K. V. S. Prasad

A Calculus of Value Broadcasts

Computation can be modelled as a sequence of values, each broadcast by one agent and instantaneously audible to all those in parallel with it. Listening agents receive the value; others lose it. Subsystems interface via translators; these can scramble values and thus hide or restrict them. Examples show the calculus describing this model to be a powerful and natural programming tool. Weak bisimulation, a candidate for observational equivalence, is defined on the basis that receiving a value can be matched by losing it.

A Prospectus for Mobile Broadcasting Systems

Computer messages are often broadcast over ethernets, and sent point-to-point between them: globally asynchronous, locally synchronous (GALS). This paradigm is captured here by a primitive calculus, MBS (mobile broadcasting systems). MBS processes talk in rooms by local broadcast, and walk between rooms at unspecified speeds. Names are like object names in the π-calculus, but its “get/put b on channel a” becomes in MBS “go to a and hear/say b”. Speakers wait for departing processes, who are grouped by destination, and walkers can enter only silent rooms. These rules, and a primitive to make a room wait for a walker from a given room, seem adequate for programming.

Broadcasting in Time

In the calculus of broadcasting systems (CBS), speech is autonomous, but hearing takes place only when the environment speaks. This paper develops a timed CBS (TCBS) where no time may pass if there is speech pending. A process wishing to speak can be forced, by attaching a time-out to it, to first listen for a specified length of time. TCBS subsumes CBS with priorities, and has an expansion theorem even if time is dense. A delay prefix operator can be derived up to weak bisimulation. TCBS casts light on issues in handshake communication: time abstracted bisimulation, and the relations between time and priority, between expansion theorems and density of time, and between delays and time-outs.

Programming with Broadcasts

[Pra91, Pra92] develop CBS, a CCS-like calculus [Mil89] where processes communicate by broadcasting values along a single channel. These values are hidden or restricted by translation to noise. This paper types CBS and restricts it to processes with a unique response to each input. Nondeterminism arises only if two processes in parallel both wish to transmit. These restrictions do not reduce the programming power of CBS. But strong and weak bisimulation can now be defined exactly as in CCS, yet capture observationally meaningful relations. Weak bisimulation is a congruence.

A calculus of broadcasting systems

Local area networks (LANs) and everyday speech inspire a model of communication by unbuffered broadcast. Computation proceeds by a sequence of messages, each transmitted by one agent and received by zero or more others. Transmission is autonomous, but reception is not. Each message is received instantaneously by all agents except the transmitter, but is read only by those who were monitoring it at the time; others discard it. As in CCS, agents learn about the environment only through the messages they read. Programming such a system is hard because we have to ensure that messages are read.

Rule-based modelling of iron homeostasis in tuberculosis

To establish itself within the host system, Mycobacterium tuberculosis (Mtb) has formulated various means of attacking the host system. One such crucial strategy is the exploitation of the iron resources of the host system. Obtaining and maintaining the required concentration of iron becomes a matter of contest between the host and the pathogen, both trying to achieve this through complex molecular networks. The extent of complexity makes it important to obtain a systems perspective of the interplay between the host and the pathogen with respect to iron homeostasis. We have reconstructed a systems model comprising 92 components and 85 protein-protein or protein-metabolite interactions, which have been captured as a set of 194 rules. Apart from the interactions, these rules also account for protein synthesis and decay, RBC circulation and bacterial production and death rates. We have used a rule-based modelling approach, Kappa, to simulate the system separately under infection and non-infection conditions. Various perturbations including knock-outs and dual perturbation were also carried out to monitor the behavioral change of important proteins and metabolites. From this, key components as well as the required controlling factors in the model that are critical for maintaining iron homeostasis were identified. The model is able to re-establish the importance of iron-dependent regulator (ideR) in Mtb and transferrin (Tf) in the host. Perturbations, where iron storage is increased, appear to enhance nutritional immunity and the analysis indicates how they can be harmful for the host. Instead, decreasing the rate of iron uptake by Tf may prove to be helpful. Simulation and perturbation studies help in identifying Tf as a possible drug target. Regulating the mycobactin (myB) concentration was also identified as a possible strategy to control bacterial growth. The simulations thus provide significant insight into iron homeostasis and also for identifying possible drug targets for tuberculosis.

Broadcasting with Priority

Adding priorities to CCS is difficult, and involves two-stage operational semantics or other complications. By contrast, priorities can be added very simply to a calculus of broadcasting systems (CBS). The reason is the input/output distinction made in CBS, with output actions being autonomous. Priority makes sense only for autonomous actions.

Formal Representation of the High Osmolarity Glycerol Pathway in Yeast

The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system. This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system. In the commonly used Systems Biology Markup Language (SBML), such a model would need to explicitly enumerate all state variables. The Kappa modelling language which we use supports representation of complexes without such enumeration. To conclude, we compare Kappa with a few other modelling languages and software tools that could also be used to represent and model the HOG system.

Developing an interlingual translation lexicon using WordNets and Grammatical Framework

The Grammatical Framework (GF) offers perfect translation between controlled subsets of natural languages. E.g., an abstract syntax for a set of sentences in school mathematics is the interlingua between the corresponding sentences in English and Hindi, say. GF “resource grammars” specify how to say something in English or Hindi; these are reused with “application grammars” that specify what can be said (mathematics, tourist phrases, etc.). More recent robust parsing and parse-tree disambiguation allow GF to parse arbitrary English text. We report here an experiment to linearise the resulting tree directly to other languages (e.g. Hindi, German, etc.), i.e., we use a language independent resource grammar as the interlingua. We focus particularly on the last part of the translation system, the interlingual lexicon and word sense disambiguation (WSD). We improved the quality of the wide coverage interlingual translation lexicon by using the Princeton and Universal WordNet data. We then integrated an existing WSD tool and replaced the usual GF style lexicons, which give one target word per source word, by the WordNet based lexicons. These new lexicons and WSD improve the quality of translation in most cases, as we show by examples. Both WordNets and WSD in general are well known, but this is the first use of these tools with GF.