Steady progress in bioinformatics software component technology, OiB'98 concludes
HINXTON, UK - Last year, conclusions of the Objects in Bioinformatics '97 conference were summarised as "Java and CORBA are good, reusable and collaborative components are the hype, and standardisation is the key issue". This year, components have gone from hype to real-life use and standardisation of those components has matured rapidly.
Organised by Alan Robinson of the European Bioinformatics Institute (EMBL-EBI), the Objects in Bioinformatics '98 conference was held here at the Wellcome Trust Genome Campus on August 3-4 and attracted more than 220 participants from both academic and commercial background in bioinformatics.
This year's conference had as main theme the implementation and application of distributed object technology (such as CORBA) to genomics and bioinformatics, and the work of the Life Sciences Research Task Force (LSR) of the Object Management Group (OMG) in promoting standards.
OMG and LSR
The morning of the first day especially focused on this theme, with presentations on both the OMG and the LSR. The conference kicked off, however, with a briefing on the progress in the bioWidgets project at the University of Pennsylvania. Jonathan Crabtree, of the Centre for Bioinformatics there, clearly demonstrated the viability of the components approach with a number of newly developed Java applications that make use of the same components. Built upon the bioWidgets architecture, the tool BlastView visualises BLAST results and is capable of executing follow-up analyses through flexible integration of external tools and databases. Other tools like AnnotView and AlignView use exactly the same widgets for presentation of data.
Jon Siegel, director of Program Management of the Objects Management Group, presented an overview of the OMG and how it will facilitate interoperability through object-oriented standards. Based upon the Common Object Request Broker Architecture (CORBA), the OMG offers a framework through which various domains can propose and implement standardised interfaces and services to domain-specific data and components.
One of these domains is geared towards bioinformatics and sequence analysis: Life Sciences Research (LSR), which was instigated just after OiB'97. Timothy Slidel (EMBL-EBI, now at SmithKline Beecham), co-chair of the LSR Task Force, informed the audience of the progress that has been made in the last year. The Request for Information (RFI) received 22 responses from both academia and commercial companies, many of these responses where bioinformatics related. The Clinical Trials working group then issued a BioMolecular Sequence Analysis Request for Proposals (RFP), to which the initial responses will be submitted before October 19.
A further talk on the OMG outlined how these standards are applied and put into use, exemplified by the work in the CORBAmed domain on a Person Identification Service (PIDS) which is now adopted in for example hospitals for their patients index.
Dave McAllister (Silicon Graphics) continued with a slightly different view on components. First of all, in his opinion Java and JavaBeans are not the answer to a component model, they are only to be used for lightweight clients based upon such a model. Other programming languages are better suited for heavyweight applications. Tied into this, the software development tools are still prehistoric: they are not suitable for today's distributed applications. Such tools need to become object-oriented themselves. This issue of the lack of proper and modern software development tools was echoed in many of the talks that followed.
CORBA and Objects applied...
The rest of the first day and the next day were spent on various talks that demonstrated the good use to which reusable components and the CORBA architecture for data exchange have been put. For example, Jeremy Parsons (EMBL-EBI) presented ongoing work that is aimed to make tools to explore EST data sources, where CORBA is used to provide an interface between the distributed (remote) data and the Java applications that view sequence chromatograms, alignments, and clusters.
A fully-packed (and dark!) auditorium.
(c) 1998 BioInformer. All rights reserved.
Another typical example was presented by Richard Baldock (MRC Human Genetics Unit) who introduced the audience to work on a digital vowel 3D-image atlas of mouse development and a gene expression database that uses the atlas as a reference. The underlying database of embryonic objects (tissues, reconstructions, and nomenclature) is implemented in ObjectStore, using CORBA to connect the database to Java applets that will enable researchers (in the near future) to query this excellent database, and even to submit new gene expression data.
Noteworthy is that, although reusable components for bioinformatics are what this conference was all about, a lot of individual solutions to certain problems were presented. Stan Letovsky (Cereon Genomics LLC) commented, "Everybody is building reusable components but everyone is building the same reusable components over and over again, which is a little bit of an antilogy. I think it's partly because we're still exploring how to design and how to build reusable components, but it is getting the point where there is not a whole lot of reason for somebody to build yet another Sequence Viewer, yet another Alignment Viewer. Action is moving elsewhere, more to the back end I would say."
Ira Baron (Millennium Pharmaceuticals) added, "The other reason that there are multiple implementations of the same sort of tool maybe simply because many of the participants here are commercial research houses or software vendors so there may be copyrighting reasons for not be able to use somebody else's implementation."
Poster sessions in the cloisters were very well attended.
(c) 1998 BioInformer. All rights reserved.
CORBA is now playing an even more important role than last year in glueing applications together; many of the presenters had adapted this architecture over any other. "I am very impressed", Ira Baron said, "I don't think there are many industries where CORBA has come into common use as quickly as in the bioinformatics community. Some of that might be a reflection that there are a lot of legacy systems in bioinformatics relative to other industries, and some of that might also be that the nature of the science in bioinformatics is very distributed, much more so than in banking or insurance for instance."
The general consensus is all in favour for reusable components, certainly in the light of the advancements that have been made in just under a year now. "A year ago we were talking of these things and we had some examples but it wasn't as mature as it is now. We now have three or four groups putting out sets of new components. So there clearly has been progress. I think the challenge for the next phase is to see to what extend we really can begin to plug and play with components from different authors", Stan Letovsky concluded. During the panel discussion, a proposal was brought forward to very soon have a standard interface for selecting (and propagating that selection) objects, to make a start with the plug and play of components of different authors.
With real interoperability and reuse of these bioinformatics components just around the corner, it is certainly no surprise that many voiced the same opinion as Ewan Birney (Sanger Centre): ". modular components are the only way to go forward in bioinformatics."
Article by: Jean-Jack M. Riethoven
Resources and further information
European Bioinformatics Institute
Objects in BioInformatics `98 Conference
The Sanger Centre
The Wellcome Trust
Object Management Group (OMG)
Life Sciences Research (LSR-DSIG)
MRC Human Genetics Unit
Mouse Atlas and Gene Expression Database
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