Explore Rancho Data Science Services
Rancho BioSciences provides data curation services for pharmaceutical and biotech companies, as well as for academic institutions, foundations, and the government. Rancho works with different life science data types, including clinical trials, genomics, gene variants, assays, chemistry, microbiome, flow cytometry, and imaging data. The data can be internal and/or public. Rancho BioSciences is platform-agnostic and has a lot of experience formatting data for many commercial, internal, and public (open-source) platforms.
AI, ML, and NLP Services
Rancho BioSciences’ full-cycle AI applications include data preparation, model training, and insights generation. We customize our data science workflows to address unique research needs, including support for clinical trials, extracting information from unstructured text, and processing and integrating multi-dimensional omics datasets. By analyzing large volumes of data using state-of-the-art AI models, our clients gain valuable insights that enable them to accelerate scientific progress, improve research efficiency, and drive innovation.
Our comprehensive suite of AI services empowers businesses by providing them with an expertly crafted synergy of domain experts, data scientists, and data engineers. Our full-cycle AI solutions span every essential part of the project — from data collection to robust model training — seamlessly merging cutting-edge technology and industry-specific knowledge. Together, we unlock the potential hidden within your data, enabling you to accelerate growth and drive innovation.
Get training data
Data curation is our core business. We work across all life science data types, are platform-agnostic, and have robust manual and automated workflows to extract data from public or private sources. We can then harmonize the data, run it through a rigorous QC protocol, and prepare high quality machine-readable datasets for training or benchmarking your AI/ML algorithms.
Examples of training datasets include datasets for target liability, clinical trial patient cohorts, reagents (cell line, antibody, etc.), gene-disease associations, and perturbation.
Training AI/ML
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Rancho BioSciences’ team can identify relevant data entities and attributes that are important for training and optimizing these algorithms.
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Rancho BioSciences has experienced data scientists and SMEs who can build tailor-made ML/AI models, such as for:
- Predictive toxicology
- Survival analysis
- Cellular phenotype classification
- Disease signature analysis
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Rancho BioSciences validates performance of AI/ML algorithms to ensure accuracy and reliability.
Applying AI to get insights
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A combination of large language models (LLM) and classical NLP techniques is used to extract valuable information from text (e.g., pathology reports).
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An embedding-based publication scoring algorithm enables scientists to easily find relevant information based on incomplete information.
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Rancho terminology mapping solution uses embedding, LLM, and Fuzzy to construct a semantic layer and enrich private datasets.
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We are building Natural Language Query (NLQ) applications for our customers with AI-generated queries and scoring in diverse corporate data environments.
Bioinformatics
Our Bioinformatics team can help answer scientific questions by analyzing your complex data. Whether you need a short-term boost in data analysis resources or engage a specialized team for a long-term project, Rancho can support your requirements with projects including:
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Single-cell transcriptomic analysis in R and Python. Routine analysis includes QC, dimensional reduction, clustering, and differential expression. In-depth cell profiling with atlas-based cell annotation, trajectory inference, and RNA velocity.
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Processing and analysis of multimodal data. Gene expression, proteomics, and metabolomics differential expression/abundance.
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DNA or histone binding site analysis (ChIP-seq)
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Genetic variant detection (single nucleotide variants, insertions/ deletions, copy number variants, genome structure variants)
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Association of genetic variants or gene expression profiles with disease, drug response, or clinical outcome
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Development of predictive models using machine learning or logistic regression
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Pathway analysis and functional enrichment analysis
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Phylogenetics and sequence analysis
By processing and integrating disparate data types, we can generate a comprehensive biological picture of a disease. This further informs practical biotech and pharmaceutical research and development, including applications in:
Precision Medicine:
Matching drug profiles and human genetic profiles, stratification of patient cohorts, biomarker identification
Drug discovery:
Mechanism of action studies, accelerating discovery pipelines by intelligently screening results, pharmacology applications
Translational medicine:
Drug repositioning for new indications, companions, and diagnostics, enabling cross-discipline communication
CDISC Services
Rancho Biosciences’ CDISC Services
Rancho BioSciences is a leading international data service company specializing in the curation and management of life science data, across clinical and preclinical domains. We recognize the critical significance of adhering to CDISC standards in clinical research and preclinical toxicology. These standards not only streamline drug development and regulatory submission processes but also uphold the highest standards of data quality and interoperability.
Our dedicated suite of services is uniquely poised to assist organizations in navigating the intricate landscape of CDISC standards.
