The field of genomics is rapidly evolving, and tools like Rosalind are leading the charge in simplifying complex data analysis processes. Recently, Rosalind held a GeoMx Data Analysis Masterclass, aimed at educating researchers on advanced analysis techniques for gene expression data. If you missed it, here’s a summary of key takeaways from Session Two on AOI (Area of Interest) and Gene Removal.

In a move that will expand the boundaries of single-cell genomics, ROSALIND is excited to announce its partnership with CS Genetics, a leading innovator in genomics technology. Together, we aim to democratize access to single-cell research by combining the cutting-edge CS Genetics’ SimpleCell™ platform with ROSALIND’s powerful data analysis capabilities.

Welcome to our exciting journey through the world of spatial transcriptomics, an innovative approach transforming the way we conduct research. Spatial analysis, particularly using platforms like GeoMx, opens new avenues for discovering insights that traditional methods may overlook. Today, we dive into one of the most crucial aspects of data analysis: quality control.

Rosalind is excited to introduce the GeoMx Data Analysis Masterclass Series, an educational initiative aimed at equipping researchers with advanced skills for GeoMx spatial data analysis. Hosted by Dr. Jessica Noll, an expert in spatial biology, this session laid the foundation for a comprehensive five-part series aimed at elevating your understanding of spatial data analysis and its applications.

Spatial biology is revolutionizing how we view and analyze biological data. Dr. Noll highlighted how Rosalind’s platform has emerged as a powerful tool to simplify complex data analysis in this rapidly evolving field. By integrating various types of data—DNA, RNA, and protein—into a single cloud-based platform, Rosalind enables users across academia, biotech, and pharma to conduct in-depth analysis while collaborating with peers globally.

Earlier this month, we launched NanoString Masterclass Series, designed to enhance scientific understanding and practical skills in advanced nCounter data analysis. Dr. Ryan Friese (VP of Rosalind Customer Experience) hosts the series to share his best practices from years of working hands-on with scientists in BioPharma and Academia as a Field Application Scientist for NanoString.

Earlier this month, we launched NanoString Masterclass Series, designed to enhance scientific understanding and practical skills in advanced nCounter data analysis. Dr. Ryan Friese (VP of Rosalind Customer Experience) hosts the series to share his best practices from years of working hands-on with scientists in BioPharma and Academia as a Field Application Scientist for NanoString.

Earlier this month, we launched NanoString Masterclass Series, designed to enhance scientific understanding and practical skills in advanced nCounter data analysis. Dr. Ryan Friese (VP of Rosalind Customer Experience) hosts the series to share his best practices from years of working hands-on with scientists in BioPharma and Academia as a Field Application Scientist for NanoString.

Rosalind is proud to introduce the NanoString Masterclass Series, an educational initiative aimed at equipping researchers with advanced skills for nCounter data analysis. This program is designed to offer scientists in-depth knowledge on how to leverage Rosalind’s enhanced analysis capabilities, such as custom normalization, advanced Cell Type Profiling, and the strategic pruning of low expressors, among other features. 

This inaugural session sets the stage, offering a glimpse into the powerful combination of Rosalind’s platform with NanoString technology. The session highlighted how researchers could transition from sample processing to insightful data analysis within a 24-hour framework, emphasizing efficiency and depth of analysis.

We invite all researchers, from individual academics to teams within biotech and pharmaceutical companies, to join these sessions to enhance their analytical practice. Our commitment is to support the scientific community with precise, efficient, and reproducible data analysis.

As the world of biotechnology continues to evolve at a rapid pace, BioPharma institutions are confronted with the complex task of managing a deluge of multi-omic data sets. Knowledge Libraries are a revolutionary feature of the Rosalind platform designed to streamline data management and bolster collaborative research efforts. Knowledge Libraries are included with every Rosalind Enterprise Subscription. 

