Systems Biology Graphical Notation: Activity Flow language Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps

Systems Biology Graphical Notation: Process Diagram Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Transformation Techniques for OCL Constraints

Constraints play a key role in the definition of conceptual schemas. In the UML, constraints are usually specified by means of invariants written in the OCL. However, due to the high expressiveness of the OCL, the designer has different syntactic alternatives to express each constraint. The techniques presented in this paper assist the designer during the definition of the constraints by means of generating equivalent alternatives for the initially defined ones. Moreover, in the context of the MDA, transformations between these different alternatives are required as part of the PIM-to-PIM, PIM-to-PSM or PIM-to-code transformations of the original conceptual schema

RelBAC: Relation Based Access Control

TheWeb 2.0, GRID applications and, more recently, semantic desktop applications are bringing the Web to a situation where more and more data and metadata are shared and made available to large user groups. In this context, metadata may be tags or complex graph structures such as file system or web directories, or (lightweight) ontologies. In turn, users can themselves be tagged by certain properties, and can be organized in complex directory structures, very much in the same way as data. Things are further complicated by the highly unpredictable and autonomous dynamics of data, users, permissions and access control rules. In this paper we propose a new access control model and a logic, called RelBAC (for Relation Based Access Control) which allows us to deal with this novel scenario. The key idea, which differentiates RelBAC from the state of the art, e.g., Role Based Access Control (RBAC), is that permissions are modeled as relations between users and data, while access control rules are their instantiations on specific sets of users and objects. As such, access control rules are assigned an arity which allows a fine tuning of which users can access which data, and can evolve independently, according to the desires of the policy manager(s). Furthermore, the formalization of the RelBAC model as an Entity-Relationship (ER) model allows for its direct translation into Description Logics (DL). In turn, this allows us to reason, possibly at run time, about access control policies

A practical approach to object based requirements analysis

Presented here is an approach developed at the Unisys Houston Operation Division, which supports the early identification of objects. This domain oriented analysis and development concept is based on entity relationship modeling and object data flow diagrams. These modeling techniques, based on the GOOD methodology developed at the Goddard Space Flight Center, support the translation of requirements into objects which represent the real-world problem domain. The goal is to establish a solid foundation of understanding before design begins, thereby giving greater assurance that the system will do what is desired by the customer. The transition from requirements to object oriented design is also promoted by having requirements described in terms of objects. Presented is a five step process by which objects are identified from the requirements to create a problem definition model. This process involves establishing a base line requirements list from which an object data flow diagram can be created. Entity-relationship modeling is used to facilitate the identification of objects from the requirements. An example is given of how semantic modeling may be used to improve the entity-relationship model and a brief discussion on how this approach might be used in a large scale development effort

Evaluation of graphical control flow management approaches for Event-B modelling

Integrating graphical representations with formal methods can help bridge the gap between requirements and formal modelling. In this paper, we compare and evaluate two graphical approaches aiming at describing control flows and refinement in Event-B, and we use a fire dispatch system case study to perform this evaluation. The fire dispatch system case study provides a good example of a complex workflow through which we try to identify a process that facilitates defining the structural and the behavioural parts of the Event-B model. In our case study, we focus on building the dynamic part of the model to evaluate the two diagrammatic notations: UML Activity Diagrams and Atomicity Decomposition Diagrams. Based on our evaluation, we try to identify the advantages and limitations of both approaches. Finally, we try to compare how both graphical notations can affect the Event-B formal modelling of our case study

A Theory of Structured Propositions

This paper argues that the theory of structured propositions is not undermined by the Russell-Myhill paradox. I develop a theory of structured propositions in which the Russell-Myhill paradox doesn't arise: the theory does not involve ramification or compromises to the underlying logic, but rather rejects common assumptions, encoded in the notation of the $\lambda$-calculus, about what properties and relations can be built. I argue that the structuralist had independent reasons to reject these underlying assumptions. The theory is given both a diagrammatic representation, and a logical representation in a novel language. In the latter half of the paper I turn to some technical questions concerning the treatment of quantification, and demonstrate various equivalences between the diagrammatic and logical representations, and a fragment of the $\lambda$-calculus