Rancho BioSciences is Your Trusted Partner for CDISC Standards and Data Management Excellence:
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Expertise: Our team possesses profound expertise in handling diverse life science data, encompassing both clinical and preclinical domains.
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Combining Automation and Human in the loop: We leverage a combination of cutting-edge commercial tools and internal resources, complemented by meticulous manual curation and quality control conducted by our subject matter experts.
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In-Depth Knowledge: We have a deep understanding of CDISC formats, including SDTM and SEND, ensuring that your data maintains its integrity and remains fully compliant with CDISC standards.
What is CDISC?
In the rapidly evolving realm of clinical research, ensuring data standardization and interoperability is crucial. The Clinical Data Interchange Standards Consortium (CDISC) has established itself as the gold standard in this sphere, laying down comprehensive guidelines and structures for the collection and submission of clinical trial data that have been adopted by regulatory agencies. With the myriad of components developed within the CDISC suite, including SDTM (Study Data Tabulation Model), ADaM (Analysis Data Model), and CDASH (Clinical Data Acquisition Standards Harmonization), researchers and pharmaceutical organizations are better equipped than ever to create more efficient, transparent, and consistent clinical trials. Moreover, with the SEND (Standard for Exchange of Nonclinical Data) framework in place, the same rigorous standards can be applied to nonclinical animal study data, ensuring a seamless and holistic approach to both clinical and preclinical research phases.
Regulatory agencies worldwide, such as the FDA (U.S.) and PMDA (Japan), have recognized the significance of CDISC standards. They mandate the use of these standards in data submissions, reinforcing the importance of a structured approach to clinical data. This underscores the necessity for expertise in CDISC for any entity involved in the clinical trial and drug approval process.
At Rancho Biosciences, we pride ourselves on our deep understanding and proficiency in CDISC services. With a dedicated team of professionals well-versed in the nuances of CDISC components and regulatory requirements, we stand at the forefront of clinical data standardization, ensuring our clients' data is robust, compliant, and positioned for success in regulatory submissions. Whether you are initiating a new clinical trial or navigating the complexities of meeting CDISC standards, our expertise is here to guide you every step of the way.
Offered Services:
CDISC Data Services:
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Establishing Data Models: Rancho crafts data models tailored to your unique requirements, ensuring fluidity and consistency with CDSIC in data workflows.
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Terminology Management: Establishing controlled terminology within your data models that align with CDISC data interoperability standards.
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Data Harmonization: We unify datasets from varied sources or studies, ensuring uniformity in sync with CDISC standards.
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Applying AI: Automated Mapping Suggestions: Leveraging semantic embeddings to map documents and your unique data to CDISC-controlled terminology, our state-of-the-art AI tools offer automated mapping advice, hastening the SDTM mapping progression.
Data Capture Deployment Services:
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CDISC Adoption Advisory: Our specialists guide organizations through deployment of CDISC-compliant data capture systems, stressing compliance and streamlined change management.
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Business Analysis Expertise: Bridging the divide between scientific requisites and vendor solutions, our analysts play an indispensable role, further liaising with vendors for customized demos and configuration quotes for your team by establishing system requirements.
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SEND LIMS & EDC Product Management: Entrust us with the complexities of system configuration management, be it SEND LIMS or EDC setups, ensuring alignment between users, vendors, and CDISC standards.
Data Science Services:
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Insight Generation from CDISC Data: We delve deep into CDISC-compliant datasets, gleaning actionable insights that directly influence your clinical strategies.
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Quality Monitoring Tools: Implementation of state-of-the-art processes and tools for ongoing data quality assessment, ensuring consistency and adherence to standards.
At Rancho BioSciences, we are committed to delivering top-tier data curation and management solutions ensuring CDISC compliance and data excellence.
Rancho BioSciences provides expert data curation services to support biomedical research, drug discovery, and precision medicine.
Data Curation Services
Why is Rancho Biosciences different:
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Expertise: Others crowd source or hire temporary curators while Rancho has a team of experienced, trained Ph.D. and M.D. scientists and curators who get the tools they need to deliver results.
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Innovation: Rancho Biosciences is committed to staying at the forefront of biomedical data science and technology, with a focus on innovation and continuous improvement, such as supporting emerging AI/ML trends in the industry
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Quality: delivers high-quality services and data that are accurate, reliable, and relevant, with a focus on quality control and validation. We have a strict QC process that is rigorous and is based on years of our collective experience. We develop QC tools to help us, and we often are called to arbitrate or review what other vendors provided.
