OmicSoft Suite v12.4 Release Notes

OmicSoft Suite v12.4 delivers important bug fixes and improvements requested by customers.

Key improvements include:

• Software installation management
• New MSI installer allowing application administrators to install static versions in App Stores: https://resources.omicsoft.com/software/OmicSoftStudioInstaller/OmicSoft_Studio_Installer_12.4.1.1.msi
• New logo for OmicSoft Studio
• OmicSoft Server on the Cloud
• Improved download of FASTQ from the NCBI SRA repository (server on the Cloud configuration required)
• Parallel download of FASTQ files from NCBI to your S3 bucket, server, or local client
• Download SRA metadata simultaneously with your data
• Multiple AWS instance types can be specified in oscript
• For advanced users of oscript and Server on the Cloud, /InstanceType supports comma-delimited lists of instance types
• OmicSoft Server on the Cloud — IAM Instance Profile authentication supported
• Alternative to including Access Key in ArrayServer.cfg configuration
• OmicSoft Server on the Cloud AMIs are no longer specified by default. Please select the appropriate AMI and specify Ami and AmiSnapshot parameters in the [Cloud] section of your ArrayServer.cfg
• Ubuntu 20 AMIs
• Amazon Linux 2 AMIs
• Server management
• LDAP integration now supports restriction to specific user groups
• SIEM logging of server activity supported – contact your account manager for details
• Data resources
• Single Cell Land improved download speed
• 1 annotator (includes 1000Genomes and ExAc) is now available for annotating VCFs on Human Genome 38
• Additional improvements and bug fixes, enumerated in the Change Log (visible under the OmicSoft Studio Help menu > View Change Log

 

Compatibility

OmicSoft Suite v12.4 components are compatible with previous OmicSoft Suite v12 components.

• OmicSoft Server v12.4 is compatible with OmicSoft Studio v12.3, v12.2, and v12.1
• OmicSoft Studio v12.4 is compatible with OmicSoft Server v12.3, v12.2, and v12.1
• oshell v12.4 is compatible with OmicSoft Server v12.3, v12.2, and v12.1
• LandExplorer v.4.3 is compatible with OmicSoft Server v12.3, v12.2, and v12.1

OmicSoft Suite v12 components are not compatible with OmicSoft Suite v11.7 or older components.

 

Retired Functionalities

1. The BAS Server was retired starting OmicSoft Suite v12.0.
2. OmicSoft Viewer was retired starting OmicSoft Suite v12.0, and link-sharing functionalities are removed.
3. The legacy “Studio on the Cloud” feature has been deprecated for Studio-only users. However, OmicSoft Server supports Cloud NGS analysis with the Server on the Cloud Contact your account manager if you are interested in learning more.

 

Known issues

1. Users cannot create mapped folder pointing to /users/ virtual subfolders
2. If a Cloud-mapped S3 bucket contains an object ‘/’, it will be displayed as a folder ‘/’ that cannot be opened. Delete this folder in the S3 bucket.
3. Users cannot search for transcripts names when creating omic data queries
4. If updating from OmicSoft Server v12.1 or v12.2 on Windows, previous installation services must be uninstalled before the new WiX installer for OmicSoft Server Service 12.4 is installed.

• The new WiX installer for v12.4 should be used for new installations of OmicSoft Server Service or directly updating from OmicSoft Server v12.3.
  5. Update Cloud Folder Mapping will create a new folder instead of updating the name of the existing cloud folder.
  6. On Mac OmicSoft Studio, some charts cannot be exported using Export to PowerPoint or Export to Excel
  7. After filtering and recoloring cohorts in Survival views, colors are sometimes inverted between legend and X-axis labels.
  8. RNA-seq→TMA view is visible in HPA_B37 although no samples are available with RNA-seq + TMA data; no data are displayed.
  9. Web site for ArrayExpress is not rendered properly in Add Expression Data > ArrayExpress Experiment
  10. Open in PowerPoint always opens a new PowerPoint^® file; this function no longer supports appending to an open file.

 

If you have further questions, please contact your local QIAGEN^® representative or contact our Technical Support Center at www.qiagen.com/support/technical-support

 

OmicSoft Suite v12.3 Release Notes

QIAGEN OmicSoft Lands API expands access to curated ‘omics data

 

The new QIAGEN OmicSoft Lands API enables powerful searches across QIAGEN OmicSoft Lands data. Query data on any metadata field across Land databases, without needing to ingest data into your own SQL database.

 

Figure 1. QIAGEN OmicSoft Lands API schematic. Queries are submitted using SQL syntax via Python or R packages, which are processed by the QIAGEN OmicSoft Lands API query engine to find matching data within the QIAGEN curated ‘omics Land databases. Matching data are returned to the Python/R environment for analysis and visualization. Retrieved data can be downloaded as flat files or directly loaded into Python/R data frames.

Data

The QIAGEN OmicSoft Lands API provides direct access to OmicSoft’s collections of deeply-curated datasets, taking advantage of extensive controlled vocabularies and our human-centered curation approach to unlock powerful cross-project queries.

Learn more: Why is a curated ‘omics data portal important?

 

Data structure

OmicSoft’s structured tables of metadata and data can be queried on one or more fields and joined to return exactly the data needed to answer your biomarker-related questions.

QIAGEN OmicSoft OncoLand and DiseaseLand datasets have structured and curated metadata at project, sample and comparison level and are linked to ‘omics measurements for each sample, such as RNA-seq gene expression (gene, transcript, exon, junction, fusion and mutation), microarray expression (probe and gene), miRNA-seq, DNA-seq mutation calls, copy numbers and more.

Figure 2.  Schema of QIAGEN OmicSoft OncoLand and DiseaseLand datasets. Curated metadata (left) are represented within multiple tables with keys to join at the project and sample level, as well as comparisons between sample groups. Each curated data type (middle) is represented by a separate table, which can be filtered on associated metadata, data values or associated annotation (right).

Single-cell datasets within QIAGEN OmicSoft Single Cell Land databases include structured and curated metadata at project, sample, cluster, cell and comparison level, linking to gene expression (raw and normalized counts) for each cell, along with cell coordinates from pre-computed dimension reduction analyses.

 

Figure 3. Schema of single-cell RNA-seq datasets in QIAGEN OmicSoft Single Cell Land databases. In addition to curated information at the project, sample and comparison level (left), single-cell datasets include metadata and data describing cells and cell clusters (right).

 

Access to curated data

The initial release provides access to subscribed datasets within QIAGEN OmicSoft DiseaseLand, OncoLand and Single Cell Land databases, including the following:

 

• 650,000+ manually curated samples
• 1400+ diseases and 700+ tissues represented across 9000+ ‘omics projects
• Rich harmonized metadata described across 6000+ metadata fields, allowing powerful queries to capture relevant samples across studies
• 124,000+ comparisons from custom statistical models to reveal differentially expressed gene signatures across studies

 

API client system requirements

We offer simple-to-install clients supporting Python (Python version 3.7 or higher) and R (R version 3.6.0 or higher). These clients are used to submit SQL queries to retrieve data slices from the hosted database.

Ask your Sales Representative to add the OmicSoft Lands API to your license.