In this paper we present an open-source web-enabled simulator for P sys-
tems. We use CLIPS embedded in C, and make the simulator available as a web application, complemented by a query language to specify the results

Bonchis, Cosmin

Ciobanu, Gabriel

Izbasa, Cornel

Petcu, Dana

idUS. Depósito de Investigación Universidad de Sevilla

WebPS: A Web-based P System Simulator withQuery Facilities?Cosmin Bonchis¸1, Cornel Izbas¸a2, Dana Petcu1,2, Gabriel Ciobanu1,31 Research Institute “e-Austria” Timis¸oara, RomaniaBd. V. Paˆrvan 4, 300223 Timis¸oara, RomaniaE-mail: cosbonchis@yahoo.com2 Department of Computer Science, Western University of Timis¸oaraBd. V. Paˆrvan 4, 300223 Timis¸oara, RomaniaE-mail: {petcu, cornel}@info.uvt.ro3 Romanian Academy, Institute of Computer Science, Ias¸iBd. Copou 8, 700505 Ias¸i, RomaniaE-mail: gabriel@iit.tuiasi.roSummary. In this paper we present an open-source web-enabled simulator for P sys-tems. We use CLIPS embedded in C, and make the simulator available as a web appli-cation, complemented by a query language to specify the results.1 IntroductionTransition P systems and deterministic P systems with active membranes (see [4])are simulated in various programming languages, and some of them are used tosolve NP-complete problems as SAT, Subset Sum, Knapsack, and partition prob-lems. P systems with active membranes, input membrane and external outputare simulated in CLIPS, and used to solve NP-complete problems (see [5]). Newvariants of these simulators provide symport-antiport rules, and catalysts. A morecomplex simulator written in Visual C++ for P systems with active membranesand catalytic P systems is presented in [2]. It provides a graphical simulator, inter-active definition, visualization of a defined membrane system, a scalable graphicalrepresentation of the computation, and step-by-step observations of the membranesystem behavior.A parallel and cluster implementation for transition P systems in C++ andMPI is presented in [1]. The rules are implemented as threads. At the initializationphase, one thread is created for each rule. Since each rule is modelled as a separatethread, it should have the ability to decide its own applicability in a particular? This work has been supported by the Institute e-Austria Timis¸oara, BMWA andBMB:WK ministries of Austria.64 C. Bonchis¸, C. Isbas¸a, D. Petcu, G. Ciobanuround. In order to detect if the P system halts, each membrane must inform theother membranes about its inactivity. It can do so by sending messages to others,and by using a termination detection algorithm.In this paper we present a new simulator based on CLIPS. The previous CLIPSimplementations represent P systems rules by CLIPS facts; we get a significantlyfaster execution by using CLIPS rules to implement P systems rules. In [5], the Psystem data are inserted directly into code, and so they cannot be easily modified,as opposed to our implementation where a P system is an input data, providinga lot of flexibility. P systems as input data are described by XML documents;this fact provides a standard method to access information, making it easier touse, modify, transmit and display. XML is readable and understandable, it ex-presses metadata easily in a portable format, just because many applications canprocess XML on many existent platforms. Moreover, by using XML, it becomeseasy to define new features and properties of P systems. XML allows an auto-mated document validation, restricting wrong input data, and warning the userbefore execution with respect to the possible errors in their P systems description.From a user point of view, all these features facilitate an efficient description andreconfiguration of the P systems.An important advantage of our simulator is given by its availability as an Webapplication; this aspect is actually emphasized by its name: WebPS. Web applica-tions do not require an installation. As any Web application, it can be used fromany machine anywhere in the world, without any previous preparation. A simpleand easy to use interface allows the user to supply an XML input both as textand a file. A friendly way of describing P systems is given by a helpful interac-tive JavaScript-based P system designer. The interface provides a high degree of(re)usability during the development and simulation of the P systems. The initialscreen offers an example, and the user may find useful documentation about theXML schema, the rules, and the query language. The query language helps theuser to select the output of the simulation.The simulator is open-source, actually free software, as it is being offered athttp://psystems.ieat.ro under the GNU General Public License. This allowsanyone to contribute with enhancements and error corrections to the code, andpossibly develop new