Watch our Webinar on Knowledge Libraries:

The Challenge

Biopharmaceutical research generates a vast amount of data in research and clinical trials from many domains including genomics, transcriptomics, and proteomics. Managing this heterogeneous data, especially integrating it from disparate sources, presents a significant challenge. Beyond mere data management, safeguarding data security and privacy is a critical task, requiring vigilant prevention of unauthorized access while enforcing requiring compliance. Implementing robust data governance policies and strategies is essential to ensure data accessibility, integrity and accountability. Moreover, effective collaboration facilitated through well-organized data storage plays a crucial role in maximizing the potential of this rich data landscape for impactful scientific discoveries.

March is always extra special here at Rosalind as we celebrate Women’s History Month. Our team takes great pride in recognizing women who have made significant contributions to the world of science. 

The ROSALIND Tracker is a real-time dashboard for the United States rapid genotyping "Project ROSA" program for SARS-CoV-2. This research was supported by the National Institute of Biomedical Imaging and Bioengineering or the National Institutes of Health as part of the Rapid Acceleration of Diagnostics (RADxˢᵐ) initiative.

The partnership aims to democratize single-cell spatial analysis data captured on the Rebus Esper™ system and increase biological understanding.

ROSALIND is cloud-native platform that harnesses industry-leading best practices and the strength of Google Cloud Platform to ensure the highest level of cybersecurity available for enterprises Pharma, academic institutions, and the Federal Government.

These new partnerships are intended to bring powerful new Single Cell Analysis Services to Cancer Researchers. ROSALIND adds a Web-based solution to offer advanced biological analysis and interpretation of Single Cell Clusters in tumor genome profiling experiments. 

This new web-based system, developed with NIH funding, will aid in monitoring emerging SARS-CoV-2 variants and the performance of diagnostic tests

This first-of-its-kind solution delivers end-to-end single-cell analysis in an intuitive web-based interface

In Her Honor...    

An Interview with Janice and Harrison of Jericho High School

Knowledge Graph architecture unifies information and creates a foundation for FAIR (Findable Accessible Interoperable and Reusable) data management and advanced search capabilities. The impact for research is an exponential expansion and acceleration in extracting insights.

Single Cell Gene Expression studies are becoming an essential tool for understanding the complex interplay of cells in both healthy and diseased tissue. Thanks to huge strides forward in technologies enabling the partitioning and sequencing of individual cells, we are seeing an explosion of new Single Cell studies across a variety of fields. In many cases, it seems that the ability to produce data is outpacing the ability extract meaning from the data. ROSALIND is seeking to close this gap by accelerating upstream data processing and providing an intuitive user interface for downstream analysis of cell clusters.

ROSALIND utilizes cloud-scale data processing and an intuitive graphical user interface to make processing of 10x Genomics cell ranger datasets both faster and easier. Alignment, quantification, and download of default clustering results can be performed easily by non-expert users without the need for onsite computer processing power.

ROSALIND also supports downstream analysis of cell clusters generated in the 10x Loupe Browser. Cell clusters defined in Loupe can be compared with one another at the level of individual genes, pathways, drugs, other key terms. This unlocks the next era of Single Cell research which will focus on developing deep understanding of the biology of each cell type cluster in a given context and the identification of actionable markers.

We are excited to participate in the Single Cell Sequencing revolution and look forward to building on the capabilities we have already established by responding to the needs of our user base. We encourage you to try ROSALIND’s new Single Cell Analysis features and let us know what you think.  Video tutorials can be found within the ROSALIND user interface and we are available to perform demos of the new functionality.

Related Posts

• OnRamp Bio and NanoString Announce Global Availability of ROSALIND® for nCounter Users
• Canopy Biosciences partners with OnRamp Bio to provide ROSALIND interactive data analysis for comprehensive gene expression services
• JOIN THE CORONAVIRUS COMMUNITY RESEARCH SPACE to begin exploring and contributing to the global community understanding of COVID-19 data.
• For all Research affected by Social Distancing: Remote Science in the Era of Social Distancing demonstrates how working remotely does not mean that science must stop.
• For Scientists on ROSALIND: Collaborating on Genomic Data is a walkthrough on how to set up real-time collaboration on genomic data (like Google Docs).
• For Directors and Managers: The Value is in Collaboration (not the pipeline) discusses how collaboration is key to empowering research in your lab.
• For every Researcher, Public Data exploration shows how we have made it 100x easier to work with public data than ever before.
• To learn more about our latest capabilities, Empowering Scientists with the ROSALIND Platform is an overview of all analysis types, species and features currently available to the general public on ROSALIND.

