Automated Function Prediction
Bioinformatics and Disease
BioLINK
Bio-Ontologies

Alternative Splicing
Bioinformatics Open Source Conference (BOSC'2005)
Joint Meeting: BioPathways and SIGSM

Abstract: The deluge of genomic information begs the following question: what do all these genes do? Many genes are not annotated, and many more are partially or erroneously annotated. Given a genome which is partially annotated at best, how do we fill in the blanks? We are faced with the problem of predicting protein function from sequence, genomic, expression, interaction and structural data. For all these reasons and many more, automated function prediction is rapidly gaining interest among computational biologists. We are pleased to announce that the first Automated Function Prediction (AFP) meeting will be held as a Special Interest Group satellite meeting (SIG) of ISMB 2005. This will be an opportunity for computational biology groups involved in function prediction to discuss the latest research in the field. Additionally, we will be challenging publicly available function prediction servers to predict the function for a set of select targets. The results of this challenge will be discussed at the meeting.

The organizing committee of AFP is currently seeking speakers for AFP 2005. Talks are sought in, but not limited to, the following topics:

• Function prediction using sequence based methods. This would include "classic" methods such as detection of functional motifs and inferring function from sequence similarity.
• Function from genomic information: prediction by genomic location; locus comparison with other organisms; function gain and loss.
• Phylogeny based methods
• Function from molecular interactions
• Function from structure
• Function prediction using combined methods
• "Meta-talks" discussing the limitations and horizons of computational function prediction.
• Towards a function prediction competition: assessing function prediction programs

We are also seeking servers for the function prediction assessment. If your group has such a server, we would be very happy if you contact us. Servers will be challenged with a select set of targets, the results assessed and discussed at the meeting in an open and collaborative fashion. Obviously, this first meeting will be more concerned with defining this complex and challenging problem, and planning the means to attack it. We would like to stress that the data submission, result collection and assessment will be done by the AFP assessment team.

Finally, we are seeking sponsors for the meeting. Organizations which would like to get involved are welcome to contact the organizing committee for sponsorship details.

Contact: Iddo Friedberg, idoerg@burnham.org

Abstract: This is an exciting time in the field of alternative splicing, combining new discoveries from genomics, bioinformatics, and molecular biology. Long considered to be an interesting but less common form of regulation, alternative splicing has emerged as a ubiquitous mechanism of regulation, thanks to genomics studies of human and other data. Whereas the Human Genome Project has produced a net result of 25,000 – 30,000 genes, alternative splicing evidently produces over 100,000 distinct transcript forms. Identifying, quantifying, and analyzing the regulation, function and evolution of these forms constitutes a “Human Transcriptome Project”, and will require as remarkable and as concerted an effort as the Human Genome Project. Above all, it will require close collaboration between bioinformaticists and experimentalists, to build a community of shared tools, databases, nomenclature and standards that permit everyone to contribute what they do best, while benefiting from what everyone else has done. This SIG aims to establish a permanent forum for bioinformaticists and experimentalists to come together in this field.

The purpose of this SIG is to cover the latest results and questions in this exciting field, and to bring together bioinformaticists and experimentalists, focusing on questions that demand their collaboration. The SIG will include studies of alternative splicing both in human and other organisms, and will consist of two days of talks (approximately 20 minutes each), and a poster session. Talks will be grouped in four major areas:

1. Technologies: new experimental approaches for high-throughput discovery, quantification, and functional analysis of alternative splice forms in both mRNA and protein. These include splice-variant measurement technologies such as microarrays; laboratory protocols/assays; validation techniques; and novel instrumentation platforms.
2. Biology: Biological mechanisms of splicing and regulation; biological functions such as the impact of splice variants on protein structure and biological pathways; phenomena such as nonsense-mediated decay and disease associations.
3. Bioinformatics: algorithms and analysis of alternative splicing, including topics such as analysis of alternative splicing evidence, products, and functional impact; comparative genomics; alternative splicing regulation; and data-mining.
4. Databases, Standards, and Community Building for the “Human Transcriptome Project”: our research community is in effect building a catalog of the 100,000+ transcript forms found in human (and other transcriptomes), including their precise structures, products, regulation, functional and experimental annotation. This massive project, comparable in scale to the Human Genome Project, requires the efforts of the entire community, as well as agreed standards for sharing data, i.e. a common database, data standards, and shared tools. What data and tool standards do we need? What nomenclature must we agree on? How can we unify our efforts via a common database? How can we integrate data from genomics, bioinformatics and traditional experiments? How can we enable community annotation, curation and validation?

