3 min read

Getting More Out of Single Cell Experiments with ROSALIND®

By Jay Gerlach on Nov 10, 2020 8:20:56 AM

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.

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Topics: Transcriptome BioInformatics Rosalind Pathways
2 min read

Making the invisible… visible.

By Cassandra Wesselman on Nov 6, 2020 12:31:54 PM

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.

OnRamp 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 flagship product, ROSALIND®, 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.

OnRamp 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

Topics: Transcriptome BioInformatics Rosalind Pathways
2 min read

Term-based Exploration - Deeper Insights with Gene Set Variation Analysis

By Tim Wesselman on Oct 27, 2020 8:13:36 AM

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.

Topics: Transcriptome BioInformatics Rosalind Pathways
7 min read

Join the COVID-19 Research Community

By Tim Wesselman on Jan 25, 2020 1:14:00 PM

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.

JOIN THE CORONAVIRUS COMMUNITY SPACE

 

Topics: Rosalind Collaboration Gene Signatures Pathways Community