What is Corporate Leadership? While operating responsibly should always take priority, Corporate Leadership requires us to focus on the very nature of our activities, going even deeper than our actions around Corporate Social Responsibility. This aspect of leadership defines the character of an entity, the impressions often left in its wake, and holds the tone across the organization and all its choices.

In the Life Sciences industry, corporations have unique advantages that smaller research and academic institutions often struggle with: resources and velocity. Private Equity and income generation provide more attainable financial support, and dedicated teams with cyclical workstreams allow for expediency when reaching for outcomes. The effective application of these resources to timely and impactful initiatives related to human health, environmental science, and the convergence of biology and technology is crucial for corporations looking to lead our society towards a better world.

Corporate leadership also paves the path forward to enable those who will hold the torch of leadership. This includes whose and what programs are supported and uplifted to succeed and allocating resources to focus on important efforts that help make what may have been unseen, acknowledged.

Our company is proud to be a founding member of the Rosalind Franklin Society’s Council on Corporate Leadership. This Council focuses on recognizing and fostering the contributions of women and minorities across scientific professions and institutions. The importance of fostering such work is fundamental to our core values, having named our company in honor of Rosalind Franklin and her pioneering spirit as we strive to empower all scientists in collaborative discoveries that transform our world.

The mission of the Council on Corporate Leadership is to create a more diverse landscape for scientific achievements, in a way that powerfully recognizes important work by every scientist.    

In the coming months, the Council on Corporate Leadership will be building its base of corporate partners and engaging them on strategies to recognize great achievements while addressing inequities of women and minorities in science. The Council will convene at a dedicated colloquium during the RFS annual board meeting this December, featuring Nobel Laureates, senior scientists as well as young researchers and leaders of promise. The Council will also be supporting the financing and allocation of the Rosalind Franklin Award given annually to pioneering women in the industrial, biotechnology, and agriculture sectors who have made significant contributions to the advancement of the bio-based economy and biotech innovation.

Rosalind is very excited to be part of this important new initiative and we encourage our colleagues to get involved. Those interested in becoming a corporate partner should reach out to Cassandra Wesselman by emailing: cassandra@rosalind.bio

Opening a new door to discovery, ROSALIND now empowers scientists to explore experiment results by key terms (Pathways, Signatures, Diseases and Drugs) that are significantly enriched across all samples using GSVA scores. You can access Term Exploration within the Discovery and Analysis section of each experiment. ROSALIND has been pre-computing these scores for the past several months, so many existing experiments already have this new analysis ready for exploration.

Every experiment and scientific question seeks to find insights on biological processes and pathways. Prior to now, this scientific journey always began with an exploration of genes to uncover the changes to underlying pathways. Now, you can begin exploring Pathways and significant Terms regardless of comparisons or cut-offs.

Our latest ROSALIND update v3.16 is now live and delivers enhancements for collaboration, 10X Single Cell RNA (scRNA-seq), Pathway Enrichment and more.

VIENNA and SAN DIEGO, June 17, 2020 /PRNewswire/ -- Lexogen, a transcriptomics and Next Generation Sequencing company, and OnRamp Bioinformatics, a provider of cloud-based genomic analysis and collaboration tools, announced availability for the QuantSeq 3' mRNA-Seq data analysis pipeline on ROSALIND™, the globally recognized discovery platform for scientists and researchers. The partnership enhances QuantSeq 3' mRNA-Seq data analysis with ROSALIND's visual data exploration and deep pathway interpretation with more than 50 knowledge bases.

