Model Repository Research Articles

Identifying refactoring opportunities in process model repositories

Context In order to ensure high quality of a process model repository, refactoring operations can be applied to correct anti-patterns, such as overlap of process models, inconsistent labeling of activities and overly complex models. However, if a process model collection is created and maintained by different people over a longer period of time, manual detection of such refactoring opportunities becomes difficult, simply due to the number of processes in the repository. Consequently, there is a need for techniques to detect refactoring opportunities automatically. Objective This paper proposes a technique for automatically detecting refactoring opportunities. Method We developed the technique based on metrics that can be used to measure the consistency of activity labels as well as the extent to which processes overlap and the type of overlap that they have. We evaluated it, by applying it to two large process model repositories. Results The evaluation shows that the technique can be used to pinpoint the approximate location of three types of refactoring opportunities with high precision and recall and of one type of refactoring opportunity with high recall, but low precision. Conclusion We conclude that the technique presented in this paper can be used in practice to automatically detect a number of anti-patterns that can be corrected by refactoring.

The FaceBase Consortium: A comprehensive program to facilitate craniofacial research

The FaceBase Consortium consists of ten interlinked research and technology projects whose goal is to generate craniofacial research data and technology for use by the research community through a central data management and integrated bioinformatics hub. Funded by the National Institute of Dental and Craniofacial Research (NIDCR) and currently focused on studying the development of the middle region of the face, the Consortium will produce comprehensive datasets of global gene expression patterns, regulatory elements and sequencing; will generate anatomical and molecular atlases; will provide human normative facial data and other phenotypes; conduct follow up studies of a completed genome-wide association study; generate independent data on the genetics of craniofacial development, build repositories of animal models and of human samples and data for community access and analysis; and will develop software tools and animal models for analyzing and functionally testing and integrating these data. The FaceBase website (http://www.facebase.org) will serve as a web home for these efforts, providing interactive tools for exploring these datasets, together with discussion forums and other services to support and foster collaboration within the craniofacial research community.

Discovering the Information Needs of Humanists When Planning an Institutional Repository

Through in-person interviews with humanities faculty members, this study examines what information needs are expressed by humanities scholars that an institutional repository (IR) can address. It also asks what concerns humanists have about IRs, and whether there is a repository model other than an institutional one that better suits how they work. Humanists make relatively low use of existing IRs, but this research indicates that an institutional repository can offer services to humanities faculty that are desired by them, especially the digitization, online storage, curation, and sharing of their research materials and publications. If presented in terms that make sense to humanities faculty, and designed consciously with their needs and concerns in mind, an IR can be of real benefit to their teaching, scholarship, collaborations, and publishing.

Repository-Scale Modeling of the Long-Term Hydraulic Perturbation Induced by Gas and Heat Generation in a Geological Repository for High-and Intermediate-Level Radioactive Waste: Methodology and Example of Application

The current design of a deep geological repository for high- and intermediate-level radioactive waste in France consists of a complex system of different underground structures (ANDRA, Dossier 2005 Argile, les recherches de l’Andra sur le stockage geologique des dechets radioactifs a haute activite et a vie longue, collection les Rapports. Châtenay-Malabry, France, 2005). For a comprehensive understanding of the long-term hydraulic evolution of the entire repository, numerical non-isothermal two-phase flow and transport simulation, taking into consideration the generation, accumulation, and release of hydrogen gas and decay heat, are compulsory. However, a detailed numerical model of the entire repository system would require a tremendous computational effort and pose a laborious task with respect to the operation of the model. To handle these difficulties, we have developed an efficient method for the numerical modeling of a complete repository system and its geologic environment. The method consists of the following steps: (i) subdivision of the repository plane into a large number of “sectors” based on the position of hydraulic seals and on other geometrical considerations, (ii) exploitation of existing symmetries (inside or between sectors), (iii) adoption of the “multiplying concept”, and (iv) connection of the individual sectors at the drift interfaces to form the entire repository model. Each sector is modeled as a three-dimensional (3D) block, and the entire model is computed with TOUGH2-MP. The method allows for a massive reduction in overall finite-volume elements and, at the same time, provides an adequate representation of the small-sized structures in the repository. The main characteristics of the method and its application to an entire deep geological repository system in a clay host rock are presented.

