A collaboration with the FDA: new insights using real-world evidence

This latest study applies our method of assessing disease progression in real-world cancer datasets to a large cohort of patients with advanced NSCLC treated with PD-1/PD-L1 inhibitors...


Understanding the Biological Data Driving Bioinformatics

In the realm of scientific exploration, bioinformatics stands at the crossroads of biology and information technology. Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. It combines biology, chemistry, physics, computer science, computer programming, information engineering, mathematics, and statistics to analyze and interpret biological data.  It’s a discipline that relies heavily on biological data to gain insights into the complexities of living organisms. In this article, we explore the various types of biological data utilized in bioinformatics and how these data sets drive advancements in genomics, proteomics, and beyond.

Types of Biological Data

Biological data can be classified into different types according to their level of organization, complexity, and format. Some of the most common types of biological data are:  
  • Sequence data – This data represents the linear order of nucleotides in DNA or RNA molecules or amino acids in proteins. Sequence data can be used to study the structure, function, and evolution of genes and proteins as well as their interactions and regulation. It can be obtained with various techniques, such as DNA sequencing, RNA sequencing, and mass spectrometry.
  • Structure data – This is data that represents the three-dimensional shape and arrangement of atoms or molecules in biological macromolecules, such as proteins, nucleic acids, or protein–nucleic acid complexes. It can be used to study the physical and chemical properties of biological macromolecules as well as their interactions and functions, and it can be obtained with techniques such as X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy.
  • Expression data – Expression data measures the amount or activity of genes or proteins in a given biological sample, such as a cell, tissue, or organism. This data can be utilized to examine the gene and protein expression patterns and profiles as well as their regulation and response to various stimuli or conditions. Expression data can be obtained through various methods, including microarrays, quantitative PCR, and proteomics.
  • Interaction data – This data identifies and characterizes the physical or functional interactions between biological molecules, such as proteins, nucleic acids, metabolites, and drugs. The data can be employed to study the biological networks and pathways that mediate various biological processes and functions. A variety of techniques can be used to obtain interaction data, including yeast two-hybrid, co-immunoprecipitation, and affinity purification.
  • Phenotype data – This is the data that describes the observable characteristics or traits of a biological entity, such as a cell, tissue, organism, or population. Phenotype data is useful for studying the effects of genetic or environmental factors on the morphology, physiology, behavior, or disease susceptibility of biological entities. Microscopy, imaging, and clinical tests are common techniques used to obtain this type of data.

Sources of Biological Data

Biological data can be obtained from various sources, such as:  
  • Experimental data – This is the data generated from laboratory experiments or field studies designed and conducted by researchers to test a specific hypothesis or question. Experimental data can provide direct and reliable evidence for a biological phenomenon or mechanism, but it can also be limited by the availability of resources, time, and ethical constraints.
  • Public data – This is data collected and shared by researchers or organizations through public databases or repositories that are accessible online. It can provide a large and diverse amount of information for a biological topic or problem, but it can also be heterogeneous, incomplete, or inconsistent in quality and format.
  • Simulated data – This form of data is the product of computational models or simulations based on mathematical or statistical assumptions or rules. Simulated data can provide a theoretical or hypothetical scenario for a biological system or process, but it can also be inaccurate, unrealistic, or oversimplified.

Genomic Data: The Blueprint of Life

At the heart of bioinformatics lies genomic data—the complete set of genes within an organism’s DNA. This data provides a comprehensive blueprint of life, enabling scientists to understand the hereditary information passed from one generation to the next. Genomic data is instrumental in studying the structure, function, evolution, and regulation of genes, unraveling the secrets of our genetic code.

Transcriptomic Data: Decoding Gene Expression

While genomic data reveals the genes present in an organism, transcriptomic data unveils how these genes are expressed. It represents the RNA transcripts produced by active genes, shedding light on the dynamic nature of cellular processes. Understanding transcriptomic data is crucial for deciphering the intricate mechanisms that govern various biological functions, helping researchers pinpoint when and where specific genes are active. By obtaining genome-wide transcriptome data from single cells using high-throughput sequencing (scRNA-seq), researchers are able to use scRNA-seq analysis to detect cell subpopulations within certain conditions or tissues.

Proteomic Data: Unraveling the Protein Landscape

Proteomic data focuses on the study of proteins, the functional workhorses of cells. This data reveals the types, quantities, modifications, and interactions of proteins within a biological system. By analyzing proteomic data, scientists gain insights into the intricate networks that govern cellular activities. This is particularly valuable in understanding diseases, as aberrations in protein expression or function often underlie pathological conditions.

Metabolomic Data: Tracing Metabolic Fingerprints

Metabolomic data provides a snapshot of the small molecules present in a biological system, offering a glimpse into the metabolic activities of cells. This data is crucial for understanding how organisms process nutrients, produce energy, and maintain homeostasis. Metabolomic analysis is especially valuable in studying diseases with metabolic components, such as diabetes or metabolic syndrome.

