Academia

Academic research and science is the blueprint for success. BC Platforms is specialized on delivering solutions for large scale collaborative research projects. Our platform supports the work around efficient genomic analysis, data management, and networking by bringing diverse partners together with constantly growing genotypic and phenotypic datasets. Our client scientists are able to mine data sets, perform analyses, and share their results in a secure manner. The full workflow from the physical sample all the way to final report can be done using our system. The system runs over 35 most commonly used statistical algorithms and BC|API (Application Programming Interfaces) enables direct programming on top of our open platform. BC Platforms is constantly seeking different collaboration projects with academic research groups.

Use Case

BC|RQUEST is a modern ICT-enabled marketplace that brings together biobanks and pharmaceutical companies to engage in new forms of collaboration. BC|RQUEST is a service platform for pharmaceutical research teams, and biobanks to communicate with each other. The service provides data discovery users (research teams) with tools to browse and analyse the summary level information from data providers (biobanks), who have subscribed to the service. Biobanks connect their data collections to the service via a secure link that collects summaries of query results, never exposing the actual content. BC|RQUEST is a safe and confidential environment for pharmaceutical researchers to seek suitable patient cohorts within validated data cloud of multiple biobanks world-wide. The service gives both sides communication tools to conduct research proposals, coordinate collaboration, and request data and samples under DTA and NDA.
The BC|PIPE NGS implements automated workflow from NGS device output i.e FASTQ file (Illumina, for device other vendors all the features might not be supported) to (g)VCF to be stored to BC|GENOME. Two additional modules are available: BC|Q for tracking data quality, and security option for providing full log of data processing steps. For NGS alignment and variation calling pipeline, two options are provided: Microsoft Genomics Service or Sentieon software solution. BC|PIPE NGS implements fully automated, highly scalable NGS data secondary analysis pipeline.
BC|PIPE GT is a QC workflow tool designed for Illumina genotyping data. The tool analyses the quality of genotypes, samples, and chips creating a report of the items falling below QC thresholds. BC|PIPE GT also filters bad quality items, reporting them, and generating a genotype file ready for analytical processing in bioinformatics applications. BC|PIPE GT uses Illumina iScan devices' GTC file as input, utilising the EGT and chip manifest files for array structure and composition. This QC pipeline is designed to be implemented as part of a standard operating procedure for genotyping in laboratories.
BC|INSIGHT presents commonly used analytical and bioinformatics tools as easily accessible user interfaces. Bioinformaticians and analysts can create script-aided workflows utilizing either the off-the-shelf supported, peer-reviewed packages, or they are free to integrate in-house scripts (like R) and tools for the graphical user interface. BC|INSIGHT operates on data available via BC|GENOME platform, and relies of the platform's data integrity features. This creates a discoverable track chain of events for analytical tasks and projects. Users and administrators are able to rerun and iterate old analytical tasks, change parameters and data, and create repeatable, and traceable bioinformatics workflows.
BC|CORE is a patient consent management tool, and patient (participant) code register. BC|CORE helps biobanks and repositories to organise their data access policies around various patient consent models. BC|CORE supports versioning of consents, and dynamic access changes to patient data, when changes are registered to the consent manager. Patient alias registry provides pseudonymisation and anonymisation in different data collections for patient confidentiality. Alias registry is secured and uses configurable  encryption algorithms to mask identifiable data, where required. BC|CORE is an add-on module for BC|GENOME and BC|CLIN products. BC|CORE provides compliance with biobank legislation and regulations concerning consent-based data access. It holds technical mechanisms to comply accurately with consent and sample registration events during sample collections, and provides mechanisms to modify access to patient data upon consent changes and withdrawal of consent.
BC|SAFEBOX is a security and confidentiality construct. It facilitates the analysis of sensitive patient data in environments where copying and exporting data or results is restricted. BC|SAFEBOX provides a secure server environment to perform research tasks as with BC|GENOME. In this environment the researcher is restricted into operating only within the platform, and in the immediate network connecting the platform to a calculation resource. Data and results can only be exported or sent out under distinct agreement between parties. The module provides a very high security environment in complex collaboration projects, isolating data analysis with technical means. BC|SAFEBOX can enable access to biobank data without moving it out from the biobank network, or from the country.
BC|SAMPLE is a multipurpose sample tracking and processing tool for research use. BC|SAMPLE supports sample –oriented workflows, location tracking, plate creation and processing. The application provides data importing and exporting in various formats, including customised instrument formats. BC|SAMPLE has tools for basic laboratory sample processing like creating aliquots or pipetting worksheets, and plate worksheets. The application stores repeated sample processing results for easy viewing of sample status and history. BC|SAMPLE integrates with other BC products, allowing sample data to be cross-referenced with clinical information. BC|SAMPLE conforms to the same data security features and standards as other BC products, providing project, role and dataset-level permission control, and full trail of sample ownership and history. It minimises the number of hands-on workflow steps in data recording and provides semi-automated workflows for repeating tasks.
BC|CLIN is a flexible and scalable platform for managing patient data collections. BC|CLIN has tools for designing and implementing web-based patient questionnaires for longitudinal studies, and tools for queries, reports, and stratification. The platform contains summary statistics applications, and export options to statistical programs. BC|CLIN facilitates standardized data input, reducing risk of human error, and increasing the quality of the data collection. BC|CLIN conforms to strict data security standards and controls data access at group, role and dataset levels. The application makes collection of patient data with questionnaires and fill-in forms easy and straightforward. BC|CLIN increases data integrity and quality in long-living data collections and acts as a harmonised data hub. The product helps clinical projects to comply with data security and patient confidentiality regulations and standards.
BC|GENOME is a data and research management platform for clinical genomic studies. The platform manages NGS, GWAS, PheWAS, variant analysis, linkage, and other data formats, and offers tools for complex queries in clinical and genetic data for multiple purposes. BC|GENOME scales up from small candidate gene studies to massive international collaboration environments. The platform is used to organise data projects, and to administer user and user-group access to sources. BC|GENOME provides fine-grained access management and auditing tools for building quality certified processes. BC|GENOME helps data and research managers to maintain and increase data integrity, quality, and efficiency of work. Flexible integration options allow access to external SQL and no-SQL sources, HL7 communications (EHR), cloud storage systems, and computational infrastructures (SunGrid, SLURM, Torque). All project data is managed in one location, sharing with other projects in a high-security environment.