BC Platforms (Biocomputing)
The purpose of the platform is to provide a database structure for handling and analyze genetic, sequence and related phenotypic data, facilitating analysis of data so that most researchers will be able to perform analyses without being programmers or bioinformaticians. The system stores personal data in a secure way where tracking of changes is available. It is also possible to customize access such that new EU data directive and GDPR is followed in that each researcher only have access to the data needed. Login will be done with double authentication (under implementation).
The system has many genetic statistical programs and tools for quality control, imputation and statistical analysis implemented in a user friendly way, tools such as PLINK, Haploview, Eigenstrat, Impute2, Minimac etc. In addition it is possible perform analysis using R or SAS scripts. For next generation sequencing data functional annotation is available. Data can be exported in many different formats. There is a separate module for handling storage of samples. Further there is a module for managing pedigree information.
Each group using the system has paid an annual fee billed directly from BC platforms covering license fee of the software they use. The amount payed depends on the software modules used. In addition to this cost each research group are billed by the CMM–IT department in relation to how much server space they use on the server. For further details and pricing please contact henrik.plym-forshell@bcplatforms.com.
Responsible person: Ingrid Kockum
Requests regarding storage can be directed to helpdesk@cmm.se.
BC PLATFORMS SOFTWARE MODULES
BC|GENOME
BC|GENOME is a data and research management platform for clinical genomic studies. Genomic and phenotypic data is collected and stored on the platform, and users have access to data and tools through an application account. All common data types for NGS, GWAS, variant analysis, linkage, and other statistics can be managed on the platform. BC|GENOME scales up from small candidate gene studies to massive international collaboration environments.
BC|SAMPLE
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.
BC|CLIN
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|SAFEBOX
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.
BC|PREDICT
The BC|PREDICT software product provides comprehensive decision support in the analysis of sequencing data. It accepts the output from any sequencing platform and turns the genome information into actionable clinical intelligence. It is easy to use and helps a laboratory attain better productivity in developing and using genetic biomarker tests and custom gene panels.
BC|CORE
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 or anonymisation in different data collections for patient confidentiality. BC|CORE is an add-on module for BC|GENOME and BC|CLIN products.
BC|INSIGHT
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.
BC|PIPE GT
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. Removes 90% or more of manual QC work previously performed with Illumina Genome Studio.
BC|PIPE NGS
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. An additional module for tracking data quality in the NGS process is available (BC|Q), offering extensive longitudinal reporting of performance. 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.
BCRQUEST.com
BCRQUEST.com is a modern ICT-enabled marketplace that brings together biobanks and pharmaceutical companies to engage in new forms of collaboration. BCRQUEST.com 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.