Epigenomic Data: Uncovering the Marks on DNA

Epigenomic data explores the chemical modifications that influence gene expression without altering the underlying DNA sequence. These modifications, such as DNA methylation and histone acetylation, play a pivotal role in regulating various cellular processes. Examining epigenomic data allows researchers to unravel the intricate epigenetic landscape that influences development, aging, and disease.

Structural Data: Peering into Molecular Architecture

To truly understand the intricacies of biological systems, scientists rely on structural data. This includes information about the three-dimensional shapes of molecules, such as proteins and nucleic acids. Structural data is essential for elucidating the molecular mechanisms underlying biological processes, facilitating the design of targeted drugs and therapies.

Microbiome Data: Exploring the Bacterial Universe Within

The human body is home to trillions of microorganisms collectively known as the microbiome. Microbiome data involves the study of the genetic material of these microbes, providing insights into their diversity, abundance, and functional roles. Understanding the microbiome is crucial for comprehending its impact on human health, from digestion to immune function.

Integrative Data: Connecting the Dots Across Domains

In the ever-expanding landscape of bioinformatics, the real power lies in integrating diverse datasets. Integrative data analysis involves combining information from genomics, transcriptomics, proteomics, and more to gain a holistic understanding of biological systems. This multidimensional approach enables researchers to unravel complex biological phenomena and identify novel connections.

Harnessing the Power of Biological Data

In the era of precision medicine and personalized therapies, the significance of biological data in bioinformatics cannot be overstated. It serves as the compass guiding researchers through the intricate landscapes of genomics, proteomics, and beyond. As technology continues to advance, the wealth of biological data available will undoubtedly propel scientific discoveries, ushering in a new era of understanding and manipulating the very fabric of life. Decoding the language of biological data opens doors to transformative possibilities, promising a future where we can harness the power of life’s code for the betterment of humanity. If you’re eager to harness the power of comprehensive data management in the life sciences and unlock new possibilities for your research or healthcare initiatives, look no further than Rancho BioSciences. Our bioinformatics services and expertise can propel your projects to new heights. Don't miss the opportunity to take your data-driven endeavors to the next level. Contact Rancho BioSciences today and embark on a journey of innovation and discovery.

Rancho will be in Basel this week at BioTechX, booth# 806. Stop by to hear all about our brilliant services. Saving Lives Through Data!

Rancho Biosciences, the premier Data Science Services company headquartered in San Diego, California, is thrilled to announce its participation in Europe's largest biotechnology congress, BioTechX, a pivotal event that serves as a bridge between pharmaceutical companies, academia, and clinicians. The event aims to foster meaningful collaborations and catalyze innovation within the biotechnology and pharmaceutical industries.

As a leading player in the field of data science, Rancho Biosciences is dedicated to revolutionizing drug development and healthcare through the application of advanced technologies and data-driven strategies. The company is proud to spotlight its key service highlights at BioTechX, which include:

AI in Drug Development and Discovery: Rancho Biosciences harnesses the power of artificial intelligence to uncover groundbreaking insights and streamline the drug discovery process. They offer pre-packaged data sets specifically designed to train AI and machine learning algorithms.

Data Integration + FAIR: Rancho Biosciences goes beyond data management; they standardize and optimize data to be analysis-ready. Their commitment to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) ensures data remains valuable and accessible. Their technology enables rapid data processing without compromising quality.

Bioinformatics R&D: With a team of world-class bioinformaticians, Rancho Biosciences brings extensive experience and domain knowledge to the table. They are dedicated to training and mentoring new talent for their clients.

Single Cell Genomics and NGS: Rancho Biosciences leads the way in curating single cell data sets, including deep annotations, and they have developed an SC Data Model to harmonize thousands of data sets. They also offer data sets with fewer metadata fields optimized for AI applications, all at competitive pricing.

Data Management, Storage, and Architecture: Learn how Rancho Biosciences can help organizations implement state-of-the-art infrastructure and strategies to manage large datasets effectively. Their services encompass building Data Lakes, knowledge portals, workflows, and more to meet the unique needs of their clients.

Digital Transformation: Rancho Biosciences isn't just observing the digital evolution of biotech; they are leading it. Attendees will discover how to harness the potential of digital tools and technologies to reshape and revolutionize the biotech landscape.

Real World Evidence: Rancho Biosciences' expertise in leveraging real-world data is changing the game by enhancing clinical outcomes and informing patient care and treatment methodologies.

Analytics Platforms: Explore the depths of data with Rancho Biosciences' robust analytics tools designed to decipher complex datasets and derive actionable insights for drug development.

About Rancho Biosciences:

Founded in 2012, Rancho Biosciences is a privately held company that offers comprehensive services for data curation, management, and analysis to organizations engaged in pharmaceutical research and development. Their client portfolio includes top 20 pharmaceutical and biotech companies, research foundations, government labs, and academic groups.

For further information and press inquiries, please contact:

Julie Bryant, CEO


For more information about Rancho Biosciences and their participation in BioTechX, please visit or stop by their booth# 806 at the event.

