On the Use of Agents in a BioInformatics Grid
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Luc Moreau ½ , Simon Miles , Carole Goble , Mark Greenwood , Vijay Dialani , Matthew Addis , Nedim Alpdemir ,
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Rich Cawley¾ , David De Roure , Justin Ferris , Rob Gaizauskas , Kevin Glover , Chris Greenhalgh , Peter Li ,
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Xiaojian Liu½ , Phillip Lord , Michael Luck , Darren Marvin , Tom Oinn , Norman Paton , Stephen Pettifer , Milena
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V Radenkovic¿ , Angus Roberts , Alan Robinson , Tom Rodden , Martin Senger , Nick Sharman , Robert Stevens ,
5 ¾ Brian Warboys ¾ , Anil Wipat , Chris Wroe
(1) University of Southampton, (2) University of Manchester, (3) University of Nottingham, (4) EMBL Outstation - European Bioinformatics Institute, (5) University of Newcastle, (6) University of Sheffield
Project site: www.mygrid.org.uk Contact Author: Luc Moreau ([email protected])
Abstract process it. In many resources, each record is analogous to an in- MyGrid is an e-Science Grid project that aims to help bi- dividual publication with not only raw data, but also ad- ologists and bioinformaticians to perform workflow-based ditional annotations supplied by a small number of human in silico experiments, and help them to automate the man- experts (curators) or automated systems. Annotations are agement of such workflows through personalisation, noti- typically semi-structured text that make some use of key- fication of change and publication of experiments. In this words and controlled vocabularies, and have to be parsed paper, we describe the architecture of myGrid and how it computationally or read by people. Therefore, as well as will be used by the scientist. We then show how myGrid can a large number of data types, much of the valuable knowl- benefit from agents technologies. We have identified three edge is locked into semi-structured text, under the premise key uses of agent technologies in myGrid: user agents, able that the scientist will read and interpret it. to customize and personalise data, agent communication In the past, this complexity has been dealt with largely languages offering a generic and portable communication by the intelligence of the practising biologist. This has been medium, and negotiation allowing multiple distributed enti- possible because biologists working on a specific organism, ties to reach service level agreements. or a specific aspect of it, have needed access to only a small number of these resources. Interestingly, much of the growth of molecular biology 1 Introduction has been contemporaneous with the development of the Web, which probably explains why many resources have MyGrid is a Grid middleware project in a bioinformatics been designed with the intention that a scientist will interact setting. In biological sciences, it is not principally the size with a Web page, dealing with a single query at a time, and of the data that matters but the complexity involved in using read the results displayed as reports in a browser, navigating it: the complexity of the data itself, the number of reposito- between links in different databases by mouse-clicking. We ries and tools that need to be involved in the computations call this approach “query by navigation”. Where databases required to answer the kind of questions posed by the scien- are published, they are usually released as flat files, even in tist, and the heterogeneity of the data and operation of tools. those cases, such as SWISS-PROT and EMBL [15], where Rather than a few international facilities (e.g. CERN and the production systems are relational databases. Fermi Lab) producing vast amounts of data that need to be Although the volume of data is not yet a computational accessible, the pressing issue with bioinformatics is coping problem, the advent of high throughput experiment tech- with a very large number of sites (potentially thousands of niques means that human analysis is now reaching its limits. individual laboratories) around the world, each using cheap, With sequence databases reaching hundreds of MBytes and commodity technology to continuously generate substantial microarray expression data producing tens of GBytes, the quantities of different kinds of data, and design new tools to limits of the non-scalable query by navigation are rapidly being reached, if not already passed. at the level of scripts through the use of an appropriate pro- The particular focus of myGrid, therefore, is on increas- gram transformation.) ingly data-intensive bioinformatics and the provision of a The workflow enactment engine can send requests to ex- distributed environment that supports the in silico experi- isting running services or can activate tools and interact with mental process. The vision is of a “lab book” environment them: services need to be discovered and processes need where the e-Scientist can construct in silico experiments, to be created. For the former, a service directory is used and find and adapt others, store partial results in local data as a repository of service instances that are currently ac- repositories and have their own view on public reposito- tive, whereas the latter makes use of a job activation and ries, and be better informed as to the provenance and the scheduling system. Generally, scripts may require space to currency of the tools and data directly relevant to their ex- store temporary results, or may try to ensure that compu- perimental space. For a less skilled user, myGrid should tational resources are reserved at the same time as storage help in finding appropriate resources, offering alternatives space to ensure the prompt execution of the workflow: allo- to busy resources and guiding the user through the com- cation and reservation are handled by the resource manage- position of resources into complex workflows. In order to