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Overview

Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

Exciting Updates and Latest News

Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

Filtering by Category: Product Release

[Land Update] Next Generation Of OmicSoft Lands on AWS Cloud

Vivian Zhang

In April 2017, Gary Ge from OmicSoft presented the webinar, Next Generation Of OmicSoft Lands on AWS Cloud, which described OmicSoft's transition into a cloud-based Land system. For those who missed the webinar, please watch the recording here, or read through this article on how our new Land technology may improve our service.

OmicSoft’s Land technology has enabled collection and management of large public data sets in curated knowledge bases in the fields of cancer genomics (OncoLand), cardiovascular, metabolic and immunology (DiseaseLand), as well as genetic research (GeneticsLand). With more data being curated daily, and more users requesting content faster, we have been focused on creating a better solution for public Land delivery.

With the rapid growth of our Land database, we now provide 32 Lands including OncoLand and DiseaseLand to customers. Previously, we delivered and updated all content of approximately 1.5TB data each quarter. The delivery often takes 1 to 5 days, and requires server-based parallel publishing, which takes a lot effort for both OmicSoft and company IT/OmicSoft product administrators.

In 2014, OmicSoft released Studio on the Cloud, and continues to improve its cloud implementation since inception. Studio on the Cloud allows users to seamlessly run all Array Studio analytics from Amazon, combining the storage of S3 (Amazon Simple Storage Service) with the analytical power of EC2 (Amazon Elastic Compute Cloud). Omicsoft has seen an increasing number of clients that implement mixed mode solutions (cloud solution in addition to their SGE/PBS/LSF cluster). 

With new technology breakthroughs, OmicSoft now offer the cloud-based Land. Our cloud Land designe enables Land streaming from Amazon AWS. It makes Land data delivery much easier. Here is a comparison on Land delivery performance:

 

The design has the following features: 

• 10x performance improvement for dynamic query
• Stream to client’s ArrayServer with server cache
• Quick land delivery with minimal local storage footprint
• Faster future content updates
• Potential On-demand content updates (particularly for DiseaseLand) 
• Allowing virtual land of public cloud lands and local server internal lands

To date, most of our clients have chosen to switch to cloud-based Land delivery. Please speak to the OmicSoft support team, or your company administrator to understand how cloud-based Land delivery can benefit your research.

[Ten Year Anniversary Release] Array Suite 10.0: Accelerating Bioinformatics Research For Ten Years

Vivian Zhang

OmicSoft, now a QIAGEN company, is excited to announce Array Suite 10.0, the ten year anniversary release to its flagship software product. Array Suite provides the backbone of OmicSoft's software and data service offerings, including OncoLand, DiseaseLand and GeneticsLand. In the past ten years, Array Suite has helped numerous users from major pharma and biotech companies (as well as research instutitions) accelerate their bioinformatics and genomics research. 

Founded in 2007, OmicSoft had a vision to focus on biomarker data management, visualization, and analysis. Array Suite (Array Studio and Array Server) differs from standard desktop solutions or open source solutions, with Array Studio providing the graphical user interface for NGS and OMIC analysis and visualization and Array Server providing the enterprise back-end solution for pipelines, project management, sample/file management, data storage and OMIC data warehouse (Land database).  In January 2017, QIAGEN enhanced its portfolio with the acquisition of OmicSoft, allowing us to imagine new possibilities for integration with the larger QIAGEN bioinformatics portfolio.  We will update everyone on these enhancements, and how they will benefit our users, in the near future.

"Although much has changed in the past ten years, in both software and the company itself, I'm proud that OmicSoft Corporation has remained unchanged it it's fundamental desire to implement useful tools, driven by our customer's needs, in the -OMICS space.  I am confident that this will continue into the future with our acquisition by QIAGEN, and I look forward to many more years of Array Studio helping to drive exciting breakthroughs and research by our customers" - Matt Newman, VP Business Development

OmicSoft is extremely proud of it's customer-centric product development and customer support, and we look to continue this into the future, as we have for the past 10 years.  With our latest update, this trend continues. Array Suite 10.0 includes revolutionary updates, with multiple technology breakthroughs including: Cloud-Based Lands, Single Cell RNA-Seq support, ENCODE integration and many other updates to both analytics and framework.