interfaces for the C and CLIPS level APIs. These interfacescan be local (graphical or command-line), or yet other Web-based ones.Next section presents the WebPS structure, and argue why it is better thansome previous simulators. Several examples implemented in the WebPS systemare described in Section 3. Finally, further development directions are identified.2 WebPS Software ArchitectureThe software structure of the simulator has three distinct levels. The inner level isthe CLIPS level. This level integrates part of the knowledge about the theoreticaldescription of P systems, the result being a library of CLIPS functions, meta-rulesWebPS: A Web-based P System Simulator 65and templates. Since CLIPS is easily embeddable in C (as its name ”C LanguageIntegrated Production System” suggests), we can control the CLIPS level froma C program, and we include some example to illustrate how this is done. TheC level is strengthened by introducing a C library for modelling and simulatingP systems based on the CLIPS library. The Web application level offers a user-friendly interface to the simulator, and can become, after the addition of debuggingand visualization features a powerful P system development tool.2.1 CLIPS levelThis is the core level of the simulator. We address here some crucial issues, namelyhow we implement in a sequential context the maximally parallel and nondeter-ministic execution of P systems.Maximally parallel executionThe maximally parallel execution requirement relies on constraining our simulationcycle to the following distinct steps:1. React step: where the activated reaction rules are sequentially executed.2. Spawn step: where the new objects created by rules inside their membranesare asserted as object facts; they become visible for a future React step.3. Communication step: where the objects injected or ejected by communica-tion rules in different membranes are asserted as objects facts.4. Divide step: it handles possible divisions processes of membranes.5. Dissolve step: it handles dissolving processes of membranes.By constantly recording the state of the P system after each React, Spawn andCommunication steps, we can get a trace of an execution.Nondeterministic executionCLIPS uses RETE algorithm to process rules; RETE is a very efficient mechanismfor solving many-to-many matching problem [3]. The nondeterministic executionrequirement is fulfilled by the CLIPS random mechanism. We have looked closelyat the random strategy, and we found it makes the same choice for the sameconfigurations in different executions. By calling the random function of CLIPS,the random mechanism uses the random number generator. The failure is relatedto the improper seeding of the random number generator. We have corrected thiserror, and properly seed the random number generator by using /dev/urandom,the entropy gathering device on GNU/Linux systems. This aspect can be alsouseful for other CLIPS implementations possibly affected by the same failure.66 C. Bonchis¸, C. Isbas¸a, D. Petcu, G. CiobanuData representationAn important choice regarding an implementation is given by data representation.We decide to represent P system objects and membrane structure as CLIPS facts(with set-fact-duplication option of CLIPS set to on), and the P systems reactionrules as CLIPS rules. This contrasts the previous implementations which haverepresented reaction rules as CLIPS facts; while their choice might allow generalmeta-rules for execution, we get a flexible and efficient framework by representingreaction rules as CLIPS rules. The efficiency is gained by making direct use of theCLIPS pattern-matching mechanism, and rule activation capabilities. This choiceis also confirmed by the efficiency of the dissolve and divide operations which implya lot of moving and copying. Initially we think to represent membranes as modules,but later we see that this representation decreases the efficiency and flexibility ofthe whole system.We present the Backus-Naur form of reaction rules, as well as their conversionsinto CLIPS knowledge-base components:<rule> ::= <object_list> -> [ <output_list> ][ "|" <promoters_inhibitors_list> ]<object_list> ::= <object_name> { "+" <object_name> }<output_list> ::= <output> \{ "+" <output> }<output> ::= <output_object> |<division_marker> |<dissolve_marker><output_object> ::= <object_name>[ "(" <target_membrane> ")" ]<division_marker> ::= "%"<dissolve_marker> ::= "#"<promoters_inhibitors> ::= [ <promoter_inhibitor>{ "+" <promoter_inhibitor> } ]<promoter_inhibitor> ::= <promoter> | <inhibitor><promoter> ::= <object_name><inhibitor> ::= !