ment service. provide such an environment, myGrid unequivocally needs to address the “Grid problem”, i.e. the flexible, secure, co- 2.2 User Interaction ordinated resource sharing, among dynamic collection of individuals and institutions — Virtual Organisations [9]. In The user, through an interface, may interact with the this context, the Grid becomes egocentrically based around workflow enactment engine, suspending and resuming the Scientist: myGrid. workflows, observing their progress, analysing their logs. The contributions of this paper are threefold. First, we Suspended workflows are serialised and stored in a reposi- present a service-based architecture to support the vision of tory, potentially shared with other users. the “lab book” environment. Second, we illustrate how this architecture can be used during the enactment of workflows. Third, we review how a bioinformaticsgrid can benefit from User Directory Service Functionality Workflow Definition agent technologies. Groups, Roles Directory Metadata Repository
Workflow Provenance
2 The MyGrid Service-Oriented Architec- Ontological Definitions Validation Authentication Service ture Ontological Reasoning Authorisation Directory
Provenance In this section, we describe the different services that are Repository provided by myGrid, and sketch their interactions. (They Notification Workflow are displayed in Figure 1.) The experimental in silico pro- Enactment cess is expressed as a workflow script by the scientist. Ser- Serialised Workflow vices can be viewed as being provided by agents and work- Repository flow can be seen as an agent interaction script. Some initial User Workflow Workflow Agent Personalisation Resolution work in this vein has already been done [2, 3]. Information Extraction
Distributed 2.1 Workflow Enactment User Repository Databases Job Scheduling Queries Resource Management At the heart of the myGrid runtime system, we find the workflow enactment engine which, given a workflow script, is able to execute (or enact) the script. Scientists and their institutions may have preferences that must be taken Figure 1. myGrid Services into account when enacting a workflow script: e.g., some databases are preferred over others, or specific tools and pa- Some workflows may take days, if not weeks, to com- rameters are routinely chosen. It is the role of the workflow plete their execution. Users therefore need to be notified resolution service to customise a script’s “free variables”, when workflow execution terminates. We prefer not to as- possibly making use of a workflow personalisation service sume the existence of user agents able to handle incoming able to obtain preferences from a user (or a user agent act- notifications. Indeed, users are not logged on permanently, ing on their behalf). There exist several strategies to resolve and we feel that always running user agents would overload a workflow: eagerly before enactment, or lazily if and when the system unnecessarily. Instead, we make use of a no- required by the enactment engine. (Both can be expressed tification service able to forward messages to user agents, when present, or to store messages in their absence. The by local and remote databases. use of the notification service is of course not restricted to Above, we have discussed the existence of metadata that the user agent, but may be used by any services in myGrid. is structured according to ontologies. In biological sciences, In particular, we use the notification service to give notifi- it is also customary to create annotations in free text form. cations to users about changes in data, workflows, services. Such metadata contains invaluable information assembled Sharing information between users, discovering infor- by database curators. MyGrid also provides support for cor- mation, finding out users or institutions that are investigat- relating such an information with medical literature through ing given topics are all key functionalities of myGrid. Sev- an information extraction service. eral directories are used for that purpose: the user direc- MyGrid provides support for provenance in two differ- tory holds information about users, groups, roles and insti- ent ways. First, provenance information, in particular re- tutions; the workflow repository contains information about lated to workflow enactement, can be logged in the prove- scripts and their functionality. nance annotation service; such a service is also used to store provenance information for services having no built-in sup- 2.3 Ontologies port for provenance. Additionally, the workflow provenance validation service is able to re-enact workflows to establish All information about workflows and users is what we change over time. call metadata and is structured according to a set of on- tologies — an ontology is generally defined as a shared un- 2.5 Security and Fault Tolerance derstanding of a specific domain [10]. Information about services are also expressed using such ontologies, and are The myGrid authentication service extends the PKI in- stored in the service functionality metadata service; the lat- frastructure to provide X.509 certificates for users and ob- ter service contains metadata about classes of services, and jects (called identities henceforth) needing verification. It must be distinguished from the service directory which lists supports a notion of logical domain which is defined by the active service instances. set of identities it manages. The confederation of several Not only are ontologies a shared understanding of some logical domains forms an enterprise infrastructure. Each domains, but their logical foundations also allow users to logical domain has associated domain administrators who perform reasoning over such domains. Examples of reason- are authorised to create and revoke identities within their ing include classification (i.e., the computation of a concept logical domains. hierarchy based on the specialisation