MAGPIE: Simplifying access and execution of computational models in the life sciences

Abstract

Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathematical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the exchange within specific model classes has been supported by standardisation and database efforts, the generic application and especially the re-use of models is still limited by practical issues such as easy and straight forward model execution. MAGPIE, a Modeling and Analysis Generic Platform with Integrated Evaluation, closes this gap by providing a software platform for both, publishing and executing computational models without restrictions on the programming language, thereby combining a maximum on flexibility for programmers with easy handling for non-technical users. MAGPIE goes beyond classical SBML platforms by including all models, independent of the underlying programming language, ranging from simple script models to complex data integration and computations. We demonstrate the versatility of MAGPIE using four prototypic example cases. We also outline the potential of MAGPIE to improve transparency and reproducibility of computational models in life sciences. A demo server is available at magpie.imb.medizin.tu-dresden.de.

KETOS: Clinical decision support and machine learning as a service – A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services

“…Finally, the platform allows researchers to rely on standardized data, which makes models with larger amounts of input parameters possible, as the data can be collected automatically. This would not be supported by for example the MAGPIE [6] platform, where our colorectal cancer example with 65 features would not be feasible, as a clinician would need to input all variables to call a prediction function. Further, it can be used as a method to supply restricted data access to researchers while at the same time making use of a large pool of data without compromising patient privacy.…”

“…It uses a service-oriented architecture for early detection and diagnosis of this particular disease. More recently, Baldow et al [6] developed MAGPIE, a platform allowing researchers to develop Unix command line executable computations, which are embedded into Systems Biology Markup Language (SBML). MAGPIE focuses on the development of models, which have to be supplied manually with parameters when executed.…”

Data integration between clinical research and patient care: a framework for context-depending data sharing and in silico predictions

“…To demonstrate the generic software framework (cf. Generic overall design and data flows), we: a) integrated a specific implementation of a model and simulation server (termed MAGPIE (19)) to manage and execute computational models. b) equipped MAGPIE with two mathematical models from the field of haematology (chronic myeloid leukemia, CML).…”

Mathematical basis for the assessment of antibiotic resistance and administrative counter-strategies

“…Moreover, due to its intermediate complexity it is able to serve as a performative boundary object [ 21 ], thence constituting a clinically relevant basis for a modelling for policy [ 22 ]. This holds all the more if implemented on a boundary infrastructure [ 23 ] as, for example, the modelling platform MAGPIE [ 24 ] that enables experts with different expertises to dock on. In other words, the proposed method has the potentiality to be translated to the point of decision making as a monitoring system.…”