Regardless of whether you need to integrate NGS-type test ordering with hospital systems such as Cerner and Epic or require a custom web-based interface to facilitate the order filling workflow, our team is capable of providing the solution that best fits your specific requests. We leverage standard vocabularies such as SNOMED-CT and HL7, and are also prepared to assist with 21 CFR Part 11, HIPPA compliance and deploying applications on a CAP/CLIA environment.
Sequencing and Lab Integration
Efficient and reliable lab procedures are essential for maintaining high standards of patient care. To overcome the challenges that may arise in this area, SemanticBits has developed advanced systems of tracking biospecimens. These systems integrate with lab information management systems to streamline test processes. Once sequencing is complete, we can automatically kick off informatics pipelines and pull data directly from sequencing instrumentation like Illumina. This helps labs operate at the highest level, the benefits of which are passed on to patients.
Our experience working with public and private cloud platforms, such as AWS, Eucalyptus, and Illumina’s new BaseSpace cloud offering, allows us to help you deploy and utilize tools such as Galazy and CloudBioLinux in these environments. This in turn results in the proper configuration of common bioinformatics tools such as GATK and Pindel, HPC tools like HTCondor and Sun Grid Engine, as well as the Hadoop ecosystem, include MapReduce, YARN and Hive.
Having successfully built systems that integrate patient genomes with data sets, such as RefSeq, Ensembl, dbSNP, COSMIC, and 100 Genomes, we’re confident in our ability to help you build highly flexible UIs for author reporting as well as structured knowledge bases of clinical interpretations. Additionally, we can build a custom genome browser or integrate with existing ones in order to visualize any variants that might occur throughout operational processes.
Interpreting genomic data can be one of the most difficult aspects of the clinical genomic workflow. The process, besides being costly, involves accounting for hundreds of patient genomes per day, and the number of variables involved can result in additional complications. To combat this, SemanticBits makes smart use of available technology to implement sophisticated data management infrastructures that integrate genomic data with actionable clinical interpretations, facilitating personalized medicine and improved patient care.
Integrating hundreds of patient genomes per day to genomic annotations, variant annotations and clinical interpretations presents a significant computational challenge. In addition to our experience building systems that integrate patient genomes with data sets, our team also has implemented modern technology to build and maintain a large, diverse and rapidly changing rule-based knowledge base of clinical interpretation, which in turn facilitates clinical decision making.