relation), or consis- In myGrid, a sub-component of the user agent acts as tency checking (i.e., checking that a statement is not incon- a credentials repository, permitting simultaneous access to sistent in a logic). An ontology-based reasoning facility is multiple logical domains. This facility allows a user to provided by myGrid to help users compose new workflows. have simultaneous access to multiple virtual organisations Additionally, the ontology service allows users to reason [9] and obtain the access rights to multiple resources across about concepts of the application domain in order to under- sites. stand their inter-relationships. MyGrid supports role-based access control [17] and dy- namic mapping between users and roles. Within each logi- 2.4 Data and Metadata cal domain, there exists a hierarchy of user roles and access rights; roles are statically associated with access rights. The Most myGrid repositories are be implemented as model is extensible by allowing the definition of new roles databases. Additionally, biological information is stored in and access rights. In an enterprise security infrastructure, multiple and heterogeneous databases. Distributed query one needs to support identities from different logical do- systems over such databases are an essential component to mains, which may have different access models: this re- facilitate information integration. In myGrid, databases is quires the definition of a mapping of roles and access rights accessed though a service interface [16], whereby struc- of a domain onto roles and access rights of another domain. tured data stores support consistent interfaces for database MyGrid computations may be long-lived and involve a access, manipulation and metadata description. As a com- very large number of computing resources. Hence, they ponent within the personalisation framework of myGrid, need to be designed with fault tolerance in order to be ro- database services are used to provide individual users with bust. To this end, myGrid provides a set of interfaces, which access to (i) locally produced data sets; (ii) the results of services are required to implement, and which provide ro- analyses run by the user over local or remote data; and (iii) bustness to applications involving the use of multiple ser- distributed querying over local and remote data resources. vices. The complete description is beyond the scope of this The distributed query processor benefits from the consis- paper, and we refer the reader to a companion paper [4]. tent service interfaces and metadata descriptions provided The approach may be summarised as follows: implemen- tors of a service have to implement an interface (for check- scientist to the sharing of resources between research com- point and rollback); the architecture dynamically extends munities. Within an e-Science community, it is not just the the service interface by methods for fault tolerance; applica- available data that is valuable, but also knowing the accept- tions making use of different services have to declare their able/proven ways of combining that data to generate new inter-dependencies, which are used by a fault-manager to insights. control checkpoints and rollbacks; an extension of the com- munication layer is able to log and replay messages. 3.1 Prototype Experiment
3 MyGrid Workflow Enactment in Practice In our prototype, a myGrid user has access to a per- sonal repository containing their domain data (and results), We have implemented a prototype of this architecture, a workflow repository containing the available workflow based on a subset of the services described in Figure 1 and scripts and a service directory of the available service in- exclusively relying on Web Services technology. In this sec- stances. Each data item in the personal repository has an tion, we show how the scientist is able to enact workflows associated concept type (a term in the ontology); such con- in myGrid. cept types are used to initiate the enactment of in silico ex- An in silico experiment typically involves using several periments, as we now explain. bioinformatics databases and algorithms available on the Potential workflows are identified through a conversa- World Wide Web. Currently, these resources are integrated tion with the ontology service. A specific user interface is by a “query by navigation” process, i.e. by cutting and past- used to incrementally build up an abstract description of a ing across browser windows. Alternatively, a script (such workflow, starting with the selected concept type. Once the as perl script or bat file) may be written to facilitate the abstract workflow description is complete, it can be classi- frequent repetition of in silico experiments. There are a fied to give a workflow service type identifier (also a term number of limitations of this current state of practice that in the ontology). This is used to retrieve the identifiers of workflows in the myGrid environment address. workflow scripts that match this required type, and from the First, there is the problem of knowing what in silico ex- identifier, the workflow script itself. In this way, the user in- periment to perform. A user typically has an understanding teracts with the ontology service to determine the concepts of what they are trying to achieve in bioinformatics terms that match their task; then, they get a list of all the workflow and might know some specific Web resources or script, scripts of this type and choose the one to run (perhaps using based on past experience. How they acquired this experi- some metadata to help in the selection). ence, how they keep their knowledge up-to-date, and how they adapt previous experiences to new tasks are essential 3.2 Workflow Details elements of the experimental process, which we intend to make explicit. Inspired by WSFL [11], the workflow definition consists Second, there is the problem of incorporating new re- of a set of service