Modeling Approaches for Investigating Gas Migration from a Deep Low/Intermediate Level Waste Repository (Switzerland)

In low/intermediate-level waste (L/ILW) repositories, anaerobic corrosion of metals and degradation of organic materials produce mainly hydrogen, methane, and carbon dioxide. The Swiss reference concept for the L/ILW repository consists of parallel caverns sealed off from a single access tunnel in a deep low-permeability claystone formation. The potential buildup of excess gas pressures in the backfilled emplacement caverns was investigated in a series of two-phase flow models. In the first step, a large-scale model was constructed, implementing the 3D radial tunnel and cavern geometry with a simplified rectangular geometry. In the second step, the potential impact of the detailed geometry of the engineered barrier system (EBS) and the associated heterogeneity inside the cavern was examined using detailed models of the repository caverns, tunnel seals, access tunnel, and surrounding host rock. The simulation results from the large-scale 3D repository model show that during the early post-closure period simulated pressures can vary significantly between different parts of the repository. The simulated pressure increase in the emplacement caverns remained below the fracture pressure of the rock for realistic assumptions. Gas flow is largely limited to the EBS and the excavation disturbed zone (EDZ); thus, gas flows through and around the repository seal into the adjacent tunnel system, which is also demonstrated in the detailed repository-cavern model. The repository seal model described the detailed two-phase flow pattern of early time resaturation of the repository by water inflow from the ramp and subsequent counter flow associated with the gas flow from the repository cavern. Overall, the results of the detailed models complement and confirmed the results of the large-scale 3D model in terms of the timing of the pressure peaks and the migration of gas from the cavern into the surrounding host rock and through the repository seal.

Revision history aware repositories of computational models of biological systems

BackgroundBuilding repositories of computational models of biological systems ensures that published models are available for both education and further research, and can provide a source of smaller, previously verified models to integrate into a larger model.One problem with earlier repositories has been the limitations in facilities to record the revision history of models. Often, these facilities are limited to a linear series of versions which were deposited in the repository. This is problematic for several reasons. Firstly, there are many instances in the history of biological systems modelling where an 'ancestral' model is modified by different groups to create many different models. With a linear series of versions, if the changes made to one model are merged into another model, the merge appears as a single item in the history. This hides useful revision history information, and also makes further merges much more difficult, as there is no record of which changes have or have not already been merged. In addition, a long series of individual changes made outside of the repository are also all merged into a single revision when they are put back into the repository, making it difficult to separate out individual changes. Furthermore, many earlier repositories only retain the revision history of individual files, rather than of a group of files. This is an important limitation to overcome, because some types of models, such as CellML 1.1 models, can be developed as a collection of modules, each in a separate file.The need for revision history is widely recognised for computer software, and a lot of work has gone into developing version control systems and distributed version control systems (DVCSs) for tracking the revision history. However, to date, there has been no published research on how DVCSs can be applied to repositories of computational models of biological systems.ResultsWe have extended the Physiome Model Repository software to be fully revision history aware, by building it on top of Mercurial, an existing DVCS. We have demonstrated the utility of this approach, when used in conjunction with the model composition facilities in CellML, to build and understand more complex models. We have also demonstrated the ability of the repository software to present version history to casual users over the web, and to highlight specific versions which are likely to be useful to users.ConclusionsProviding facilities for maintaining and using revision history information is an important part of building a useful repository of computational models, as this information is useful both for understanding the source of and justification for parts of a model, and to facilitate automated processes such as merges. The availability of fully revision history aware repositories, and associated tools, will therefore be of significant benefit to the community.

The Physiome Model Repository 2

The Physiome Model Repository 2 (PMR2) software was created as part of the IUPS Physiome Project (Hunter and Borg, 2003), and today it serves as the foundation for the CellML model repository. Key advantages brought to the end user by PMR2 include: facilities for model exchange, enhanced collaboration and a detailed change history for each model. PMR2 is available under an open source license at http://www.cellml.org/tools/pmr/; a fully functional instance of this software can be accessed at http://models.physiomeproject.org/.

Physiological Model Creation and Sharing

Background: Mathematical modelling in medicine (physiology) takes place in research, clinical practice and learning. There are several suitable modelling languages and tools for physiological model implementation. Graphical simulators are created in order to make models used in teaching more illustrative. Objectives: It is important to make model developers’ cooperation easier. For this reason it should be possible to interconnect models written in different languages. Elearning simulators must be well available for students and teachers. Necessity to install the application can be an obstruction. Methods for sharing models written in Modelica language should be enhanced. Methods: Standardised interface FMI allows interconnection of models written in different languages. E-learning models are developed on .NET platform. It enables them to run in web browser. The editor for models written in Modelica is being developed. It will run in browser and will be interconnected with web based model repository. Results: Simulation runtime, solver and simulation centre was implemented in .NET languages. They are used in web e-learning applications. They will be also used together with web-based model repository, that is being developed now. Conclusions: New tools will simplify model creation and interconnection. They will also improve collaboration of model developers.