Contact: Christopher Lee, leec@chem.ucla.edu; Shoba Ranganathan, shoba@els.mq.edu.au; Stefan Stamm, stefan@stamms-lab.net; Hui Wang, Hui_Wang@affymetrix.com

Abstract: Bioinformatics has become a fundamental tool for understanding the molecular basis of disease. It is now commonplace for candidate drug targets to be both suggested and validated through genomic research. Expression profiles derived through microarray analysis routinely give insight into disease aetiology. The study of polymorphisms provides information on the basis of inherited disease and susceptibility to common disease. There are many other examples.

Information: The CCP11 SIG on Bioinformatics and Disease will present keynote lectures from protagonists in the field. Primarily, however, it is an opportunity for younger scientists, postdocs and students to present 20 minute talks on their bioinformatic success stories in this area.

Submission of Papers: Abstracts of proposed talks should be submitted no later than May 16, 2005 to Clare Sansom (c.sansom@mail.cryst.bbk.ac.uk). They shall be passed on to the Programme Committee who will then invite successful researchers to speak at the event. All unsuccessful abstracts will be considered for poster presentation.

Contact: Clare Sansom, c.sansom@mail.cryst.bbk.ac.uk

Abstract: Recent years have seen an interesting confluence between the worlds of bioinformatics and natural language processing. Molecular biologists, confronted with new high-throughput sources of data, have recognized that language processing can provide them with tools for handling a flood of data that is unprecedented in the history of the life sciences. The natural language processing community, in turn, has become aware of the resources that the computational bioscience community has made available, and there has been growing interest in applying natural language processing techniques to mine the biological literature to support complex applications in the biological domain, ranging from identifying relevant literature (information retrieval) to extraction of experimental finding to populate biological knowledge bases to summarization, to present key facts to biologists in succinct form.

A number of successful conferences and workshops have resulted, with significant progress in the areas of entity identification, concept normalization, and system evaluation coming through competitions like the KDD Cup, BioCreAtIvE and through shared resources like the Genia corpus.

This workshop will continue the interaction between these communities and bring researchers in natural language processing in the bioinformatics and biomedical domains together with scientists in bioinformatics and biology.

Contact: Christian Blaschke, blaschke@almabioinfo.com

Abstract: The Bio-Ontologies workshop has been a satellite meeting to the annual ISMB conference since 1998, and is now operated as a Special Interest Group at the ISMB Conference. Bio-Ontologies is well established as one of the key meetings for dissemination of latest information and research on ontologies in the life sciences and has drawn the key researchers in the field.

Ontologies provide a mechanism for organising, sharing and reconcilingdata. Within recent years there has been a great deal of interest in the use of ontologies within bioinformatics, particularly in providing computationally accessible annotation, or standard data models for complex data for microarray or pathway information.

Meetings such as last years workshop and SOFG have made it clear that there are many important uses of ontologies and a clear realisation of the importance of implementing mechanisms for integrating source ontologies rather than duplicating effort or causing confusion by extending a given ontology to include everything.

However, with the increase in scope and use of ontologies within bioinformatics, issues of scalability, expressivity and best practices for modelling are becoming more important. We are particularly
interested, therefore, in work involving multiple source ontologies, and which cut across the different levels of granularity implicit within biological systems.

Contact: bio-ont-sig@cs.man.ac.uk

Abstract: The 7th BioPathways meeting will be held on June 23rd and 24th, in Detroit, Michigan, USA as a satellite of ISMB 2005. The meeting is organized by the BioPathways Consortium (www.biopathways.org), an open forum aimed at fostering computational approaches to the modeling, reconstruction, analysis and simulation of biological networks.

As in previous years, the meeting will include plenary sessions, presenting invited talks on various aspects of computational pathway biology such as systems scale analysis of molecular networks, reconstruction of pathways from heterogeneous types of high throughout data, the evolution of molecular pathways, and the representation and visualization of pathway data. Each plenary session will include several long invited presentations (45'), followed by a panel discussion on the theme.
To encourage presentation of cutting-edge research and work-in-progress in computational approaches to molecular pathways, we will also include a contributed session, consisting of short presentations of relevant tools. Selected tools will also be featured on the BioPathways Consortiums web site. Particular emphasis will be made on works along the themes of the plenary sessions, as well as research in pathway visualization and reconstruction, all of which are subjects followed by the consortium's workgroups.

Contact: Aviv Regev, ARegev@CGR.Harvard.edu; Vincent Schachter, vs@genoscope.cns.fr

Abstract: The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology.

Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community.

Contact: Darin London, dlondon@ebi.ac.uk