<object_name><symport_rule> ::= "( <object_list>, out | in )"<antiport_rule> ::= "( <object_list>, out;<object_list>, in )"It is useful to note that the simulator supports divide, promoters/inhibitors, andsymport/antiport rules for membranes. For example, the P system transition rulea+b-¿c+d(2)+e(0) with priority 11 from membrane 1 is converted into the follow-ing CLIPS rule:(defrule MAIN::1_a+b->c+d[2]+e[0](declare (salience 11))(do (what react))(or (parent-child (parent 1) (child 2))WebPS: A Web-based P System Simulator 67(parent-child (parent 2) (child 1)))(or (parent-child (parent 1) (child 0))(parent-child (parent 0) (child 1)))?a-0 <- (obj (name a) (membrane 1))?b-1 <- (obj (name b) (membrane 1))=>(assert (newobj (name c) (membrane 1)))(assert (inject (name d) (membrane 2)))(assert (inject (name e) (membrane 0)))(retract ?a-0) (retract ?b-1))The membrane structure is reflected by the parent-child facts. An object a ofmembrane 1 is represented as a CLIPS fact on line 8: (obj (name a) (membrane1)). While the reactants a and b are consumed, the new objects c, d , and e arecreated during the Spawn and Communication steps, respectively. The rulepriorities are mapped directly to CLIPS rules salience values, and therefore arerestricted to integer values in the interval [-10000, 10000].2.2 C levelIn the C level we use CLIPS API, although we plan to develop a complete librarythat encapsulates the C-CLIPS interface, namely a C library which wrap nicelyaround the CLIPS one (Figure 1). We represent a P system using XML, and weCCLIPSFig. 1. Relation between the C and CLIPS levels.define an XML Schema for this kind of document. A special library is developedto handle XML parsing of the input for the CLIPS part of the simulator. In thefollowing example is described a P system conforming to the XML schema. Thisexample system presents a P system for multiplication of the number of a objectsin membrane 1 with the number of b objects in membrane 0 , the result being thenumber of d objects in membrane 0 .<?xml version="1.0"?><psystem><membrane name="0"><object name="b" count="3" />68 C. Bonchis¸, C. Isbas¸a, D. Petcu, G. Ciobanu<rule body="b+v->e+v+d" priority="1" /><rule body="e+u->b+u+d" priority="1" /><rule body="v->u(1)" /><rule body="u->v(1)" /><membrane name="1"><object name="a" count="4" /><object name="v" count="1" /><rule body="a+v->v(0)" /><rule body="a+u->u(0)" /></membrane></membrane><query text="count of (objects from 0 where (objects d))" /></psystem>2.3 Web levelThe Web level of the simulator allows to choose between a user-friendly P systemdesigner written in JavaScript and a traditional HTML input form transmittingan XML description by uploading a file or by editing. Aside from the XML Psystem description editing, the user can specify a number of executions of the Psystem. Our JavaScript P system Designer aims to facilitate the description of theP system without requiring the user to write XML, but generating it based onthe user’s interaction with a dynamic interface. After the user introduces a XMLPHP scriptCGI program(C)CLIPS library LibCGI PS−XML C libraryJavaScriptP system DesignerHTML input formfor XMLFig. 2. Structure of the Web level.description, it is transmitted to a PHP script which does some further processing,and sent then to a CGI program written in C (Figure 2). The C program usesa specific P system XML library called PS-XML, as well as LibCGI and CLIPSWebPS: A Web-based P System Simulator 69library in order to simulate the evolution of the P system. Finally it returns theresults to the user. It is possible to select various information provided as results,and in oprder to help the user to select the desired information we define a querylanguage called PsQL.PsQL (P systems Query Language)We define PsQL as an SQL-like language for querying the state of a P system. Wedeveloped a CLIPS library for parsing and interpreting this language. At the Weblevel, the queries can be included in the XML input; these queries are activatedafter the execution of the specified P system. If it does not exist any query, the Psystem is simulated, but no output is generated. At the CLIPS level it is possible tospecify queries for the P system in a dynamic manner, not just before starting thesimulation. At the syntactic level, PsQL is a Lisp-like language, and it is supportedby a small CLIPS library of list-handling functions.The Backus-Naur (partial) description of PsQL is presented in the followinglines:<query> ::= <expression> |<count-query> |<membranes-query> |<objects-query><count-query> ::= "(" count-of <objects-query> |<membranes-query> ")"<objects-query> ::= "(" objects-from <membranes-spec>[ where <where-spec> ] ")"<membranes-query> ::= "(" membranes-from <membranes-spec>[ where <where-spec> ] ")"The full description is available at http://twiki.ieat.ro/twiki/bin/view/Institut/PSystemsQueryLanguage. We plan to extend PsQL with trace facili-ties; having queries on the possible traces during an execution represents