Jacek Sroka

A formal semantics for the Taverna 2 workflow model

This paper presents a formal semantics for the Taverna 2 scientific workflow system. Taverna 2 is a successor to Taverna, an open-source workflow system broadly adopted within the e-science community worldwide. The new version improves upon the existing model in two main ways: (i) by adding support for data pipelining, which in turns enables input streams of indefinite length to be processed efficiently; and (ii) by providing new extensibility points that make it possible to add new operators to the workflow model. Consistent with previous work by some of the authors, we use trace semantics to describe the effect of workflow computations, and we show how they can be used to describe the new features in the Taverna 2 model.

On representing coalitional games with externalities

We consider the issue of representing coalitional games in multi-agent systems with externalities (i.e., in systems where the performance of one coalition may be affected by other co-existing coalitions). In addition to the conventional partition function game representation (PFG), we propose a number of new representations based on a new notion of externalities. In contrast to conventional game theory, our new concept is not related to the process by which the coalitions are formed, but rather to the effect that each coalition may have on the entire system and vice versa. We show that the new representations are fully expressive and, for many classes of games, more concise than the conventional PFG. Building upon these new representations, we propose a number of approaches to solve the coalition structure generation problem in systems with externalities. We show that, if externalities are characterised by various degrees of regularity, the new representations allow us to adapt coalition structure generation algorithms that were originally designed for domains with no externalities, so that they can be used when externalities are present. Finally, building upon Rahwan et al. [16] and Michalak et al. [9], we present a unified method to solve the coalition structure generation problem in any system, with or without externalities, provided sufficient information is available.

Petri net + nested relational calculus = dataflow

In this paper we propose a formal, graphical workflow language for dataflows, i.e., workflows where large amounts of complex data are manipulated and the structure of the manipulated data is reflected in the structure of the workflow. It is a common extension of Petri nets, which are responsible for the organization of the processing tasks, and Nested relational calculus, which is a database query language over complex objects, and is responsible for handling collections of data items (in particular, for iteration) and for the typing system. We demonstrate that dataflows constructed in hierarchical manner, according to a set of refinement rules we propose, are sound: initiated with a single token (which may represent a complex scientific data collection) in the input node, terminate with a single token in the output node (which represents the output data collection). In particular they always process all of the input data, leave no ”debris data” behind and the output is always eventually computed.

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

BackgroundConstraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.ResultsHere, we present Acorn, an open source (GNU GPL) grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.ConclusionsAcorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.

MUFINS: multi-formalism interaction network simulator

Systems Biology has established numerous approaches for mechanistic modeling of molecular networks in the cell and a legacy of models. The current frontier is the integration of models expressed in different formalisms to address the multi-scale biological system organization challenge. We present MUFINS (MUlti-Formalism Interaction Network Simulator) software, implementing a unique set of approaches for multi-formalism simulation of interaction networks. We extend the constraint-based modeling (CBM) framework by incorporation of linear inhibition constraints, enabling for the first time linear modeling of networks simultaneously describing gene regulation, signaling and whole-cell metabolism at steady state. We present a use case where a logical hypergraph model of a regulatory network is expressed by linear constraints and integrated with a Genome-Scale Metabolic Network (GSMN) of mouse macrophage. We experimentally validate predictions, demonstrating application of our software in an iterative cycle of hypothesis generation, validation and model refinement. MUFINS incorporates an extended version of our Quasi-Steady State Petri Net approach to integrate dynamic models with CBM, which we demonstrate through a dynamic model of cortisol signaling integrated with the human Recon2 GSMN and a model of nutrient dynamics in physiological compartments. Finally, we implement a number of methods for deriving metabolic states from ~omics data, including our new variant of the iMAT congruency approach. We compare our approach with iMAT through the analysis of 262 individual tumor transcriptomes, recovering features of metabolic reprogramming in cancer. The software provides graphics user interface with network visualization, which facilitates use by researchers who are not experienced in coding and mathematical modeling environments.

A formal model of dataflow repositories

Dataflow repositories are databases containing dataflows and their different runs. We propose a formal conceptual data model for such repositories. Our model includes careful formalisations of such features as complex data manipulation, external service calls, subdataflows, and the provenance of output values.

Translating Relational Queries into Spreadsheets

Spreadsheets are among the most commonly used applications for data management and analysis. They combine data processing with very diverse supplementary features: statistics, visualization, reporting, linear programming solvers, Web queries periodically downloading data from external sources, etc. However, the spreadsheet paradigm of computation still lacks sufficient analysis. In this article, we demonstrate that a spreadsheet can implement all data transformations definable in SQL, merely by utilizing spreadsheet formulas. We provide a query compiler, which translates any given SQL query into a worksheet of the same semantics, including NULL values. Thereby, database operations become available to the users who do not want to migrate to a database. They can define their queries using a high-level language and then get their execution plans in a plain vanilla spreadsheet. The functions available in spreadsheets impose limitations on the algorithms one can implement. In this paper, we offer O(n log2 n) sorting spreadsheet, using a non-constant number of rows, and, surprisingly, Depth-First-Search and Breadth-First-Search on graphs.

Towards a Formal Semantics for the Process Model of the Taverna Workbench. Part II

Workflow development and enactment workbenches are becoming a standard tool for conducting in silico experiments. Their main advantages are easy to operate user interfaces, specialized and expressive graphical workflow specification languages and integration with a huge number of bioinformatic services. A popular example of such a workbench is Taverna, which has many additional useful features like service discovery, storing intermediate results and tracking data provenance. We discuss a detailed formal semantics for Scufl - the workflow definition language of the Taverna workbench. It has several interesting features that are notmet in other models including dynamic and transparent type coercion and implicit iteration, control edges, failure mechanisms, and incominglinks strategies. We study these features and investigate their usefulness separately as well as in combination, and discuss alternatives. The formal definition of such a detailed semantics not only allows to exactly understand what is being done in a given experiment, but is also the first step toward automatic correctness verification and allows the creation of auxiliary tools that would detect potential errors and suggest possible solutions to workflow creators, the same way as Integrated Development Environments aid modern programmers. A formal semantics is also essential for work on enactment optimization and in designing the means to effectively query workflow repositories. This paper is the second of two. In the first one [13] we have defined, explained and discussed fundamental notions for describing Scufl graphs and their semantics. Here, in the second part, we use these notions to define the semantics and show that our definition can be used to prove properties of Scufl graphs.

Towards a Calculus for Collection-Oriented Scientific Workflows with Side Effects

In this paper we propose a calculus that can be used to describe the semantics of collection-oriented scientific workflow systems such as the Taverna workbench. Typically such systems focus on the specification and execution of workflows with a relatively simple control flow and a more complex data flow that involves large nested collections of data. An essential operation in such workflows is the instantiation of a certain nested workflow for each element of a collection. We argue that if such workflows call external services, their semantics must be described not only in terms of input-output behavior but also take side effects into account. Based on this assumption a trace semantics is defined that corresponds to the observational equivalence of two workflow specifications. We show that under such a semantics a relatively small calculus with a structural semantics can be defined and used to describe such workflows. This is demonstrated by giving a translation of Taverna workflows in terms of this calculus.

XQTav: an XQuery processor for Taverna environment

UNLABELLED Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the internet. It is gaining popularity fast, because of supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav-an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query-like algorithms (e.g. filters and inner joins). Moreover, XQtav may be used to automatically generate an XQuery script that is equivalent to Tavernas workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments. AVAILABILITY XQtav is an open source software. It may be downloaded from http://xqtav.sourceforge.net/. The page also contains various tutorials and examples, including the one described in this report.