*Data-retrieval: the HIVE is capable of retrieving data from a variety of sources such as local, cloud-based or network storage, sequencing instruments, and from http, ftp and sftp repositories. Additionally, HIVE implements the sophisticated handshake protocols with existing large scale data platforms such as NIH/NCBI to download large amounts of reference genomic or sequence read data on behalf of users in an easy and accurate manner.
*Data-warehousing: HIVE honeycomb data model was specifically created for adopting complex hierarchy of scientific datatypes, providing a platform for standardization and provenance of data within the framework of object-oriented data models. By using an integrated data-engine, honeycomb, HIVE contributes to the veracity of biomedical computations and helps ensure reproducibility, and harmonization of bio-computational processes.
*Security: HIVE-honeycomb employs a hierarchical security control system, allowing the determination of access privileges in an acutely granular manner without overwhelming the security subsystem with a multiplicity of rules. It provides on the fly encryption/decryption of PII and is compliant with the highest security protocols as requested for systems authorized to operate in regulatory FISMA moderate environments.
*Integration: HIVE provides unified Application Program Interface (API) to search, edit, view, secure, share and manipulate data and computations of all types.  As an Integrator platform HIVE provides developers means to develop (C/C++, Python, Perl, JavaScript, R) and integrate existing almost any open source or commercial tools using generic adaptation framework to integrate command line tools. Additionally session controlled web-API provides means to drive HIVE to perform data quality control and complex computations on behalf of remote users. Currently there are tens of big data analytics tools  in production HIVE and dozens more being developed; these include but are not limited to DNA-, RNA-, Transposon-, Chip-, Immune-sequencing), de novo assembly, population genomics metagenomic sequencing, differential profiling, statistical, classification and clusterization utilities to study bacteria, viruses, human germline and somatic profiles, quasispecies, infections, pathogens.
*Computations: Unlike many virtual computing environments, HIVE virtualizes services, not processes: it provides computations as a service by introducing agnostic abstraction layer between hardware, software and the computational tasks requested by users. The novel paradigm of relocating computations closer to the data, instead of moving data to computing cores has proven to be the key for optimal flow of tasks and data through network infrastructure.
*Visualization: HIVE provides number of scientific visualization components using technologies as HTML5, SVG, D3JS within its Data Driven Document context. The native data and metadata and computational results provided in JSON, CSV-based communication protocols, which are used to generate interactive, user driven, customizable tools allow bioinformaticians to manipulate terabytes of extra-large data using only an Internet browser.