NEW YORK (GenomeWeb) – BioTuring has released a browser that it says will make analyzing and visualizing publicly available single-cell RNA sequencing data as well as bulk RNA sequencing data as easy as surfing webpages.
Currently, the platform, called BioTurning Browser, offers access to information from nearly 400 publications, including single-cell data and bulk RNA-seq data from nearly 16,500 samples, the company said. BioTuring plans to continue expanding the breadth of the platform to include all publicly available single-cell RNA sequencing datasets.
In addition, the browser, which is available as of this week, comes with various add-ons for exploring the information. They include a single-cell visualization tool that provides scientists with interactive dashboards that support the three-dimensional exploration of millions of cells. The so-called Single-Cell Add-on also features a real-time cell type prediction algorithm that helps researches quickly annotate cell populations using a curated knowledge base of well-known marker genes from published studies.
The company has also developed an add-on for analyzing bulk RNA-sequencing data, called RNA-Seq Explorer, which supports analyses from raw Fastq files through to publication-ready plots. It includes tools for aligning and quantifying RNA transcripts, studying differential gene expression, and investigating gene expression at the transcript level.
Later iterations of the browser will include functionality for pseudo-time trajectory reconstruction, differential expression, and the ability to search for specific single cell populations. The company also plans to develop and release more add-ons for the browser, including one for analyzing Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) data, according to Son Pham, BioTuring’s director.
BioTuring is offering its browser free of charge for use with public datasets. However, it will charge customers who want to use it to visualize their own datasets, either on their own or in the context of the publicly available data. Pham said that the company plans to charge an undisclosed fee for six-month licenses for personal use of the browser. "We are working on our pricing strategy now and will be offering introductory pricing below market rates for a brief period of time," he said.
The exact price will depend on which add-ons the customer wants to use. For example, "an add-on for essential single-cell analysis can be around $3,000 per year, with special discounts for academic labs," Pham explained. Users can also choose a more advanced iteration of the single-cell add-on with additional features, such as automatic cell type prediction, but they will have to pay more. Furthermore, the company can create customized add-ons to meet specific needs. For example, "we can partner with single-cell transcriptome or ATAC-seq companies to build add-ons for their specific sequencing protocols," Pham said.
Ultimately, BioTuring's goal is to make single-cell and RNA sequencing data accessible to as many people as possible, especially biologists and clinicians, according to Pham. One of the key benefits of single-cell sequencing is that "we can see diseases in single-cell resolution and we can also see the effects of drugs in single-cell resolution," but "we are dealing with petabytes of data," he said. Several dozen or even several hundred samples can quickly result in thousands of data points. "It is a great area for [applying] machine learning, [artificial intelligence], knowledge-based curation, and modern data visualization [technologies]."
Single-cell sequencing is already being used in a variety of settings. For example, a recent study from researchers at Max Planck Institute for Evolutionary Anthropology and elsewhere used a combination of single-cell RNA sequencing and reporter-based lineage tracking to study molecular processes involved in limb regeneration of the axolotl (Ambystoma mexicanum), an amphibian known for its ability to regrow lopped-off arms or legs. In another recent study, researchers from the Sanford Burnham Prebys Medical Discovery Institute used single-cell analysis to identify copy number variants that occur in developing brains.
The browser is not the only tool in BioTuring's product portfolio. In April of this year, the company launched BioVinci, which offers statistical tools and algorithms for analyzing and visualizing data and for generating custom plots for publication. The company offers a trial version of the BioVinci software for customers to test. After that, they will have to pay an annual fee for continued access. The company offers different pricing for student, academic, and commercial customers, and depending on the number of devices that will run the software.
Pricing starts at $60 for an annual license for students and $99 for an annual academic license. However, the company is willing to offer discount pricing to academic institutions that purchase licenses for students. The company also offers six-month licenses for short-term projects for each customer category. To date, researchers in more than 150 institutions have used BioVinci for their projects, according to the firm.
Another BioTuring product, called Hera, is designed for RNA transcript quantification. According to the company's website, the most recent iteration of Hera outperforms similar tools, such as Kallisto and Salmon. Hera is also used in the RNA-seq add-on to the BioTuring Browser. As a standalone solution, Hera is free for academic institutions to use, Pham said.
BioTuring's products are used by customers such as the Lieber Institute for Brain Development, which focuses on translating research into basic genetic and molecular mechanisms of schizophrenia and related developmental brain disorders into clinical advances. The institute houses a repository of human brain material gleaned from over 3,000 human brain tissues and has been involved in several investigations. This includes studies performed as part of the BrainSeq consortium, an initiative between the Lieber Institute and pharmaceutical companies AstraZeneca, Astellas, Eli Lilly and Company, Lundbeck, Johnson & Johnson, Pfizer, and Roche. The consortium is trying to characterize genetic and epigenetic regulation of transcription in distinct brain regions across the human lifespan in samples from cases of major neuropsychiatric disorders and controls.
"We have generated huge human datasets about gene expression regulation in the human brain across the lifespan … and in a variety of neuropsychiatric disorders," said Daniel Weinberger, CEO of the Lieber Institute and a professor in the departments of psychiatry, neurology, and neuroscience at Johns Hopkins University School of Medicine. As such, "we became extremely interested in the BioTuring toolbox."
Lieber Institute researchers have developed their own software for visualizing expression data, including BrainCloud, a free application for exploring temporal dynamics and genetic control of transcription in human brains.
However, the user-friendliness, fast analytics, and the quality of the visualizations offered by BioTuring's products could not be matched, according to Weinberger. In fact, the institute was so impressed with the functionality of the BioTuring software that it decided to invest in the company, he said. Furthermore, researchers at the institute have worked with the company to customize the browser for internal use, as well as to make some internal single-cell sequencing datasets available on the BioTuring Browser. In terms of specific customizations, the institute has developed a pipeline for RNA-seq analysis, differential gene expression, and eQTL analysis that it wants implemented in BioTuring. It also has developed software for RNA editing, based exclusively on messenger RNAs that it wants included in the BioTuring platform.
"We have about 10 biologists here that are not data scientists who are using BioTuring daily" and are "able to look at very high-dimensional data on their own desktops without the need for data scientists for every analysis or visualization that they want to do," Weinberger said, adding that the browser is a much more "sophisticated and complete suite of programs."
Jarrod Harman, a researcher at LSU Health New Orleans, echoed similar sentiments regarding the ease of use of BioTuring's products. He is an ophthalmology research associate in the laboratory of Jeffrey Gidday and a graduate student in physiology at the Louisiana State University School of Medicine in New Orleans and currently uses the BioVinci software as part of his research.
Besides the user-friendliness of BioVinci, Harman pointed out the drag-and-drop interface and the ease of creating templates that can be reused for different datasets. Other benefits include the software's functional outputs, such as publication-ready plots. It also provides guidance on the best templates and plots for users who may not be familiar with the best applications to use for their sequence data. "The way that they have it set up in their software, you can read when is a good time to use this application, what types of tests and what types of studies use these applications," he said. "Then it gives you templates and transformations that you can essentially copy and paste to format your data the same way. For me, that opened an entire new category of graphical functions that I was, prior to this software, incapable of doing."
Besides software, BioTuring also provides bioinformatics consulting services that are focused on RNA-sequencing data. Its list of services includes gene function annotation, including gene ontology and gene enrichment analysis, as well as gene and transcript quantification. The company also offers differential expression analysis, SNP calling, and annotation services.