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Flexibility: Rancho Biosciences provides flexible and customized solutions that are tailored to the specific needs of each customer. By collaborating closely with clients to gain a deep understanding of their needs and goals, our team develops fit-for-purpose solutions that are unique to each project. We do not believe in a one-size-fits-all approach, and strive to deliver high-quality, customized services that exceed our clients' expectations.
At Rancho BioSciences, we cover nearly all types of Life Sciences data. Our curators have expertise in curating, annotating and enriching:
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Genomic data: DNA sequencing data, gene expression data, and genomic variations
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Clinical data: clinical data from clinical trials, biobanks, and other sources, including patient demographics, diagnoses, procedures, and medications
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Real World data: information collected in non-experimental, everyday settings including patient medical records, insurance claims data, electronic health records, pharmacy records, and data collected from wearable devices
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Imaging data: medical and R&D imaging data, including radiology images, MRI scans, and other types of imaging data used in clinical practice or research
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Omics data: large-scale datasets generated by high-throughput technologies in various areas of the life sciences, such as genomics, proteomics, metabolomics, and transcriptomics
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Assay data: experimental data generated by various types of laboratory assays, such as biochemical assays, cell-based assays, and high-throughput screening assays including CRISPR screens, Cell Painting assays and other.
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Biomarker data: quantitative measurements of specific molecules or information, such as proteins, genes, metabolites, medical imaging such as MRI or CT scans and others to evaluate anatomical and functional changes in cells or organism
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Pathway data: data on biochemical and molecular interactions in biological pathways, protein-protein interactions
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Chemical data: chemical structures, chemical properties, and chemical interactions
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Pharmacological data: drug targets, drug interactions, and drug metabolism (ADME, PK/PD, toxicity, metabolomics, and others.)
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Other types of life science data: environmental data, microbiology, toxicology, etc.
Rancho Biosciences uses automated and manual curation services:
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AI/ML/NLP development and application:
- Rancho BioSciences prepares high quality machine-readable datasets for training of your AI/ML algorithms.
- Rancho BioSciences validates performance of AI/ML algorithms to ensure accuracy and reliability.
- Ranchos BioSciences team can identify relevant entities and attributes of data that are important for training and optimizing these algorithms.
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Data Harmonization: This involves identifying and resolving differences in data formats, structures, and semantics between different data sources, and creating a common data model that allows for easy integration and analysis of the data.
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Aligning data to CDISC (SDTM, SEND and other domains), OMOP and other standard data models.
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Quality assurance: ensuring integrity of data delivered by other vendors.
- Rancho Biosciences scientists are life science domain experts who help to guide AI/ML development and data interpretation.
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Terminology services:
- Semantic data integration: Rancho Biosciences can integrate heterogeneous data sources using semantic technologies and standards.
- Customized terminology and ontology services: Rancho Biosciences can develop customized terminology and ontology services to meet the specific needs of clients, such as building a custom ontology for a specific project or application.
- Nomenclature mapping and cross-referencing: Rancho Biosciences can map and cross-reference data to standard nomenclatures, such as LOINC or SNOMED, to ensure consistency and interoperability.
- Training and support services: Rancho Biosciences can provide training and support services for clients to help them understand and effectively use biomedical terminologies and ontologies in their research or clinical practice.
- Data enrichment: Rancho Biosciences can enrich data with additional information, such as synonyms, cross-references, and metadata, to improve data quality and usability.
Our team at Rancho BioSciences has developed robust and reproducible curation workflows that utilize both automated and manual approaches. These workflows are designed to ensure that the data is accurate, complete, and of the highest quality. The team has extensive experience in curating various types of data, and their expertise allows them to tailor their workflows to the specific needs of each project.
Data Engineering
Rancho combines deep scientific knowledge and technical expertise in software engineering to provide both custom and off-the-shelf solutions.
Engineering services include, but not limited to:
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Pipelines and Process Automation
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Data Management and Migration Solutions
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Data Integration
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Data Visualizations
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Custom Analytical Tools
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FTEs To Assist Teams With Software Engineering Needs
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Technical Consulting
Rancho leverages its managed toolkit to customize solutions that meet client needs while cutting down on delivery time and cost.
Data Management, Data Governance, and Data Modeling – What Is Data Governance, Data Modeling, and Data Management?
Data management is an IT practice encompassing an organization's practices across the data life cycle.