Here is a list of some of our exciting updates:

1. Cloud-Based Lands  
2. Single Cell RNA-Seq support  
3. ENCODE integration in Omicsoft genome browser  
4. New gene set analysis
5. Streaming large tables  
6. Smart labeling in multi-charts
7. Smart caching for cloud/HTTP bam sources
8. New analytic modules including variable selection and prediction  
9. Significant improvements on plasmid-host integration  
10. Various genome browser improvements

For more details, please join our webinar, Omicsoft Array Suite 10.0 Release on May 3rd, 2017. Jack Liu from Omicsoft will present to you the top ten new features and more. Register here.

Bridging Bioinformatics|Genomics|Genetics Research: 2016 Omicsoft User Group Meeting

Vivian Zhang

 

  • Who Attended:
    • More than 30 leading pharmaceutical and biotech companies. 
    • More than 100 attendees who are experts and scientists in the field of bioinformatics/genomics/genetics.
  • What Occurred:
    • Numerous discussions among attendees on the future of biomarker discovery, as well as best practices of data management, visualization and analysis.

 

  

Omicsoft Corporation successfully held our kick-off Omicsoft User Group Meeting in Cambridge, MA on Wednesday May 4, 2016.

We would like to thank all speakers and attendees, all of whom are extremely important in helping build out our platform successfully.  We've received extremely positive feedback from the meeting, and hope to do it again in the future.  Feedback on our software and services help drive our business, and the direct interaction with our customers during the event proved invaluable to us. 

Highlights from the meeting:

  • Introduction of GeneticsLand for management of genetics data
  • Introduction to the future SingleCell Land
  • Overview on curation processes
  • Updates on current data subscription Lands

For more details, please visit our 2016 User Group Meeting webpage.

 

Above is just a glance of some exciting moments at our meeting. If you missed the meeting, we have uploaded our speaker presentations and videos on our 2016 User Group Meeting webpage.

If you have any question with regard to the meeting, please contact us. 

 

[Land Update]GeneticsLand: Data Warehouse for Variant Level Data

Vivian Zhang

 

What is GeneticsLand?


GeneticsLand is a data warehouse for variant level data and provides a turnkey solution to genetic data storage, analysis, and annotation to facilitate a wide range of genetic-based activities in drug discovery and development. 

It allows user to import and export VCF files, array based data, imputed array data, eQTL data, association results, and variant annotated data. GeneticsLand is a subscription, adding value regularly with new content after purchase.. It is a search engine that not only stores millions of samples but also provides fast, easy and accurate search of variants, genes, chromosomal region and phenotype data.


Why use GeneticsLand?

 

Big Data:  GeneticsLand can store up to one million VCF samples per "Land" (database), (assuming 100 million SNPs per sample and essentially unlimited array based files). It can support thousands of association studies. At the same time,  data storage is compressed, significantly reducing IT storage burden.

Fast: GeneticsLand can access 100 trillion data points and perform advanced visualizations and dynamic annotation in real time.  Queries of 10 billion data points can occur in much less than 1 second (0.01 seconds in benchmark testing).

Integrated Solution: GeneticsLand will provide biologist-friendly and high level client for genomic/genetic data integration (including a future web-based client), accelerating target identification and validation using our sophisticated queries and visualization system. Our adjacent products, including OncoLand, ImmunoLand and CVMLand, work together with GeneticsLand to provide comprehensive genomic research tools that empower researchers in all disease fields. 

SNEAK PEEK OF GENETICSLAND

 

Search variant/genes for individual genotypes, SNP allele frequencies (population genetics), and annotations:

Access curated public association data: 

Visualize public and private eQTL data:

Correlate numerical clinical variables to genotypes:

How could GeneticsLand help you with your genetics research?

  • Big Picture - centralized storage and search engine
  • Everyday work
    • Search variant/gene for annotations
    • Search frequencies for a given variant/gene/region cross projects
    • Access individual genotype data (for data managers) cross projects
    • Access public association data (e.g. GRASP2)
    • Access public variant data
    • normalized data from any# of studies through exportinf
    • Instant region/genome plots for association studies

Stay tuned for more information in the coming days and weeks! 

Contact us at: sales@omicsoft.com for any questions or request for demo.

