The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets

SUMMARY

As large-scale metabolic phenotyping studies become increasingly common, the need for systemic methods for pre-processing and quality control (QC) of analytical data prior to statistical analysis has become increasingly important, both within a study, and to allow meaningful inter-study comparisons. The nPYc-Toolbox provides software for the import, pre-processing, QC and visualization of metabolic phenotyping datasets, either interactively, or in automated pipelines.

AVAILABILITY AND IMPLEMENTATION

The nPYc-Toolbox is implemented in Python, and is freely available from the Python package index https://pypi.org/project/nPYc/, source is available at https://github.com/phenomecentre/nPYc-Toolbox. Full documentation can be found at http://npyc-toolbox.readthedocs.io/ and exemplar datasets and tutorials at https://github.com/phenomecentre/nPYc-toolbox-tutorials.

Multi-task learning with a natural metric for quantitative structure activity relationship learning

The goal of quantitative structure activity relationship (QSAR) learning is to learn a function that, given the structure of a small molecule (a potential drug), outputs the predicted activity of the compound. We employed multi-task learning (MTL) to exploit commonalities in drug targets and assays. We used datasets containing curated records about the activity of specific compounds on drug targets provided by ChEMBL. Totally, 1091 assays have been analysed. As a baseline, a single task learning approach that trains random forest to predict drug activity for each drug target individually was considered. We then carried out feature-based and instance-based MTL to predict drug activities. We introduced a natural metric of evolutionary distance between drug targets as a measure of tasks relatedness. Instance-based MTL significantly outperformed both, feature-based MTL and the base learner, on 741 drug targets out of 1091. Feature-based MTL won on 179 occasions and the base learner performed best on 171 drug targets. We conclude that MTL QSAR is improved by incorporating the evolutionary distance between targets. These results indicate that QSAR learning can be performed effectively, even if little data is available for specific drug targets, by leveraging what is known about similar drug targets.

On-demand virtual research environments using microservices

The computational demands for scientific applications are continuously increasing. The emergence of cloud computing has enabled on-demand resource allocation. However, relying solely on infrastructure as a service does not achieve the degree of flexibility required by the scientific community. Here we present a microservice-oriented methodology, where scientific applications run in a distributed orchestration platform as software containers, referred to as on-demand, virtual research environments. The methodology is vendor agnostic and we provide an open source implementation that supports the major cloud providers, offering scalable management of scientific pipelines. We demonstrate applicability and scalability of our methodology in life science applications, but the methodology is general and can be applied to other scientific domains.

Interoperable and scalable data analysis with microservices: applications in metabolomics

MOTIVATION

Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.

RESULTS

We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.

AVAILABILITY AND IMPLEMENTATION

The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

PhenoMeNal: processing and analysis of metabolomics data in the cloud

BACKGROUND

Metabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.

FINDINGS

PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.

CONCLUSIONS

PhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and 'omics research domains.

ChemDistiller: an engine for metabolite annotation in mass spectrometry

Motivation

High-resolution mass spectrometry permits simultaneous detection of thousands of different metabolites in biological samples; however, their automated annotation still presents a challenge due to the limited number of tailored computational solutions freely available to the scientific community.

Results

Here, we introduce ChemDistiller, a customizable engine that combines automated large-scale annotation of metabolites using tandem MS data with a compiled database containing tens of millions of compounds with pre-calculated 'fingerprints' and fragmentation patterns. Our tests using publicly and commercially available tandem MS spectra for reference compounds show retrievals rates comparable to or exceeding the ones obtainable by the current state-of-the-art solutions in the field while offering higher throughput, scalability and processing speed.

Availability and implementation

Source code freely available for download at https://bitbucket.org/iAnalytica/chemdistillerpython.

Supplementary information

Supplementary data are available at Bioinformatics online.

Meta-QSAR: a large-scale application of meta-learning to drug design and discovery

We investigate the learning of quantitative structure activity relationships (QSARs) as a case-study of meta-learning. This application area is of the highest societal importance, as it is a key step in the development of new medicines. The standard QSAR learning problem is: given a target (usually a protein) and a set of chemical compounds (small molecules) with associated bioactivities (e.g. inhibition of the target), learn a predictive mapping from molecular representation to activity. Although almost every type of machine learning method has been applied to QSAR learning there is no agreed single best way of learning QSARs, and therefore the problem area is well-suited to meta-learning. We first carried out the most comprehensive ever comparison of machine learning methods for QSAR learning: 18 regression methods, 3 molecular representations, applied to more than 2700 QSAR problems. (These results have been made publicly available on OpenML and represent a valuable resource for testing novel meta-learning methods.) We then investigated the utility of algorithm selection for QSAR problems. We found that this meta-learning approach outperformed the best individual QSAR learning method (random forests using a molecular fingerprint representation) by up to 13%, on average. We conclude that meta-learning outperforms base-learning methods for QSAR learning, and as this investigation is one of the most extensive ever comparisons of base and meta-learning methods ever made, it provides evidence for the general effectiveness of meta-learning over base-learning.