a steptowards an automated verification of the P systems.3 ExamplesMultiplicationThe first example is a P system that computes the multiplication of two naturalnumbers. Figure 3 describes graphically the P system. As inputs we consider thenumber of a objects in membrane 1 , and the number of b objects in membrane0 . The result is given by the number of d objects in membrane 0 .This P system differs from other similar ones by that it does not have expo-nential space complexity, and does not require active membranes. As a particular70 C. Bonchis¸, C. Isbas¸a, D. Petcu, G. Ciobanubmb+v e+v+d > v u(1)e+u b+u+d > u v(1)ana+v v(0)a+u u(0) v01Fig. 3. P system for multiplication.case, it would be quite easy to compute n2 by just placing the same number n ofa and b objects in its membranes.Another interesting feature is that it may continue computing the multiplica-tion after reaching a certain result. Thus if initially there are m b objects and n aobjects, the system evolves and reaches a state with n ·m d objects in membrane0 . If the user wish to continue in order to compute (n + k) · m, it is enough toinject k a objects in membrane 1 at the current state, and the computation cango on. Therefore this example emphasizes a certain degree of re-usability.Recursive sumThe P system described in Figure 4 computes the recursive sum∑ni=1 ki. Thea a(0) a a(0) a a(0)k2k1 kn1 2aa...0naFig. 4. P system for recursive sum.numbers of a objects in the membranes 1...n are the summands, and the result ofthe computation is the number of a objects in membrane 0. The PsQL query todetermine this result is:(count of (objects from 0))WebPS: A Web-based P System Simulator 71While this example is rather trivial, it illustrates the expressiveness of the querylanguage (PsQL). Using PsQL queries, it is not necessary to apply the rules andexecute the specified P system. Given the initial multiset, the same recursive sumis obtained by using the following query:(count of (objects from (membranes from 0)))Dot product of two vectorsCombining the previous two examples, we can compute the dot (scalar) productx · y of two vectors x, y ∈ Nm, where m ∈ N. Let us denote the components of thevectors by xi and yi, respectively; these components are given by the number of band a in the membranes labelled by 2i and 2i+1, respectively. Then x · y is givenby the number of d objects obtained in membrane 0 after the P system halts.This P system is described in Figure 5: where k = 0,m− 1. The PsQL query for> u u(2k+2)e+u b+u+d(0)yk+1a+v v(2k+1)a+u u(2k+1)2k+2a vb+v e+v+d(0) > v v(2k+2)xk+1b2k+1b+v e+v+d(0)y1a+v v(1)a+u u(1)a v2x1be+u 1> v > u b+u+d(0)v(2)u(2)0... ...Fig. 5. P system for dot product.retrieving the result is:(count of (objects from 0))4 Conclusion and Further WorkWe present a new simulator of the P systems. It is efficient, flexible, and does notrequire any previous knowledge in P systems, or expertise in computers. Since thesimulator has some novel and interesting features related to efficiency, ease of useand generality, it can become a useful tool for the community, both theoreticallyand practically. Being GPL licensed, we expect it is eligible to become a simulatorbenchmark reference. The simulator is available at http://psystems.ieat.ro.72 C. Bonchis¸, C. Isbas¸a, D. Petcu, G. CiobanuWe intend to make the simulator available as a web service. Moreover, continu-ing the commitment to standards compliance, we will strive for SBML compatibil-ity for our specification language. Further improvements are related to better de-bugging and visualization capabilities (including a flexible fine and coarse-grainedtracer), developing a library of macros and methodologies using the principles ofmodularity, extensibility and structured design from software engineering, intro-ducing flexible rules for the development of macros for P systems.References1. G. Ciobanu, W. Guo: P systems running on a cluster of computers. Proceedings4th Workshop on Membrane Computing, LNCS 2933, Springer-Verlag, Berlin, 2004,123–139.2. G. Ciobanu, D. Paraschiv: P system software simulator. Fundamenta Informaticae,49, 1-3 (2002), 61–66.3. C.L. Forgy: RETE. A fast algorithm for the many pattern/ many object patternmatch problem. Artificial Intelligence, 19 (1982), 17–37.4. Gh. Pa˘un: Membrane Computing. An Introduction. Springer-Verlag, Berlin, 2002.5. M.J. Pe´rez-Jime´nez, F.J. Romero-Campero: A CLIPS simulator for recognizer Psystems with active membranes, Proceedings 2nd Brainstorming Week on MembraneComputing, University of Sevilla Tech. Rep 01/2004, 387–413.

WebPS: A Web-based P System Simulator with Query Facilities

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WebPS: A Web-based P System Simulator with Query Facilities

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