providers, activities, data links and con- sources. In most situations the user is interested in a spe- trol links between activities (cf. Figure 2). For many my- cific type of resource, a SWISS-PROT database, rather Grid workflows, each activity has its own service provider, than a specific resource instance such as the SWISS-PROT which includes a locator element to identify the Web Ser- database hosted at a specific institution. If their first (de- vice, to be used by the workflow enactment engine. It is fault) choice is unavailable, then the user would like to use possible for the locator to be static and directly reference an alternative of the same type. In the current state of prac- the WSDL definition of the service, but it is more usual for tice, scripts tend to include hard-coded references to spe- the locator to be dynamic. In this case, it gives the ser- cific resources. vice type identifier that is used to lookup possible services Third, there is the limited recording of how in silico ex- (using UDDI) from the service directory. Each activity is periments have been performed. Without knowing what re- described in terms of its service provider and an operation, sources have been used in the derivation of a result, there thus expressing the specific provided operation that matches is no way of knowing if it might be worthwhile re-running the abstract activity in the workflow. The data links describe the in silico experiment in the light of more recent knowl- how the outputs of an activity are mapped to the inputs of edge (or if the result should be disregarded, as more recent other activities, while the control links are used to decide knowledge has rendered some of the experimental assump- when the activities should be fired. tions invalid.) The enactment of a workflow script starts by sending the Fourth, there is difficulty in propagating good in silico script and input data to the workflow enactment service. experimental practice. This essentially incorporates the pre- This responds by returning a workflow instance identifier vious three issues and extends them beyond the individual that the user interface portal can use to query the workflow chooses the first element in the list returned from the ser- vice directory. The other is user-choice, where the list of services is sent to the user agent who makes choice on be- half of the user, possibly interacting with the user through the portal, if configured to do so. The workflow enactment service also creates a prove- nance log within the personal repository for each workflow instance. This trace includes: the initial data, the workflow script, the intermediate results, the actual service instances selected and the time taken for the service operations. These logs could be viewed through the portal to understand the detailed derivation of a particular result. The definition of an in silico experiment as a workflow means that it exists as an explicit piece of data that can be shared, copied and altered by a community of scientists. Even within the context of the simple examples in the proto- type, it was clear that what a user might consider a single in silico experiment might be supported by many workflows. There are variants of workflows that have the same type and
¯ the cost of receiving the notification, sumer wishing to receive notifications of a specified quality, then provide a final proposal to the consumer. It can nego-
¯ the topic (event category) of the notifications, tiate with any of the publishers known to the notification service, and also limit the agreed quality of service to that
¯ the frequency with which notifications are received (e.g. every time a change occurs, daily, hourly), acceptable to the notification service. We wish to make the quality of service broker able to negotiate with publishers
¯ the generality of the change described by the notifica- produced by various providers, so we use the concept of tions, pluggable negotiation algorithms, allowing the quality of service broker to select the appropriate protocol for negoti-
¯ the form in which the information in the notification ating with a publisher. message is supplied, and
¯ the accuracy of information contained within a notifi- 5 Conclusion cation. Quality of service refers to these distinctions in both what a In this paper, we have presented the myGrid architec- publisher produces and how it produces it. ture and overviewed possible use of agents. MyGrid aims A publisher of notifications will be able to produce no- to provide a personalised environment for the bioscientists, tifications matching (or exceeding, where appropriate) one which helps them to automate, repeat and therefore better or more measures of quality of service. For example, a pub- achieve their experiments. Agents are particularly useful in lisher may be able to publish notifications on a particular tailoring the myGrid system to the priorities of individual topic every minute or every hour. A consumer of notifi- scientists, personalising each step of a workflow and nego- cations may prefer, or demand, one measure of quality of tiating on their behalf. It can be seen from our discussion service over another. Whether, or how well, their demands that, along with dynamic workflow enactment, standardis- can be met by a publisher depends on the quality of service ation of data semantics via ontologies and the many other that the publisher can provide. facilities of myGrid, agents can make conducting in-silico experiments flexible and more easily controlled by the indi- PAR’02), Lecture Notes in Computer Science, Padeborn, vidual or collablorating scientists. Germany, Aug. 2002. Springer-Verlag. The examples of use of agents we have presented, while [5] T. Finin, Y. Labrou, and J. Mayfield. Software Agents, J. already offering a capability non existing in current bioin- Bradshaw, Ed., chapter KQML as an Agent Communication Language. 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