BOSC 2001 Bioinformatics Open Source Conference

Talk Abstracts
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1 Aug, 9:15 - 10:15 Ewan Birney Keynote

Are we growing up? Reports from the open bioinformatics foundation and the open bioinformatics database access project.

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1 Aug, 10:15 - 10:40 Bioperl project report
Jason Stajich / Duke University
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The Bioperl project recently released version 1.0 of our toolkit for life science programming. The components include modules which support sequences, sequence reading and writing, sequence features and annotations and features with simple and complex locations, multiple sequence alignments, phylogenetic trees, BLAST & FASTA parsing, building and accessing local sequence databases, accessing remote sequence databases, retrieving and manipulating bibliographic references, interoperating with BioCORBA and OBDA biological object standards. The toolkit has been used in a wide array of situations from simple laboratory situations and as the building blocks for enterprise solutions in EnsEMBL and the Generic Model Organism Database (GMOD).

The toolkit is built with an easily extensible architecture which can be used for quickly building perl programs to address specific research questions. Several examples of its use to answer real laboratory questions will be discussed.

License: Perl Artistic.

1 Aug, 11:00 - 11:25 Bioperl-Pipeline System
Shawn Hoon / Fugu Genome Project, Singapore
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The prominence of the in-silico laboratory coupled with the explosion of comparative genomics have made the nature of computational biological analysis increasingly complex. This is exacerbated by the plethora of software that are now available. It is not uncommon for an analysis to involve large amounts of data from disparate sources and formats, different programs with specific requirements and output formats that must be suitable for human interpretation. There thus exists a need for a flexible workflow framework that will hide such complexity, allowing scientists to focus on their analysis, while providing bioinformaticians a coherent methodology for which to extend the system. It was with this in mind that we developed the bioperl-pipeline system. Largely adapted from the Ensembl Pipeline Annotation System, some of the features in the current system include:

  1. Handling of various input and output data formats from various databases.
  2. A bioperl interface to non-specific loadsharing software (LSF,PBS etc) to ensure that the various analysis programs are run in proper order and are successfully completed while re-running those that fail.
  3. A flexible pluggable bioperl interface that allows programs to be 'pipeline-enabled'.

We are currently looking at extending the system in the following way:

  1. A 'grid-aware' system that allows jobs to be distributed over a bio-cluster network harnassing collective computing power that will be especially useful for small groups looking to perform compute-intensive analysis.
  2. A user-friendly click and drag GUI system to allow easy workflow design and job tracking.

We are now applying this framework to our compara system for high throughput multi-species studies. We will discuss the design and implementation details of the bioperl-pipeline package.

1 Aug, 11:25 - 11:35
Cancer Bioinformatics Infrastructure Objects (caBIO): An open-source, object oriented API for biomedical informatics
Peter A. Covitz, Himanso Sahni, Scott Gustafson, and Kenneth Buetow
National Cancer Institute Center for Bioinformatics

The National Cancer Institute has established a Center for Bioinformatics (NCICB) whose mission is to support the NCI's programs in basic and clinical cancer research. The NCICB is aggressively pursuing a program to develop a core infrastructure and API for biomedical information management and retrieval. The initiative employs industry-standard software engineering methodologies to develop data models, middleware, vocabularies and ontologies for biomedical research.

caBIO is the primary programming interface to the core infrastructure. caBIO objects are implemented using Java and Java Bean technology, and represent biological and laboratory entities such as genes, chromosomes, sequences, libraries, clones, pathways, and ontologies. caBIO provides uniform API access to a variety of genomic, biological, and clinical data sources including GenBank, Unigene, LocusLink, Homologene, Ensembl, Golden Path, DAS servers, CGAP, NCI Enterprise Vocabulary Services, and clinical trials protocols. Any client can retrieve HTML and XML from caBIO via HTTP. Java-based clients can further communicate with caBIO via the domain objects provided by the caBIO JAR, while server components can communicate via Java RMI. Non-Java applications can communicate via SOAP. RDF is currently used to advertise cialis services to crawlers and agents, and a UDDI registry is planned. For its presentation layer, caBIO uses servlets and JSPs under Jakarta Tomcat. All caBIO objects can be transformed into XML, and XSL/XSLT is used to present data in documents, web pages or other interfaces.

