Recon 2.2: from reconstruction to model of human metabolism.

IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001)

Functional Requirements-Based Automated Testing for Avionics

We propose and demonstrate a method for the reduction of testing effort in safety-critical software development using DO-178 guidance. We achieve this through the application of Bounded Model Checking (BMC) to formal low-level requirements, in order to generate tests automatically that are good enough to replace existing labor-intensive test writing procedures while maintaining independence from implementation artefacts. Given that existing manual processes are often empirical and subjective, we begin by formally defining a metric, which extends recognized best practice from code coverage analysis strategies to generate tests that adequately cover the requirements. We then formulate the automated test generation procedure and apply its prototype in case studies with industrial partners. In review, the method developed here is demonstrated to significantly reduce the human effort for the qualification of software products under DO-178 guidance

A Reference Architecture for Provisioning of Tools as a Service: Meta-Model, Ontologies and Design Elements

Abstract not availableMuhammad Aufeef Chauhan, Muhammad Ali Babar, Quan Z. Shen

Test Cases Selection Based on Source Code Features Extraction

Extracting valuable information from source code automatically was the subject of many research papers. Such information can be used for document traceability, concept or feature extraction, etc. In this paper, we used an Information Retrieval (IR) technique: Latent Semantic Indexing (LSI) for the automatic extraction of source code concepts for the purpose of test cases\u27 reduction. We used and updated the open source FLAT Eclipse add on to try several code stemming approaches. The goal is to check the best approach to extract code concepts that can improve the process of test cases\u27 selection or reduction