the interactivity found in the client side, even after the data has been published to the server.  Products that rely on web-only interfaces cannot hope to achieve the interactivity on the server-side that Omicsoft’s products achieve.

Scripting

OmicScript is Omicsoft’s scripting language. Most of what is done in Array Studio is scripted, and thus can be easily tracked using the Audit Trail functionality.  This is extremely important for both data integrity purposes and to be able to track and understand how an analysis is performed.

This scripting language can also be used to automate certain functions, allowing administrators to create standard pipelines of analysis that can be run with very little input from the users.

Omicscript is hugely popular amongst bioinformatics users, who prefer to rely on scripting rather than UI (user interface) for much of their work.

Array Command (Omicsoft’s analysis gene that can be run on Linux or Mac) can be used with OmicScript to automate many tasks for advanced users.

Server Pipeline

Use of Array Server’s pipeline process allows for easy storage and processing of raw data from the server.  Fully customizable, this pipeline can be used to automate a portion of your data analysis for your users, allowing a consistent normalization and QC to be done on all projects analyzed by your users.  Integrated with R, this pipeline allows much flexibility in generating and processing the data, in a manner that is consistent with your standards and workflow.

Customization

Omicsoft operates with a Feature-On-Demand philosophy. We believe the customer should influence our product, and so our products have all been designed with the influence of customers at some of the top pharmaceutical companies. Our Feature-On-Demand philosophy, where we rapidly react to the customer's ever-changing needs in the world of biomarker discovery, is the hallmark of our development strategy. We have some of the best developers around, and as a result, we are able to rapidly deliver updates and requests based on user feedback.

If there’s a feature that we are missing, don’t hesitate to ask us.  If it makes sense, you’ll see it in one of the next versions of the products.  We always allow our customers access to our next generation (beta access) of products, so it could be weeks before you are using a new feature instead of months or years.