An improved architecture design of shared repository database model

For many years ago, the term repository has been used in a restricted manner, since it only addressed metadata management in the context of database management systems. Nowadays it is used in a much broader sense and covers multiple services supporting design applications. Our concern is to make well customized repositories available for users. To reach this goal, we present this paper which has a main objective of improving the performance of shared database pattern in the Repository Model. Accordingly, the presented work aims to increase the level of performance of the shared repository pattern when large amounts of data are to be shared by reducing the number of times that is required to access the central database and also to save the cost rather than increasing the speed of response for the subsystems requests to access their desired data. Accordingly, the idea of improvement was based on the establishment of buffer where repository model is an organization model used as a storage medium of a huge database. Also, it is used in interactions between the subsystems of the system in architectural design showing the exchange of data between the subsystems in the system as a whole. The proposed model to achieve the required enhancement was simulated, and the output simulated results show its capability of reducing the access time of data, increasing the speed of accessing the data, increasing the system performance, and also increasing the efficiency of the system work. Also, the proposed model was compared with the approach of shared repository pattern and the results showed that the proposed approach outperforms better through making enhancement in reducing the access time and increasing the speed of accessiing the data. Key words: Database repository model, buffer, subsystem, RDBMS, central database, shared database.

APROMORE: An advanced process model repository

Business process models are becoming available in large numbers due to their widespread use in many industrial applications such as enterprise and quality engineering projects. On the one hand, this raises a challenge as to their proper management: how can it be ensured that the proper process model is always available to the interested stakeholder? On the other hand, the richness of a large set of process models also offers opportunities, for example with respect to the re-use of existing model parts for new models. This paper describes the functionality and architecture of an advanced process model repository, named APROMORE. This tool brings together a rich set of features for the analysis, management and usage of large sets of process models, drawing from state-of-the art research in the field of process modeling. A prototype of the platform is presented in this paper, demonstrating its feasibility, as well as an outlook on the further development of APROMORE.

Advancing systems medicine and therapeutics through biosimulation

This Interface Focus issue presents 15 different facets of the research conducted by the participants of the BioSim Network (www.biosim-network.net). BioSim was a network of excellence under the Life Sciences, Genomics and Biotechnology for Health Thematic Priority Area of the 6th European Framework Programme. The immediate goal of the network was to develop modelling and simulation approaches that can help the pharmaceutical industry achieve a more rational drug development process. In a broader perspective, the network aimed at contributing in an essential manner to the development of an integrated and quantitative understanding of biological processes. It included a total of 40 partners, including 26 academic research groups from various universities, nine SMEs and Novo Nordisk, with many of the partners having strong collaborations with the pharmaceutical industry. The network established a platform for very fruitful interdisciplinary collaboration with biological groups providing insights into genetics, biochemistry, cellular biology, pharmacology, endocrinology, neurology and physiology; clinicians and hospital groups bringing experience in treatments of depression, various forms of tremor, and cancer clinical interventions and theoreticians providing expertise in bioinformatics, systems biology (SB), network theory, statistical physics, nonlinear dynamics and complex systems theory, as well as pharmacokinetics and clinical trial planning.

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics–pharmacodynamics platform

The utility of model repositories is discussed in the context of systems biology (SB). It is shown how such repositories, and in particular their live versions, can be used for computational SB: we calculate the robustness of the yeast glycolytic network with respect to perturbations of one of its enzyme activities and one transport system. The robustness with respect to perturbations in the key enzyme phosphofructokinase is surprisingly large. We then note the upcoming convergence of pharmacokinetics-pharmacodynamics (PK-PD) and bottom-up SB. In PK alone, quite a few one-, two- or more compartment models provide valuable initial guesses and insights into the absorption, distribution, metabolism and excretion of particular drugs. These models are phenomenological however, forbidding implementation of molecule-based tools and network information. In order to facilitate a fruitful synergy between SB and PK-PD, and between PK and PD, we present a new platform that combines standard phenomenological models used in the PK/PD field with mechanism-based SB models and approaches.