St. Louis, MO /PR Newswire/—Canopy Biosciences, a multi-omic CRO providing NanoString® nCounter® and RNA Seq services to both clinical and research customers, has partnered with Onramp BioInformatics™ to offer their ROSALIND™ interactive data analysis platform for Canopy’s gene expression services.  Launched earlier this year, Canopy has been providing this intuitive platform to customers that have run NanoString and RNA Seq projects.

I’m convinced, and I know most of you are too, that we will not get to a complete understanding of diseases and biology in general without looking behind a multi-omics lens. While NGS radically democratized access to genomics information with RNA-seq, for example, the complexity of other assays like ChIP-seq and the ensuing challenges in combining different types of data analyses have limited the wide scale adoption of multi-omics approaches.

NanoString and OnRamp BioInformatics Partner to Develop Cloud-Based Analysis Solutions for nCounter Data

SEATTLE--(BUSINESS WIRE)--NanoString Technologies, Inc. (NASDAQ:NSTG), a leading provider of life science tools for discovery and translational research, and OnRamp Bioinformatics, a provider of cloud-based genomic analysis tools, today announced a collaboration for the development of new analysis tools for data generated on NanoString’s nCounter® Analysis System. The new analysis functionality is built into ROSALIND™, OnRamp’s cloud-based analysis suite that facilitates data visualization, exploration and collaboration. The companies are releasing these new capabilities through early access and immediately offering it to COVID-19 researchers performing critical host response studies on the nCounter platform.

We’ve all been reminded across various social media feeds how Isaac Newton discovered calculus while “social distancing” during the Great Plague of London or how some of Shakespeare’s greatest works happened while in quarantine. Although the thought of being able to work from home was once a dream we wished for, as Adam Ruben, Ph.D. puts it, science-ing from home isn’t easy.

If juggling your altered home-life alongside the 9-5 work routine wasn’t challenging enough, it’s even more questionable how you can advance your research now that you have limited access to your laboratory, your data and your team.

As we all grapple with the new reality of lockdowns and work-from-home mandates, there’s now a new opportunity re-define what it truly means to do collaborative research and remote science anywhere in the world.

Updated: June 25, 2020 ------
The COVID-19 Research Community Showcase

The COVID-19 Research Community unites scientists across the globe in the shared purpose of accelerating our collective understanding of COVID-19 and the SARS-CoV-2 virus. Researchers working on COVID-19 receive complimentary Community Scientist access to ROSALIND and the NanoString Early Access Program to facilitate rapid data analysis with real-time, global collaboration.

Today, we enhanced the COVID-19 Research Community through the addition of a new Showcase. ROSALIND Showcases provide a new experience for collaboration by summarizing highlights, capturing key observations and empowering community scientists with a library of COVID-related datasets, including some of the most recent research. 

The COVID-19 Research Community Showcase is accessible publicly at this link: https://rosalind.onramp.bio/showcase/covid19

Join the community effort to share, discover and accelerate our collective understanding of COVID-19.

Updated: May 20, 2020 ------
NanoString Early Access Program and the COVID-19 Community

Today, we announced our collaboration with NanoString for the development of new analysis tools for data generated on NanoString’s nCounter® Analysis System. This new analysis functionality is now built into ROSALIND™ and facilitates data visualization, exploration and collaboration for COVID-19 researchers performing critical host response studies on the nCounter platform.

As of the Early Access Program launched today, ROSALIND natively supports the NanoString COVID Panel Plus with targeted gene expression on human immune response with 10 supplemental genes (8 SARS-CoV-2 plus ACE2 human and ACE2 mouse). This new solution incorporates the methods and algorithms of NanoString nSolver and their Advanced Analysis solution within ROSALIND to accelerate insights from the nCounter instrument and empower global collaboration. 

Through the Early Access Program scientists and researchers are empowered with an end-to-end solution that streamlines the extraction, quantification, data analysis and collaboration to provide deeper insights into the gene expression of human immunology together with the viral response experienced during COVID-19.   

Updated: April 12, 2020 ------
COVID-19 Community Enablement - SARS-CoV-2 Genome & Virology

The SARS-CoV-2 genome is now available for new experiments and to support the COVID-19 Community. This facilitates analysis and discovery into the viral gene expression of COVID-19. Many of the recent NCBI public data submissions with SARS-CoV-2 samples and COVID-19 patient samples have already been processed and added to the Community Space.