Data governance is a business practice that defines how data is processed across the organization to ensure that data is FAIR (compliant, private, etc.).
Data modeling is a process of creating conceptual, logical, or physical data models for one’s data.
Life sciences companies accumulate data with an ever-increasing pace, and data that they use to create new treatments or new diagnostics is more diverse and complex than in arguably any other domains. With multiple data sources, data elements, stakeholders, and data consumers, it gets progressively harder and harder to scale and to maintain control over the data life cycle. There is a strong awareness in the scientific community that more data must produce more insight and knowledge, but this goal has been difficult to attain. Life Sciences businesses are now relying on the practice of data management and data governance as best business practices to wrangle data assets and realize value from data.
There are many resources that deliver data management and data governance solutions. There are frameworks, platforms, and solutions; there are tools that one can use and knowledge bases to consult with. We are different. We provide people—scientists with subject matter expertise trained in data modeling—who can help. Our people have dozens of years of experience in their respective fields of study and participated in multiple projects where they did data modeling or provided data governance support. We have real-life experience, and we can support your projects with minimal ramp-up time by leveraging data models we have already built and know-how.
Data Science
Rancho BioSciences combines advanced data science methods with life science expertise to provide comprehensive data solutions. Our team is highly experienced in statistical modeling, machine learning, natural language processing, and other data science techniques. At the intersection of life science and data science, our experts deliver tailored solutions to unlock your data’s potential, keeping our clients at the forefront of scientific exploration and development.
Our full-cycle AI applications include data preparation, model training, and insights generation. We customize data science workflows to address your unique research needs, including support for clinical trials and navigating unstructured text and multi-dimensional omics datasets. By analyzing large volumes of data using state-of-the-art AI models, our clients gain valuable insights to accelerate scientific progress, improve research efficiency, and drive innovation.
We can help you with:
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FAIRification of large datasets, transforming data from disparate sources and formats into Findable, Accessible, Interoperable, and Reusable data
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Interactive data visualization, including R-shiny, to help you explore your data and develop hypotheses
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Building custom AI/ML models and conducting statistical analyses to address your needs
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Extracting information and gaining insights from unstructured or poorly structured private or public sources
Imaging Data
Whether you would like to increase the value of your medical imaging data through better annotations or extract new insights via analysis, Rancho’s scientists can provide curation, organizational strategy, and analytical support across several types of imaging modalities.
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Neuroimaging
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Digital pathology
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High content experiments
Rancho can provide high-quality imaging data services that include:
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Data Modeling
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Data Aggregation and Curation
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Data Analysis & Reports
Imaging Data Services
Data Modeling
Medical imaging creates vast amounts of data that need to be properly stored and organized to maximize its value. Rancho Biosciences can create conceptual, logical, or physical data models for imaging data that leverage existing models and can be customized to your needs. Our scientists are experienced in data modeling and have subject matter expertise in different imaging modalities. When they create a model, they consider the complexity of your imaging data. Rancho Biosciences can build a stand-alone model or embed it in a larger “omics” model, linking the data to other collected biospecimens.
Data Curation
For accurate interpretation of medical images across datasets, the images need to be well documented, and their metadata standardized. With expertise in this area, Rancho scientists can ensure that data meets F.A.I.R. data standards. Rancho scientists have experience in the aggregation, automated extraction, and integration of imaging data such as H&E, single biomarker or multiplex IHC, structural and functional MRI, and PET. Our scientists have both clinical and technical knowledge that will help maximize the value of your imaging data. Rancho scientists have experience working with clinical data and research data from a variety of diseases such as Parkinson’s Disease, Alzheimer’s Disease, Traumatic Brain Injury, Huntington’s disease, and from oncology and immunology studies, and are well-versed in applying imaging data standards. Their understanding of the study process e.g., data lineage from biospecimen collection to scanning of an image, will ensure that the value of your annotations is maximized.
Data Analysis & Reports
Imaging data is highly advanced and can be technically challenging. Our scientists have real-life experience handling imaging data from various modalities and understand its complexity. Rancho scientists can build tools to visualize your data, evaluate quantified measurements from processing algorithms, create pipelines to compare different image processing algorithms through statistical testing, provide reports and QC support, and prepare your data for further downstream analysis.
Knowledge Mining
Our team of highly qualified Ph.D. and M.D. scientists can help you collect information to support your projects. If you have a need to assess a new target, or compile competitive intelligence, or assemble a dataset of toxicity endpoint – we can help. Our expertise includes:
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Data gap analysis – we will find what is missing in your data collection and come up with ideas to fill in those gaps.