 

[New Land Update] GeneticsLand: a turnkey solution for genetic data storage, analysis and annotation

Vivian Zhang

GeneticsLand will provide a turnkey solution to genetic data storage, analysis, and annotation to facilitate a wide range of genetic-based activities in drug discovery and development. It serves as a gateway to bring both internal and external genetic data in one place to allow easy access and interpretation of genetic data.

GeneticsLand utilizes a proprietary data storage framework that enables efficient storage of whole genome sequencing, whole exome sequencing, GWAS and imputed data. Data quality control and analysis adopting up-to-date best practices are implemented in GeneticsLand to allow consistent and rapid genetic data QC and analysis. By linking both current and historical internal data with most-current external databases, GeneticsLand can help researchers interpret genetic analysis results.

GeneticsLand is a tool that will be used for drug target discovery, drug target validation, pharmacogenetic and pharmacogenomics studies. Expected release 2015 Q4. Contact us at sales@omicsoft.com if you are interested in a free trial. Also, talk to us if you have public or private datasets of interest. We would love to customize the Land for your research needs.

GeneticLand Sneak peek:

Figure. Variant Region Plot 

Figure. Variant Region Plot 

GeneticsLand has the following 6 major modules:

(1)     Genetics data management:

  • Stores array-based or sequencing-based genotype data, imputed dosage data on the server with powerful search/visualization/exporting functions
  • Manages QC results and association reports

(2)    Genetic variant management: manages a huge collection of variant annotation

(3)    Array-based data analysis pipeline: Genetic data analysis pipeline based on GWAS and imputed data

(4)    NGS data analysis pipeline:

  • Uses server, cluster or cloud to run OSA4+GATK or BWA+GATK pipeline
  • Generates QC and VCF from FASTQ in a simple yet powerful pipeline.
  • Includes built-in cloud/server based BAM streaming

(5)    Genetic search engine:

  • Provides gene based search engine for full genetic information – GWAS catalog, eQTL.
  • Makes use of LD information to provide insights for target validation and interpretation of genetic contribution to drug response

(6)    eQTL management: manages public or internal eQTL data in a highly searchable/visual user interface

Screenshots of GeneticLand prototype:

Table. Vatiant Annotation

Table. Vatiant Annotation

Figure. Variant Filter Directory. (Partial display)

Figure. Variant Filter Directory. (Partial display)

Figure. LDL Association Plot

Figure. LDL Association Plot

[New Land Update] Coming Soon: MetabolicLand helps researcher battle diabetes, obesity and more

Vivian Zhang

The increasing number of public genomic datasets and customer demand for integrated database have been driving Omicsoft's Land database development. In just a few short years, our flagship Land, OncoLand, has been an overwhelming success and is now being used by most of our pharma and biotech customers. Encouraged by our OncoLand success, we are in the process of bringing a series of DiseaseLand products to our customers, including the recently released ImmunoLand and the upcoming MetabolicLand. 

MetabolicLand is designed for metabolic disease data, for example, diabetes and obesity, as well as cardiovascular diseases.  By the end of 2015, MetabolicLand will be tested and used by a few of our prestigious pharmaceutical clients. 

We will have three distinct Land products covering all disease areas:

1. OncoLand (Oncology)
2. ImmunoLand (immune related diseases and neurological diseases)
3. MetabolicLand (Metabolic and Cardiovascular diseases)

We will do our best to fit all remaining diseases that we have not yet covered into these three categories, as least as it related to genomic data.

Before its release, we would like to show you a few snapshots of our MetabolicLand. Schedule a meeting with us through sales@omicsoft.com if you are interested in metabolic disease genomic and clinical data. Also, talk to us if you have public or private datasets of interest. We would love to customize the Land for your research needs.

Figure 1. MetabolicLand Sample Distribution by 2015 Q3.

Figure 1. MetabolicLand Sample Distribution by 2015 Q3.

Figure 2. MetabolicLand mTOR Gene Expression Comparison, Disease vs. Control. 

Figure 2. MetabolicLand mTOR Gene Expression Comparison, Disease vs. Control. 

Figure 3. Available Views in MetabolicLand by 2015 Q3.

Figure 3. Available Views in MetabolicLand by 2015 Q3.

Together, let Omicsoft help improve your metabolic and cardiovascular disease research and drug development.

