CLC bio was a

bioinformatics Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, ...

software Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...

company that developed a

software suite A software suite (also known as an application suite) is a collection of computer programs (application software, or programming software) of related functionality, sharing a similar user interface and the ability to easily exchange data with eac ...

subsequently purchased by QIAGEN.

History

CLC bio started commercial activities on January 1, 2005, headquartered in

Aarhus Aarhus (, , ; officially spelled Århus from 1948 until 1 January 2011) is the second-largest city in Denmark and the seat of Aarhus municipality, Aarhus Municipality. It is located on the eastern shore of Jutland in the Kattegat sea and app ...

Denmark Denmark is a Nordic countries, Nordic country in Northern Europe. It is the metropole and most populous constituent of the Kingdom of Denmark,, . also known as the Danish Realm, a constitutionally unitary state that includes the Autonomous a ...

. Its product's development was also partly funded by collaborating with researchers on grant-funded projects. By 2012, it had additional offices in

Cambridge, Massachusetts Cambridge ( ) is a city in Middlesex County, Massachusetts, United States. It is a suburb in the Greater Boston metropolitan area, located directly across the Charles River from Boston. The city's population as of the 2020 United States census, ...

Tokyo Tokyo, officially the Tokyo Metropolis, is the capital of Japan, capital and List of cities in Japan, most populous city in Japan. With a population of over 14 million in the city proper in 2023, it is List of largest cities, one of the most ...

Taipei , nickname = The City of Azaleas , image_map = , map_caption = , pushpin_map = Taiwan#Asia#Pacific Ocean#Earth , coordinates = , subdivision_type = Country ...

and

Delhi Delhi, officially the National Capital Territory (NCT) of Delhi, is a city and a union territory of India containing New Delhi, the capital of India. Straddling the Yamuna river, but spread chiefly to the west, or beyond its Bank (geography ...

, with staff largely from research backgrounds (30% having a PhD) and had built a userbase of around 250,000 users in both academic institutions and biotechnology companies. CLC bio was acquired by QIAGEN in 2013 and merged into its bioinformatics research and development division with several other purchased platforms in 2014.

Software

CLC bio's main activities were in software development for desktop (

Mac OS X macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...

Windows Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...

, and

Linux Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...

), enterprise, and cloud software for analysis of

biological data Biological data refers to a compound or information derived from living organisms and their products. A medicinal compound made from living organisms, such as a serum or a vaccine, could be characterized as biological data. Biological data is highly ...

. CLC bio developed some of their own open source algorithms, as well as their own

SIMD Single instruction, multiple data (SIMD) is a type of parallel computer, parallel processing in Flynn's taxonomy. SIMD describes computers with multiple processing elements that perform the same operation on multiple data points simultaneousl ...

-accelerated implementations of several existing popular applications. In 2010, CLC bio was notable as the first commercial platform for bioinformatics analysis that utilized a

graphical user interface A graphical user interface, or GUI, is a form of user interface that allows user (computing), users to human–computer interaction, interact with electronic devices through Graphics, graphical icon (computing), icons and visual indicators such ...

for building, managing, and deploying analysis workflows as well as

command-line A command-line interface (CLI) is a means of interacting with software via commands each formatted as a line of text. Command-line interfaces emerged in the mid-1960s, on computer terminals, as an interactive and more user-friendly alternativ ...

tools, a

SOAP Soap is a salt (chemistry), salt of a fatty acid (sometimes other carboxylic acids) used for cleaning and lubricating products as well as other applications. In a domestic setting, soaps, specifically "toilet soaps", are surfactants usually u ...

and

REST REST (Representational State Transfer) is a software architectural style that was created to describe the design and guide the development of the architecture for the World Wide Web. REST defines a set of constraints for how the architecture of ...

API, and later, the ability to run containerized tools. As additional capabilities were added to the software platform, it was eventually split into several themed Workbenches and plugins with collections of features relevant to different applications (e.g. pathway analysis,

genomics Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...

, and other

omics Omics is the collective characterization and quantification of entire sets of biological molecules and the investigation of how they translate into the structure, function, and dynamics of an organism or group of organisms. The branches of scien ...

). Features include read mapping and de novo assembly of

high-throughput sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The ...

data, whole-genome detection of

SNPs In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in ...

and structural variations,

ChIP-seq ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with Massively parallel signature sequencing, massively parallel DNA sequencing to identify t ...

RNA-Seq RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also k ...

, small

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

analysis, genome finishing, microbial genomics, structural biology, and functions to analyze, visualize, and compare

genomic Genomics is an interdisciplinary field of molecular biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, ...

, transcriptomic, and epigenomic data.

Cloud Computing

In 2017, CLC bio launched their CLC Genomics Cloud Engine as a command-line driven platform for cloud-based bioinformatics workflow execution on Amazon Web Services. In 2019, this platform was adapted for and approved for use in AWS GovCloud. In 2020, CLC bio released a free plug-in that enables workflow execution on AWS directly from the CLC Genomics Workbench desktop software.

Hardware

Early on, the company initially presented own-developed

high-performance computing High-performance computing (HPC) is the use of supercomputers and computer clusters to solve advanced computation problems. Overview HPC integrates systems administration (including network and security knowledge) and parallel programming into ...

solutions, focusing on accelerating open source algorithms such as HMMER, Smith-Waterman and ClustalW, using

FPGA A field-programmable gate array (FPGA) is a type of configurable integrated circuit that can be repeatedly programmed after manufacturing. FPGAs are a subset of logic devices referred to as programmable logic devices (PLDs). They consist of a ...

technology. However these products are no longer under development.

References

{{DEFAULTSORT:CLC bio Software companies of Denmark Danish companies established in 2005 Biotechnology companies of Denmark Bioinformatics companies Computational science Defunct computer hardware companies Privately held companies of Denmark