NCICB makes the caBIO interfaces available on its public servers, and also makes the underlying software available for use at at local sites. More information is available at The open source license covering caBIO software can be found at

1 Aug, 11:35 - 12:00 Biopython and the Laboratory Scientist
Brad Chapman / University of Georgia
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Biopython is a collection of open-source tools in the Python programming language. Developed by a collection of programmers from around the world, the Biopython toolkit is designed to provided re-usable code for anyone answering biological questions using Python. Biopython has been around since 1999, and has a number of active contributors and users. In this talk, I will briefly describe the basic components provided in the Biopython toolkit. From there, I will describe how Biopython can be used in a academic laboratory environment, taking examples from my own lab. The emphasis will be on utilization of Biopython code for automating everyday tasks faced by wet lab researchers. I will try to show that Python and Biopython can be used productively by researchers lacking formal training in computer science. Finally, I will describe integrating Biopython into larger bioinformatics projects. Again, this will draw on my own experience using Biopython and will describe how using Biopython can help make your coding life easier when approaching a large project. The aim of the entire talk it to convince you that using open source libraries like Biopython is worth the time invested in learning it.

1 Aug, 1:50 - 2:15 The Open Source Authors' Contract
Steven Brenner / University of California, Berkeley

Most universities, national laboratories, companies, and other employers have clauses in their employment contracts that prevent or restrict the creation and use of open source software. Indeed, it seems likely that much of the biological open source software is being produced illegally, in violation of institutions' terms. While benign neglect of enforcement of the institutions' regulations has led to a situation that is generally acceptable, it is not ideal.

Several individuals have sought the ability to produce open source software by seeking exemptions or variations of their institutions' intellectual property agreements. However, this is a painstaking process, and the associated legal fees can be costly. I propose that a general contract be drawn up, which has standard terms for individuals to create open source software without undue constraints.

Since this idea was first broached a year ago, there has been widespread discussion regarding regulations governing production open source software. This talk will provide a background to the motivation for the Authors' contract, as well as recent responses which suggest productive ways forward.

1 Aug, 2:15 - 2:40 BioJava Toolkit Progress
Matthew Pocock / BioJava Consulting Limited

BioJava is an open-source software project that aims to provide an industry-quality Java library for common bioinformatics tasks. BioJava is part of the open-bio foundation. BioJava was started in the autumn of 1998, and now has over 25 developers. In the past two years, the core development team has expanded from the original team of two to five. This has brought with it a greater range of views and expertise, as well as a greater stability. In parallel with this, we are in the process of integrating unit testing to maintain the quality of the >130,000 lines of code and documentation in the core library.

BioJava has taken an active role in participating in the open-bio hackathons. Representatives have attended both legs of the hackathon (Tuscon, AZ, USA and Cape Town, SA). During this time, several important interoperabe technologies were designed and implemented. These include a registry file format for biological entities, an SQL schema for storage of sequences and their annotations, BioCorba-based corba clients and servers, bibliographic web services, web services for publishing sequence data and flat file indexing. All of these have been implemented in BioJava, and interoperate with implementations in the other open-bio language projects, as well as with some external implementations.

Over the next year, we hope to mature the library's functionality in areas related to sequence manipulation, pipeline management, alignments, Sequence GUIs and file parsers. In parallel, we shall be integrating code-generation, more flexible transaction management and ontology representations with the current free-form annotation model and BioJava interfaces to allow the representation of more fluid data types, and more maintainable and robust implementation of standard interfaces.

1 Aug, 2:40 - 2:50 GOET: the General Ontology Editing Tool
John Richter / Berkeley Drosophila Genome Project

GOET is a Java application designed to facilitate the creation of ontology schemas and data. GOET allows a user to define DAML+OIL-like schemas and then populate those schemas with data. Data can loaded from and saved to DAML+OIL flat files, as well as numerous other formats.

GOET is highly customizable via pluggable editor kits. Editor kits are Java jar files that define a custom user interface for GOET, tailored to a particular kind of data. Editor kits allow programmers to create the most efficient user interface for any given ontology. GOET comes with a generic editor kit that can edit any ontology, making it easy for users to experiment with new schemas.

GOET provides a strong toolkit for ontology editing, with automatic support for history tracking, undo/redo, cycle checking, and other important graph editing tools. This toolkit makes it easy for programmers to develop new, powerful editor kits. Other information:
GOET is being developed as part of the gmod project at
Like all gmod components, GOET is distributed under the terms of the Artistic License.

1 Aug, 2:50 - 3:00 GHMM & HMMed: A comprehensive HMM toolkit
Alexander Schliep / Max-Planck-Institut for Molecular Genetics

Hidden Markov Models (HMMs) are one of the m