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Crawling public resources to identify relevant datasets for your research needs. A custom-designed Crawling tool efficiently queries NCBI and EMBL resources and provides results in a user-friendly Excel format.
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Developing custom scoring systems and generating profile reports for target prioritization.
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Assessing therapeutic landscape to understand unmet needs, patient populations, competitors to make informed decisions about product development.
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Building knowledge bases for various life science domains, including diseases, genetic variants, microbiomes, drugs, assays and other.
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Extracting relevant information from publications such as interactions, assays, drug activity and toxicity, clinical trials, phenotypes, genetic variants, expression signatures, adverse events, biomarkers, patient population, and other domains.
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Gathering information for drug repurposing.
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Assisting with panel development by creating comprehensive lists of relevant genes based on literature and public databases and gathering information to facilitate gene prioritization.
The team's knowledge mining abilities are unparalleled, and their dedication to understanding each customer's unique requirements allows them to provide tailored solutions that deliver high-quality, actionable insights.
Proteomics
Our scientists are highly skilled across a wide range of quantitative and comparative proteomics study designs. Rancho’s team will work with you to define the scope of your project and develop a proposal detailing all deliverables, timelines, risks, expectations, and costs. From start to finish, we’ll keep the lines of communication open and provide support as needed. Our range of proteomic services include (but are not limited to):
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Peptide inference and quantification pipeline
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Single-cell proteomic solutions
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Optical proteomics
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Data modeling and ingestion
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Differential proteomics
What Can Be Delivered?
Data Models:
Delivered as ERDs, in many cases with data dictionaries. We use a variety of tools to deliver data models, LucidCharts and ER studio by IDERA being the most common.
Data Governance as a Process:
We provide scientists trained in data modeling and experienced with data governance projects to support your team operationally. We bridge scientists and IT departments and provide oversight on the data governance process at your organization. We develop community outreach to educate your team on best practices. We write SOPs, post them, and check that people adhere to the recommendations
Documentation, Strategy Documents, Investigation of Third-Party Tools:
We help clients develop short and long data strategy. Often, young companies focus on research and work hard to develop a new drug or a diagnostic—and find themselves in need to quickly become ready for a regulatory finding, but they lack the skillset in-house to approach this stage of growth. Rancho team can evaluate the current state and find solutions for future data state 0- tailored to the specific needs of the client. We do not own software or platforms and will provide our opinions based on our experience and expertise to help clients select the best solution for their situation.
Unlocking the Power of Subject Matter Experts: Rancho's Differentiator
In the fast-paced world of life sciences, subject matter experts (SMEs) make all the difference by providing the critical insights and specialized knowledge required to navigate the complexities of research, innovation, and breakthroughs. At Rancho Biosciences, our SMEs are our secret sauce of “human expert in the loop” for success.
Rancho SMEs are scientific professionals with deep knowledge and experience in diverse domains of life sciences, including biology, chemistry, genetics, and more. Our SMEs set Rancho apart from the competition through:
Unparalleled Expertise: Our team of SMEs is comprised of highly qualified professionals with advanced degrees and years of hands-on experience in their respective fields ready to tackle complex scientific challenges.
Tailored Solutions: Rancho understands that no two projects are the same. Our SMEs work closely with clients to develop customized solutions aligned to their unique scientific objectives. This guarantees that our services consistently match the specific requirements of our clients.
Interdisciplinary Collaboration: We foster a culture of collaboration and cross-disciplinary communication within our organization and client organizations. This means that our SMEs not only excel in their individual areas of expertise but also work seamlessly together to deliver comprehensive solutions. Rancho frequently works with multiple teams within one pharmaceutical and biotechnology company and fosters collaboration by connecting client teams, which results in data and technology sharing and diminishes duplicated efforts.
Scientific Rigor: Rancho's commitment to scientific rigor is unwavering. Our SMEs bring a critical eye to every project, ensuring that data is analyzed, interpreted, and reported with the highest level of accuracy and integrity.
Continuous Learning: In the ever-evolving landscape of life sciences, staying current is crucial. Rancho's SMEs are dedicated to ongoing education by keeping abreast of the latest advancements and technologies to deliver cutting-edge solutions.
Your Partner in Data Solutions
When you choose Rancho Biosciences, you are gaining a trusted partner with a deep knowledge to support all stages of Research and Development. Join us in harnessing the power of SMEs and experience the Rancho difference.