ROSALIND Pathways has added a new Virology category and collection of Knowledge Bases to enhance COVID-19 research. New entries include Pathogen-Host Interactome (P-HIPSTer) and GEO Virus Perturbations. 

New COVID-19 datasets now available in the Community Space:

• Transcriptional response of human lung epithelial cells to SARS-CoV-2 infection (PRJNA615032)
• LY6E blocks coronavirus fusion and confers immune control of viral disease (PRJNA609134)
• Washington SARS-CoV-2 isolate sequences (PRJNA610428)
• Severe acute respiratory syndrome coronavirus 2 Raw sequence reads (PRJNA605983)
• Metatranscriptomics of two COVID-19 pneumonia cases (PRJNA601736)
• Relative timing of type I interferon response and virus replication determines disease outcome during MERS-CoV infection (PRJNA545350)

Updated: March 30, 2020 ------
Support for the SARS-CoV-2 Genome is in development now and will be released next week. We will also be posting several new public datasets from multiple locations across the globe. It's imperative that we join forces globally in open data sharing on COVID-19 so that we may track the strains, measure the progression of the disease and assess the efficacy of treatments.

If you have COVID-19 datasets, upload them today for free processing and interpretation.

Originally Posted: Jan 25, 2020 ------

Seeing the news on the growing threat of a Coronavirus pandemic, I’m reminded of just how interconnected we all are on this planet. Within a few short weeks, this deadly virus managed to make its way across species and oceans to a dozen different countries, affecting thousands of people. We still don’t know how severe this strain of Coronavirus will be and it’s hard not to be driven to join the fight against it.

We live in an era of unprecedented genomic technology with brilliant scientists that work tirelessly each day to gain deeper understanding into the inner workings of our biology and the diseases that afflict us. I believe that our greatest work stands before us and will be achieved through collaboration. While technical, organizational or resource constraints often slow our progress in other areas, we can overcome these now to collaborate for the cure.

Today we've launched the Coronavirus Community Space to provide open-access of ROSALIND, our discovery and collaboration platform, for fellow scientists who wish to join a community effort to share, discover and accelerate our collective understanding of Coronavirus.

After conversations with thousands of Scientists, there is stunning lesson in their feedback that every Pharma and Biotech manager should internalize: Collaboration is more valuable than the underlying analysis pipelines.

No matter how great the pipeline, if Scientists can’t explore, interpret and consistently collaborate on a common version of the data then the value invested in the experiment is lost, or simply not realized.

Like dark data, the latent insights in these experiments remain trapped. Interestingly, Pharma and Biotech institutions with a deluge of clinical trial and research data are looking for collaboration tools for their Scientists, not the fundamental analysis pipelines. The implications for oncology research, immunology, drug discovery and disease research are significant.

• Something every Scientist should read: we walked through Collaboration Spaces on ROSALIND, highlighting how it's now possible to collaborate in real-time on genomic data (like Google Docs). Read the post here. 
• We've forever transformed Public Data exploration. Follow this link for more information.
• Learn more about the latest capabilities, supported species and levels of access in this post on empowering scientists.  

Let’s face it, collaborating on genomics data is hard.

Schistosoma mansoni causes schistosomiasis, a disease of poverty that infects approximately 200 million people worldwide. Treatment of the disease relies on praziquantel (PZQ). With the expanding use of the drug, there is a fear over the development of resistance. It is, therefore, important to discover new drugs and drug targets.

I'm really happy to announce  another poster and research project utilizing ROSALIND, our analysis and collaboration platform for genomics.

Working with Public Data is important to nearly every Scientist in our community. Unfortunately, it's harder than it should be to work with these valuable datasets.  We all see and hear the news each week of exciting discoveries and breakthroughs in leading research, yet accessing and analyzing these Public Datasets, especially from RAW (SRA), requires determination, persistence and more coding skills than should be required of Scientists today.