Artexte metadata conversion to EPrints: adaptation of digital repository software to visual and media arts documentation

The following research questions structured our analysis: Does an open access institutional repository model respond to the needs of a non-academic documentation centre? Is EPrints software a good match to support the needs of the existing metadata describing Artexte’s collection? What are the customizations required to accommodate the existing Artexte metadata using EPrints? In order to address these questions, in this study we exported the existing metadata schema and sample data in Artexte’s three databases, performed a manual evaluation of metadata quality and compared the 49 Artexte fields to those available within the EPrints schema. We identified the metadata elements that mapped by default without the need for customization or modification and those which would need to be added to EPrints using configuration files. We also identified the customized software development to accommodate Artexte metadata using EPrints: the bilingual controlled vocabulary demands an extension of the EPrints subject taxonomy model with thesaurus semantic relationships. Comparing Artexte and EPrints metadata schemas, we found that 15 out of 49 fields mapped by default without the need for modification, 25 fields would need to be added to EPrints configuration files, and one field will be removed during the migration. With only the remaining eight fields requiring some special attention, we conclude that EPrints is suitable to the needs of Artexte’s bibliographic data management.

What will be the next records management orthodoxy?

PurposeThe electronic document and records management system model (EDRMS) served for most of the noughties (the decade from the year 2000) as an orthodoxy that united the records management profession. The purpose of this paper is to address two questions: “Does the stagnation and retreat of the EDRMS model towards the end of the noughties call into doubt the theory that lay behind that model, namely DIRKS and the records continuum?”, and “Is a new records management orthodoxy likely to emerge over the course of the next five years, and if so what form might it take?”.Design/methodology/approachThe paper looks back at the author's readings of DIRKS and the records management continuum at different times over the period 1993‐2010, and links those readings with the prevailing fortunes of the EDRMS model that was build on top of that theory. It gives a personal perspective of a consultant/practitioner on the chances of a new records management orthodoxy arising in the course of the next five years.FindingsThe loss of momentum of the EDRMS model does not invalidate the insights of DIRKS and the records continuum. Both frameworks support alternative readings from those that underpinned the EDRMS model. But any future orthodoxy is likely to be less directly derived from theory. One possible future orthodoxy is the “records repository model” – where a business classification scheme is held in a back end system, and applied to content held in the various applications used by colleagues. However this model has not yet received sufficient practitioner attention, and there are unanswered questions as to how it would work in practice.Originality/valueThe paper looks at the ways in which the records management community has used orthodoxies in both theory and implementation models to keep itself united during an extended period of upheaval and change since the commencement of the networked digital age. It outlines the challenge of finding a records management orthodoxy that is both consistent with record keeping theory and also workable and sustainable in the rapidly changing world of enterprise computing.

BioModels Database: Next generation model repository

Public announce that the software system running BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) will evolve from open source to a community developed project.

BioModels Database: Next generation model repository

AbstractPublic announce that the software system running BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) will evolve from open source to a community developed project.

CellML 1.1 modularity

AbstractCellML 1.1 is an open XML-based language designed to store and exchange computer-based mathematical models. It has a simple facility to import existing models in order to create new models. The import facility encourages the development of hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.

Workspaces, exposures, and multiscale modelling

Here I present technical details on the software package PMR2, which is the software running the CellML and Physiome Project model repositories. In particular, the use of mercurial repositories to define workspaces for collaborative model development, creating modular hierarchies of embedded workspaces, and defining exposures as a means to provide permanent links to specific revisions of model workspaces. I also briefly mention the use of OpenCMISS to link CellML models into large scale, spatially distributed field modeling and simulation.

Workspaces, exposures, and multiscale modelling

AbstractHere I present technical details on the software package PMR2, which is the software running the CellML and Physiome Project model repositories. In particular, the use of mercurial repositories to define workspaces for collaborative model development, creating modular hierarchies of embedded workspaces, and defining exposures as a means to provide permanent links to specific revisions of model workspaces. I also briefly mention the use of OpenCMISS to link CellML models into large scale, spatially distributed field modeling and simulation.

Similarity of business process models: Metrics and evaluation

It is common for large organizations to maintain repositories of business process models in order to document and to continuously improve their operations. Given such a repository, this paper deals with the problem of retrieving those models in the repository that most closely resemble a given process model or fragment thereof. Up to now, there is a notable research gap on comparing different approaches to this problem and on evaluating them in the same setting. Therefore, this paper presents three similarity metrics that can be used to answer queries on process repositories: (i) node matching similarity that compares the labels and attributes attached to process model elements; (ii) structural similarity that compares element labels as well as the topology of process models; and (iii) behavioral similarity that compares element labels as well as causal relations captured in the process model. These metrics are experimentally evaluated in terms of precision and recall. The results show that all three metrics yield comparable results, with structural similarity slightly outperforming the other two metrics. Also, all three metrics outperform text-based search engines when it comes to searching through a repository for similar business process models.