Source: Rancho BioSciences, LLC

Please visit Rancho next week at The Festival of Genomics, Booth# 4. Boston Convention & Expo Center, October 4 – 5.

Rancho Biosciences, the leading Data Science Service company, will be presenting expanded Data Science Services including our LLM work and a new product, Data Crawler that allows scientists to self-serve and find data sets they are looking for easily and quickly. The Festival of Genomics conference runs October 4-5, 2023, at the Boston Convention and Exhibition Center. Rancho’s mission of saving lives through data will be on full display through case studies, impact we have had on projects, biomarker discovery and clinical trials.

Julie Bryant, CEO and Founder, said: “Our goal is to be a partner and provide value through working efficiently with data, automating wherever possible and leveraging technologies such as AI/ML/NLP/LLM to provide high quality results with value and ROI.”

Rancho Biosciences is eager to introduce our cutting-edge services and insights to the attendees and engage with peers and pioneers alike to witness firsthand how we can turn your data into a catalyst for unmatched insights.

Why Visit Rancho Biosciences at The Festival?

Expert Insights: Delve deep into the realm of different data modalities with our scientists to better understand the latest breakthroughs and applications including single cell and spatial transcriptomics.

Tailored Solutions: Discover how our domain expertise and specialized offerings can pivot your genomics research or clinical endeavors to actionable results.

Interactive Discussions: Engage in meaningful conversations and solution-driven dialogues with our team of experts, discussing challenges and crafting a roadmap where we can build knowledge bases, data portals, unique analysis tools, workflows and pipelines.

About Rancho:

Founded in 2012, Rancho Biosciences is a privately held company offering services for data curation, management and analysis for companies engaged in pharmaceutical research and development. Its clients include top 20 pharma and biotech companies, research foundations, government labs and academic groups.

For press inquiries, please contact:

Julie Bryant

Rancho leverages the power of LLM (Large Language Models)

At Rancho BioSciences, we leverage the power of large language models (LLMs) to provide a diverse range of services, enabling innovative ways to interact with data, including unstructured text, omics, and imaging data. Our expertise goes beyond the hype, delivering tangible value to our clients.

Our offerings include:

  • Natural Language Processing: Gain actionable insights and enhance decision-making through advanced understanding and analysis of unstructured text data.
  • Information Extraction: Streamline workflows and improve efficiency by accurately retrieving relevant information from vast data sources.
  • Semantic Search: Enhance search functionality with context-aware results, ensuring accurate and relevant outcomes tailored to user intent.
  • Prompt Engineering: Optimize communication and interaction with LLMs through expertly designed prompts that generate high-quality responses.
  • Fine-tuning: Customize and adapt existing foundational models for seamless integration within the client's environment, maximizing performance and effectiveness.

In addition, we specialize in natural language querying (NLQ), making internal and public datasets easily accessible across large organizations. Our approach focuses on delivering tailored solutions that meet your unique requirements, driving tangible results and exceeding expectations.

RanchoBiosciences Offers CDISC-Compliant Data Curation Services Via SDTM

The Clinical Data Interchange Standards Consortium (CDISC) was developed to ensure healthcare, clinical, and medical research data are consistently presented and interoperable as a way of improving medical research. CDISC standards also help ensure data is FAIR (Findable, Accessible, Interoperable, and Reusable), which maximizes the data’s impact in terms of sharing capabilities, reducing R&D costs and timelines, and accelerating innovation. 

The Study Data Tabulation Model (SDTM) is the CDISC-compliant standard format for data submitted to the FDA and other regulatory authorities. However, ensuring data adheres to the SDTM format can consume valuable time and resources, especially when data is derived from multiple studies. 

Rancho BioSciences has developed a semi-automated workflow combining automated and manual curation, designed to flag and correct mistagged fields. This script, which first creates a preliminary tagged summary file, goes through a rigorous manual quality control protocol to ensure all domains, fields, and code lists are updated to current SDTM standards. 

The resulting tagged summary file undergoes a final automated step, designed to eliminate unnecessary fields, reformat values to adhere to SDTM standards, and reorder columns per domain standards. Rancho BioSciences’ SDTM curation services create high-quality, accurate, and reliable data files to lead researchers towards actionable insights. 

Rancho BioSciences is partnering with public and private research institutions

Image: Mixed rat brain cultures stained for coronin 1a, found in microglia here in green, and alpha-internexin, in red, found in neuronal processes. Antibodies and image generated by EnCor Biotechnology Inc. GerryShaw, CC BY-SA 3.0 <>, via Wikimedia Commons

Rancho BioSciences is partnering with public and private research institutions to develop a comprehensive data catalog of transcriptomic studies of myeloid cells. These highly complex cells exhibit high plasticity and context-specific functions, making them difficult to study. Collecting and organizing data from existing transcriptomic studies will help researchers gain a global perspective on myeloid lineages and how they impact aging and disease.