New cancer genomics datasets (TCGA and more) with OncoLand's 2015 Q2 Release

Vivian Zhang

PR News Release

Omicsoft Corporation, an industry leader in cancer genomics, bioinformatics, and next generation sequencing storage and analysis, today announced their quarterly release of their OncoLand data service. Watch the Land 2015 Q2 Release Webinar

Omicsoft Corporation provides a data service and oncology database platform, OncoLand, that focuses on management of both public and customer cancer datasets, including clinical, next generation sequencing, gene expression, copy number, protein, and methylation data. 

In the 2015 Q2 release, the biggest Land update since it's introduction in 2013, Omicsoft highlights the following updates:

  • Introduction of a new clinical subsystem
  • 10+ Patient centric views now available
  • Introduction of new lands, such as GenentechCellLine, and more than 10,000 new sample data (requires controlled access to Genentech Cell Line study published in Nature in 2014)
  • Feature updates:
  1. Dynamic correlation (among RNA-Seq, Mutation, CNV and protein expression data)
  2. Viral and bacterial data integration
  3. Sample centric views
  4. Multiple grouping
  5. Geneset improvement
  6. Land Audit Trail
  7. "Missing data" visualizations

For more details about feature update, please watch the Land 2015 Q2 Release Webinar

Along with the OncoLand release, Omicsoft is pleased to introduce the next release of ImmunoLand. ImmunoLand incorporates public immunology data in disease areas including Arthritis, Asthma, COPD, IBD (Ulcerative Colitis, Crohn’s diseases), Lupus, Psoriasis and other skin diseases, Infectious diseases and vaccine, and Neuroimmuno-diseases (multiple sclerosis and more).

For new users, please contact sales@omicsoft.com for a free trial and consultation. For existing user, please contact support@omicsoft.com for more details. 

 

 

 

OncoLand and ImmunoLand Update Webinar (Updates to TCGA and GEO Datasets)

Matt Newman

Jack Liu, President of Omicsoft, will discuss and demonstrate live some of our biggest updates to the “Land” technology since its introduction in 2013. This includes framework updates, feature updates, as well as data updates to both OncoLand and ImmunoLand. 

Major framework updates: 

(1) deep clinical integration with the user interface and analytics with carefully curated TCGA clinical data 
(2) dynamic correlation framework providing instant integration capabilities across different data types and genes 
(3) much improved comparison support greatly enhancing our ImmunoLand subscription and future OncoLand subscriptions 
(4) integration with our breakthrough variant annotation system. 

Also included are the following features/data updates: 
(1) Built-in metagenomics integration (viral, bacterial) for TCGA, GTEx and a few other “Lands” 
(2) Sample specific views (expression, CNV and mutation) 
(3) Grouping/Profiling visualization support for multiple columns 
(4) Various “GeneSet” view improvements, including performance improvement 
(5) Cross-tissue normalized protein data: RPPA-RBN 
(6) New “Group Summary” views for powerful exporting of statistics behind the boxplots, heatmaps, etc. 
(7) Thousands of new NGS and MicroArray samples for ImmunoLand with additional disease coverage 
(8) Various data updates (TCGA, ICGC, GenetechCellLine, etc.) for Oncoland 

We will also present some of the near-future working projects, including HLA typing and dynamic cohort support. The Land updates will also be made available to our customers on July 17th as well.

We'll also update our blog in the coming days with direct links to the recorded webinar, and stay tuned for blog posts showing some of the newly released features and datasets.



Introducing Array Studio on the Cloud

Matt Newman

Omicsoft is pleased to announce the availability of Array Studio on the Cloud.  

Now, easily incorporate your data stored on S3 into your workflow with Array Studio and Array Server.

For Array Studio only users, this allows the power and scale-up opportunities of running pipelines using EC2, as well as the vast storage of S3, for the single user.

For Array Server users, this allows seamless integration of Sample Management, Pipelines, and more with that of S3 and EC2.  For the user, this is transparent, with data stored on the cloud using EC2 resources, but still allowing the use of local resources for data stored within your network.

Array Studio on the Cloud is available as an upgrade for Array Studio and Array Suite (ArrayStudio + ArrayServer) users. Contact support@omicsoft.com for more information, or sales@omicsoft.com for new users).