[Socbin] CFP: NETTAB 2005 Workflow management in bioinformatics

[Paolo Romano]

                   NETTAB 2005 Workshop on

                    Workflows management:
    new abilities for the biological information overflow

              October 5-7, 2005, Naples, Italy

                 http://www.nettab.org/2005/

                       CALL FOR PAPERS

Scope

It is well known that bioinformatics has to cope with one of the largest
amounts of information in all knowledge domains. This not only includes
biological sequences and structures, but also, increasingly, microarray
data, metabolic pathways, interaction maps and gene networks. Moreover,
this information is exponentially increasing in volume (e.g., DNA sequences
increased more than 10% during last three months), so very soon it will
no longer be locally manageable.

This huge amount of data is also largely distributed over the network, has
heterogeneous data structures and information systems and, often, even
differing semantics. The same heterogeneity applies to the many available
software applications.

The biomedical research domain is also one of the fastest evolving research
areas. New knowledge and hypotheses are accumulated daily, often leading to
new data and elaboration needs. User needs are often peculiar and different
from one application domain to another. In this context, the development of
general purpose applications is difficult, both because of the different
users' needs and quickly accumulating knowledge, and thus limitated to some
basic tools.

Biological information is made available to researchers through web sites.
Biologists connect to many sites and switch among them to submit and retrieve
preliminary and intermediate data. Final achievements are often the result
of a manual integration activity. The huge amount of information makes its
access inexhaustive and inefficient and requires the development of complex
searching and retrieval software. They can be developed to perform this
integration activity, provided that they are taught the semantics of the
information, how to link data and how to pipe retrieval and analysis steps.

According to the Workflow Management Coalition, a workflow is "a computerized
facilitation or automation of a business process, in whole or part".
Its main goal is the implemention of data analysis processes in standardized
environments. Its main advantages relate to:

- effectiveness: being an automatic procedure, it frees the bioscientist from
   repetitive interactions with the web and it supports good practice,
- reproducibility: analysis can be replicated over time,
- reusability: intermediate results can be reused,
- traceability: the workflow is carried out in a transparent analysis
   environment where data provenance can be checked and/or controlled.

Workflow systems can also support a better interactive management of flows
of data and analysis, not necessarily encoded in an automated pipeline.

Advantages of changing current biological information management from a
human-oriented to a machine-oriented approach are therefore clear. Machine
orientation is quickly improving, both as to technologies and tools and as
to its diffusion in the biomedical domain. Many Web Services have been
implemented, even by some of the most important network service institutes,
such as EBI and NCBI. Technologies related to registries of biological web
services and related implementation are also emerging, e.g. bioMOBY.

It therefore comes as no surprise that implementation of workflow management
software has already started. In recent years, we have seen Biopipe, an
add-on to bioperl for pipelines management, and GPipe, an extension of the
Pise interface. Even more recently, some quite sophisticated tools as EBI's
Taverna, maybe the most well known workflow management tool that is being
developed within MyGrid project, Wildfire and SciTegic's Pipeline Pilot.
And many others are probably coming.

Workshop aims are:
- to collect the latest ideas, achievements and proposals in the
   application of workflow management systems in bioinformatics
- to strengthen the relationships within bioinformatics community, also
   in view of a wider synergistic effort towards common scientific aims,
- to improve cooperation between bioinformatics and biomedical communities.

The workshop is organized in sessions, where invited speakers present
the state of art of the session's topic, and open discussions.
Open discussions will also be based upon submitted issues and topics.
Tutorials are also foreseen. A limited number of submissions will be
accepted for oral presentation, and others for presentation in a poster 
session.

A call for position papers, posters and oral presentation is now open.


SUBMISSION OF CONTRIBUTIONS

Authors are encouraged to submit:

Oral Presentations: submit an extended abstract (4-5 A4 pages, size
   12pt, MS Word format). Abstracts will be reviewed and acceptance
   or rejection will be communicated to authors.
   All submissions for oral presentation which are not selected
   will automatically be considered for posters presentation.

Posters: submit an extended abstract (2-3 A4 pages, size 12pt, MS Word
   format). Abstracts will be reviewed by relevance and acceptance or
   rejection will be communicated to authors.

Position papers: submit a short abstract (max 1 A4 pages in length,
   size 12pt, MS Word format) specifying research interests and issues
   to be debated during the workshop.
   Authors submitting position papers do not engage themselves to present
   a poster. Instead, they will be invited to introduce the issues they
   arose before open discussion sessions.

Abstracts can be submitted from May 1st, 2005, through the NETTAB 2005
Paper Review System availble at the workshop web site.

Contributions will be reviewed by the scientific committee for relevance,
clarity and novelty of results.

Accepted oral presentations, posters and position papers will be published
in the conference proceedings.
Authors of a selection of best papers will be asked to submit an extended
version of their paper in view of a joint submission to a peer-reviewed
international journal.

TOPICS

Submitted contributions should address one or more of the following topics:

Technologies and technological platforms of interest to the field,
with emphasis on:
- Web Services (SOAP, WSDL, WSFL, UDDI, ....)
- Web Services Choreography and Orchestration
- Semantic Web (RDF, LSID, OWL, ...)
- comparison of available technologies, limitations, pros and cons
- Knowledge representation
- Biological data and knowledge modeling tools
- Ontologies, Databases and Applications of Semantics in Bioinformatics

Workflow management systems in bioinformatics:
- implementations of web services
- implementations of registries
- reuse and versioning of web services and workflows
- workflow management systems
- web interfaces for accessing and executing workflows
- interactive systems to support work flows

Applications of workflow management systems in bioinformatics
- Methodologies for life sciences analysis:
   gene expression, genome annotation, mass spec peptide fragment
   identification, etc...
- Encoding of the above in workflows
- Case studies
- Scenarios and use cases


DEADLINES

- Oral presentations due: June 17, 2005.
- Notification to authors: July 29, 2005.
- Posters and position papers due: August 26, 2005.

Registration:
- Early registration: August 26, 2005


NETTAB Workshops

NETTAB workshops are a series of workshops focused on the most
promising and innovative ICT tools and to their usefulness in
Bioinformatics. Participation is at an international level and
speakers are among the most known researchers in the field.

NETTAB workshops:

- Focus on a well defined, emerging, promising ICT technology
   (not on a specific biological research topic)
- Introduce the basic knowledge related to the technology under
   analysis, in a non-trivial way
- Outline the promising features of the technology in bioinformatics
- Show some valuable examples in bioinformatics or different domains
- Allow for as much discussion as possible
- Demonstrate "how it works" practically, through demos or tutorials

Visit the NETTAB workshops site for information on previous editions.
See http://www.nettab.org/ .

On behalf of Organizing and Scientific Committees

Paolo Romano

Paolo Romano (paolo.romano at istge.it)
Bioinformatics and Structural Proteomics
National Cancer Research Institute (IST)
Largo Rosanna Benzi, 10, I-16132, Genova, Italy
Tel: +39-010-5737-288  Fax: +39-010-5737-295