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Need for Standards Is Key Dilemma for Software-Sharing Proposals


HINXTON, U.K.--Java and CORBA are good, reusable and collaborative components are the hype, and standardization is the key issue. These are, in short, the conclusions of the Objects in Bioinformatics '97 conference that was held at the Wellcome Trust Genome Campus here June 18-19.

Jointly organized by the European Bioinformatics Institute (EMBL-EBI) and the bioWidget Consortium, the conference focused on the growing role of reusable object-oriented software components and distributed objects in bioinformatics and the biological sciences.

"The widget and object-oriented approach is a powerful paradigm in which new applications are developed by utilizing preexisting components interacting in concert, and which offers the possibility of a new generation of bioinformatics tools. In this way development time is reduced and greater time is spent on data analysis and knowledge discovery, rather than on the writing of monolithic applications," explained Alan Robinson of EMBL-EBI, who organized the conference. "Initially, we were aiming at a small workshop of 40-50 persons, but we were overwhelmed at the number of people registering. Approximately 200 official registered scientists, software developers, and managers attended the conference, with another 50 or so unregistered visitors."

A sizable part of the first day was dedicated to the bioWidgets Consortium. Stan Letovsky of Johns Hopkins University, a member of the consortium's board of directors, described the group as a nonprofit organization with the goal to "find better and more economical ways to develop graphical displays for genomic data and biological data in general. It does this by developing a community consensus on standards for graphical components (bioWidgets), by implementing bioWidgets, and by building genomic graphical applications from the bioWidgets." Java has been selected as the language for bioWIdgets, because it is a standard language, encourages modular and cross-platform development, and is seen by the majority as cutting edge technology.

Other talks discussed the bioWidget low-level Application Programming Interface (API) and the quality assurance process that every widget has to go through to earn the label "bioWidget."

David Benton, of SmithKline Beecham, outlined a new proposal called BioMolecules that extends the model of the bioWidgets Consortium to other areas in bioinformatics, such as algorithmic engines for such common software tasks as sequence similarity searching or multiple sequence alignment, and access to local and remote databases. He proposed using CORBA for this effort and affiliating with the Object Management Group (OMG).

One of the major results of this part of the conference "is the bioWidgets API, which is going to come out within the next couple of weeks, and will probably be published in CABIOS or a similar outlet," concluded Suzanna Lewis of the University of California, another member of the board of directors of the bioWidget Consortium. Addressing the doubts some attendees had about the usefulness of the OMG BioMolecules proposal, Lewis stated, "I absolutely think the bioWidget Consortium and the OMG BioMolecules can coexist, because the two are very separate. Where the bioWidgets focus on graphical views, the OMG BioMolecules is about the datamodels, and it is the datamodel that you pass to a widget. The two are tightly coupled. I think this a very intriguing proposal and I intend to be involved myself."

For the remainder of the conference, the focus turned to case studies of the object-oriented approach in bioinformatics tools and to recent developments in distributed, collaborative, and interoperable objects. Presentations, posters, and demonstrations revealed a definite trend toward reusable, and especially interoperable or collaborative, objects. Reusable objects are software components that can be reused with ease for the same task in other unrelated applications. Objects that have a well-defined API and can work together are called interoperable objects. Collaborative objects take it one step farther: they can be queried by other objects to reveal their purpose and how to communicate with them. Distributed objects reside in different processes or physically different locations, but can be queried over the network by other objects to perform a task, such as retrieving sequence information from a database.

Although the first part of the conference was dedicated to the bioWidgets Consortium, other initiatives toward reusable componentry in bioinformatics were also presented. Stephen Chervitz of Stanford University discussed his group's Bioperl project, in which they aim to develop a set of object-oriented Perl modules to manipulate molecular information. The Bioinformatics Template Library (BTL), focused at providing a library of C++ algorithms and data structures for bioinformatics and molecular modeling, was outlined by David Moss of the Department of Crystallography at Birckbeck College in London.

Java was one of the most prevalent languages of choice in this arena, but "there seems to be a general consensus, a convergence to adopting CORBA as a way of data exchange," Lewis said.

Commenting on the different initiatives in creating bioinformatic objects, David Parry-Smith, of the Bioinformatics Group at Pfizer Central Research in the U.K., noted, "There has been a lot about widgets, interoperable objects and developing software collaboratively, reusing software, all those things that we all knew before we came here. But I think what's come out of it is that there is a strong need for standardization somewhere along the line. Not everyone is clear about where that standardization line should be. One of the issues that underlies this all is the legal side of how to actually share code. The bioWidget Consortium hasn't been able to come to an agreement about licensing yet, and other initiatives, like the Open Molecule Foundation, have had similar discussions and haven't come up with an acceptable agreement either. Without some move on that front it is going to be very difficult for us to share code, so some of these ideals of code reuse come actually to perish."

However, Lewis countered, "in my opinion it is possible to share code and I really think that whether you are commercial, academic, or nonprofit, you'll gain from sharing code and ideas and using these for a bigger creative outlet in whatever it is you're doing."

Her sentiment was shared by many presenters and attendees, who said they wanted to cooperate with the bioWidget Consortium or one of the other complementary initiatives. For academic and nonprofit organizations, the legal issues are secondary to ensuring that they aren't left behind in the thrust toward the development of a new generation of bioinformatics applications.

--Jean-Jack M. Riethoven

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