OnRamp’s ROSALIND and Active Motif offer an improved ChIP-Seq data analysis experience for researchers with state-of-the-art dynamic track plots and advanced collaboration capabilities.

OnRamp takes home the "People's Choice - Best of Show" award at BioIT-World 2018 in Boston.

Click here to try ROSALIND for free

As proud contender for Bio-IT World's "People's Choice - Best in Show", ROSALIND will have latest features presented throughout the event

Event: Bio-IT World

Dates: 5/15/18 - 5/17/18

Location: Seaport World Trade Center, Boston MA

Event URL: www.bio-itworld.com/

Building a "Comparison of Comparisons" Across Multiple Experiments using Meta-Analysis on ROSALIND

OnRamp and Advaita announce a Strategic Partnership to bring collaboration and widespread accessibility to genomic data analysis

OnRamp's CEO, Tim Wesselman, features ROSALIND™ during Plenary Keynote Panel on Emerging Technologies and Industry Perspectives

Event: Molecular Medicine Tri-Conference

Date/Time: February 14th @ 8:45a PT

Location: San Francisco Moscone Convertion Hall

Event URL: http://www.triconference.com/

In this webinar, we discussed the transcriptomic analysis of racial disparities in prostate cancer using OnRamp's ROSALIND™ platform

Dr. Robi Ludwig interviews OnRamp CEO, Tim Wesselman, to explore the future needs for genomics to scale.

Our mission is to transform how cancer researchers and biologists analyze their data (at SCALE)!

Advanced bioinformaticians deserve all of the credit for building state-of-the-art applications to analyze genomic, proteomic, and microarray data.  While these tools remain the lifeline of genomic analysis, more simplified user experiences are now required to empower today’s cancer biologists to focus on their research application, not which software application to use. 

OnRamp BioInformatics welcomes you to visit us at the ASHG Data CoLab zone Oct 18th, 19th and 20th to Meet Rosalind™. 

This new platform was built with the researcher/biologist in mind, guiding you through a simplified bioinformatics process from experimental design to interpretation for analyses including transcriptomics and epigenetics. 

Cloudian, OnRamp, ScaleMatrix Partnership Eyes Faster, Lower-Cost Genome Analysis.

Written By: Neil Versel

CHICAGO (GenomeWeb) - When ScaleMatrix, OnRamp Bioinformatics, and Cloudian decided to get together in an effort to speed up sequencing analysis and lower the cost of data storage, they saw several shortcomings in the genomic informatics market.

Good News Bad News for Personalized Medicine.

I’m reminded daily of the many advancements towards personalized medicine, but one elephant remains firmly planted in the room.

Recently I came across an encouraging article that touched on the increasingly collaborative nature of the efforts to bring about this new age of personalized medicine.  Data-sharing is reported to be on the rise in oncology, with groups like the Genomic Data Commons assembling harmonized genomic and clinical datasets, and making that information widely accessible to cancer researchers. 

Challenges and opportunities in the research setting. 

The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine.

Could health outcomes be determined by the little guys who call us home?

The San Diego MicroBiome Meetup, hosted by Clotide Telling of Illumina, Inc., kicked off with a presentation by OnRamp's Scientific Advisor, Rob Edwards. Rob's story of the discovery of the crAssphage is a truly amazing example of Metagenomics and the MicroBiome, and is testament to the power of the sequencing revolution.

Transcriptome differences in prostate cancer highlight racial disparities. 

African-American and European-American men with prostate cancer exhibit significantly different expression of genes associated with immune response and inflammation.

Systems-level, RNA analyses support the concept that inflammatory processes may contribute to racial disparities in disease progression and that vitamin D3 supplementation can modulate pro-inflammatory transcripts.

The threat to fish embryos and larvae development.

MIAMI-A research team led by scientists at the University of California, Riverside and the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science have found that ultraviolet light is changing the structure of the Deepwater Horizon (DWH) oil components into something more toxic, further threatening numerous commercially and ecologically important fishes.

Click here to read the full interview.