Software Services in Bioinformatics
Since we started in 2000, we have built bioinformatics software for most analytics platforms: microarrays, mass spectrometry, next generation sequencing, high throughput microscopy, and digital PCR. We have covered the spectrum from genomics, transcriptomics, epigenomics to systems biology. We have built high performance software for GPUs, speeded up drug discovery algorithms for pharmaceutical companies many-fold, created Natural Language Processing algorithms for mining protein interactions, and systems biology platforms for predicting drug-induced liver injury.
We have even built software that drives reporting of NGS-based somatic and germline clinical tests, from which thousands of reports have been generated. Our clients include large instrument companies, pharmaceutical companies and core laboratories. Our software has been cited in thousands of peer-reviewed publications. We’re experts on bioinformatics software; if you want something built, you probably want us. And we will deliver.
Application 1. Do you need software to support your instrument platform?
Application 2. Do you need software that performs custom analysis of NGS or microarray data?
Application 3. Do you need software that manages existing bioinformatics workflows?
Application 4. Do you need your existing bioinformatics workflows tested and/or standardized?
Application 5. Do you need to make your software clinical-grade for FDA submission?
If you answered yes to one or more of these questions, get in touch with us at email@example.com.
Variant Curation Services
Laboratories running NGS-based clinical tests are challenged with the labor of variant interpretation. To support our clinical diagnostics business, we have built up databases of curated variants across 3 different application areas:
- Somatic Tumor Profiling: This database contains over 10,000 somatic variants curated for oncogenicity, 100 genes curated for druggability and 500 drugs curated for evidence for response in multiple cancer types
- Hereditary Cancer: This database contains over 5000 variants curated for pathogenicity across multiple inherited cancers based on ACMG guidelines
- Rare Inherited Disorders: This database contains over 10,000 variants curated for pathogenicity across multiple different mendelian disorders based on ACMG guidelines.
We work with several clinical laboratories to license and/or customize these databases based on their requirements.
Application 1. Do you want to bring your NGS somatic panel reporting in-house?
Application 2. Do you want to make NGS germline panel reporting more efficient by pre-curating variants?
Application 3. Do you want to reduce costs of variant annotation dramatically?
Application 4. Do you want to keep up to date with rapidly growing literature?
If you are interested in licensing any of our databases or would like to create your own, please get in touch with us at firstname.lastname@example.org.
Our Variant Interpretation and Reporting Platform: StrandOmics
Efficient reporting of NGS-based clinical tests requires a robust and mature platform for automatic variant prioritization, clinical interpretation and report generation. Strand Omics is a fast, HIPAA-compliant cloud-based platform that drives our clinical diagnostics practice. It has been honed over 4 years and over 10,000 clinical reports and multiple peer-reviewed publications.
Strand Omics combines bioinformatics algorithms, curated databases, visualization interfaces and reporting capabilities. It has specialized workflows for both rare inherited disorders as well as somatic tumor profiling tests. The platform contains over 10,000 somatic variants curated for oncogenicity, 100 genes curated for druggability in multiple cancer types and 500 drugs curated for evidence in multiple cancer types.
It also carries over 20,000 proprietary rare disease variants curated from literature and 200,000 commercially available curated variants. The platform is also capable of integrating all relevant public databases.
- Do you want to save millions of dollars building your own variant interpretation software?
- Do you want to to inherit best practices from a team that generates thousands of reports annually?
If you are interested in licensing this platform or would like more information, please email us at email@example.com.
Strand has extensive experience in validating NGS-based panels under CAP- and CLIA-settings: be it germline panels, somatic tumor panels, or liquid biopsy panels, and be it small panels with tens of genes, to large panels with thousands of genes.
Over the past few years, Strand has developed a diagnostics setup that performs NGS tests for a variety of different conditions, including germline and somatic cancers as well as rare diseases. Our clinical diagnostics lab is accredited by the College of American Pathologists, as well as the National Accreditation Board of Laboratories (ISO15189).
Are you a laboratory offering NGS-based clinical diagnostics?
Are you an organization assessing your ability to enter clinical diagnostics?
- Would you like to validate your clinical assay to CLIA/CAP standards?
- Would you like help setting up an accurate data analysis pipeline for your assay?
- Would you like to monitor your assay performance to ensure CLIA/CAP compliance?
- Would you like help in clinical interpretation and reporting of your NGS assay?
If you answered yes to any of these questions, get in touch with us at firstname.lastname@example.org.
Analysis Services in Bioinformatics
Bioinformatics analysis can be tricky. You may have large-scale RNA-Seq data, and don’t know whether technical effects are relevant; or you may have large grouped cohorts of DNA-Seq data, and need to narrow down your variant list to a few significant ones, associated with disease; or you may want to do an integrated study on a dataset containing RNA and ChIP-Seq samples.
One of the foremost software products built by Strand for genomics data analysis from microarray experiments was called Soochika. Strand’s success with Soochika took it on a path of evolution that led to what is today’s GeneSpring, marketed by Agilent Technologies, Inc.
GeneSpring GX is a data analysis software for analyzing and interpreting data from genomics, proteomics, transcriptomics and metabolomics experiments, as well as to perform integrated biology.
GeneSpring has a huge customer base of researchers worldwide with over 25,000 citations in Google Scholar. GeneSpring has established itself as the world leader with its competitors a distant second.
Agilent and Strand continue to innovate and serve the GeneSpring customers with regular software updates to empower their research and publications.
Strand NGS enables analysis of data generated from next-generation sequencing (NGS) experiments. It supports extensive workflows for RNA-Seq, DNA-Seq, ChIP-Seq, small RNA-Seq and Methyl-Seq analysis.
NGS experiments are notorious for the volume of data that they generate – a typical experiment can generate several GBs of raw data. That puts a huge onus on having to carefully optimize every single step of every analysis algorithm.
In the rapidly evolving area of NGS, Strand continues to keep pace and serve the Strand NGS customers with the latest.