Anduril is an open source component-based workflow framework for scientific data analysis developed at the Systems Biology Laboratory,

University of Helsinki The University of Helsinki (, ; UH) is a public university in Helsinki, Finland. The university was founded in Turku in 1640 as the Royal Academy of Åbo under the Swedish Empire, and moved to Helsinki in 1828 under the sponsorship of Alexander ...

. Anduril is designed to enable systematic, flexible and efficient data analysis, particularly in the field of high-throughput experiments in biomedical research. The workflow system currently provides components for several types of analysis such as

sequencing In genetics and biochemistry, sequencing means to determine the primary structure (sometimes incorrectly called the primary sequence) of an unbranched biopolymer. Sequencing results in a symbolic linear depiction known as a sequence which succ ...

gene expression Gene expression is the process (including its Regulation of gene expression, regulation) by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, proteins or non-coding RNA, ...

, SNP, ChIP-on-chip,

comparative genomic hybridization Comparative genomic hybridization (CGH) is a molecular cytogenetic method for analysing copy number variations (CNVs) relative to ploidy level in the DNA of a test sample compared to a reference sample, without the need for culturing cells. The ai ...

and exon microarray analysis as well as

cytometry Cytometry is the measurement of number and characteristics of cell (biology), cells. Variables that can be measured by cytometric methods include cell size, cell counting, cell count, cell morphology (shape and structure), cell cycle phase, DNA c ...

and

cell imaging Cell most often refers to: * Cell (biology), the functional basic unit of life * Cellphone, a phone connected to a cellular network * Clandestine cell, a penetration-resistant form of a secret or outlawed organization * Electrochemical cell, a d ...

analysis.

Architecture and features

A workflow is a series of processing steps connected together so that the output of one step is used as the input of another. Processing steps implement data analysis tasks such as data importing, statistical tests and report generation. In Anduril, processing steps are implemented using components, which are reusable executable code that can be written in any programming language. Components are wired together into a workflow, or a component network, that is executed by the Anduril workflow engine. Workflow configuration is done using a simple yet powerful scripting language, AndurilScript. Workflow configuration and execution can be done from

Eclipse An eclipse is an astronomical event which occurs when an astronomical object or spacecraft is temporarily obscured, by passing into the shadow of another body or by having another body pass between it and the viewer. This alignment of three ...

, a popular multipurpose GUI, or from the command line. The core Anduril engine is written in Java and components are written in a variety of programming languages, including Java, R,

MATLAB MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementat ...

, Lua,

Perl Perl is a high-level, general-purpose, interpreted, dynamic programming language. Though Perl is not officially an acronym, there are various backronyms in use, including "Practical Extraction and Reporting Language". Perl was developed ...

and Python. Components may also have dependencies on third-party libraries, such as Bioconductor. Components for cell imaging and microarray analysis are provided but additional components can be implemented by users. The Anduril core has been tested on Linux and Windows.

Anduril 1.0: AndurilScript language

Hello world in AndurilScript is simply std.echo("Hello world!") Commenting follows the syntax of Java: // A simple comment /* Another simple comment */ /** A description that will be included in component description */ Components are called by assigning their calls to named component instances. Names cannot be re-used within a single workflow. There are special components for input files that include external files to the script. Supported atomic types are integer, float, boolean and string, and typing is done implicitly. in1 = INPUT(path="myFile.csv") constant1 = 1 componentInstance1 = MyComponent(inputPort1 = in1, inputParam1 = constant1) Workflows are constructed by assigning outputs of component instances to inputs of following components. componentInstance2 = AnotherComponent(inputPort1 = componentInstance1.outputPort1) Component instances can also be wrapped as functions. function MyFunction(InType1 in1, ..., optional InTypeM inM, ParType1 param1, ..., ParTypeP paramP=defaultP) -> (OutType1 out1, ..., OutTypeN outN) In addition to standard if-else and switch-case statements, AndurilScript also includes for-loops. // Iterates over 1, 2, ..., 10 array = record() for i: std.range(1, 10)

Extensibility

Anduril can be extended on multiple levels. Users can add new components to existing component bundles. However, if the new component or components carry out tasks that are not related to existing bundles, users can also create new bundles.

Moksiskaan

Moksiskaan is a

data integration Data integration refers to the process of combining, sharing, or synchronizing data from multiple sources to provide users with a unified view. There are a wide range of possible applications for data integration, from commercial (such as when a ...

framework for the

cancer research Cancer research is research into cancer to identify causes and develop strategies for prevention, diagnosis, treatment, and cure. Cancer research ranges from epidemiology, molecular bioscience to the performance of clinical trials to evaluate ...

and

molecular biology Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...

. The framework provides a relational database that represents a graph of biological entities such as genes, protein, drugs, pathways, diseases, biological processes, cellular components, and molecular functions. In addition, there is a wide set of analysis and accession tools built on top of this data. The great majority of these tools are implemented as Anduril components and functions. Moksiskaan is used mainly to interpret lists of

candidate gene The candidate gene approach to conducting genetic association studies focuses on associations between genetic variation within pre-specified genes of interest, and Phenotype (clinical medicine), phenotypes or disease states. This is in contrast to ...

s obtained from the genomic studies. Its tools can be used to generate graphs of biological entities related to the input genes. The exact for of these graphs may vary from the drug target predictions to the

time series In mathematics, a time series is a series of data points indexed (or listed or graphed) in time order. Most commonly, a time series is a sequence taken at successive equally spaced points in time. Thus it is a sequence of discrete-time data. ...

of signalling cascades. Some of the goals of these tools are closely related to IPA.

References

External links

Official Anduril websiteAnduril Code repositoryOfficial Moksiskaan website
Workflow applications Bioinformatics software