AllBio Activities

All AllBio partners will organize within the next 6 months local or national events to disseminate the idea of the AllBio project and invite for collaborations within AllBio. Further, these events should also help to understand and analyse problems in bioinformatics processes within plan sciences, microbiology and livestock research. AllBio will collect, also during these events, Test Cases AllBio will be involved to solve.


The first, and probably most important, task of WP4 will be the coordination of the ontology activities. A crucial step on the path to generalise bioinformatics facilities that were originally developed for activities in the (post-) human genome era will be the harmonisation of the ontologies for data and methods that have so far mainly been developed independently in the various life-science fields. At the highest levels, the ontologies are likely to easily be made to agree, but it is important to cope with a multitude of small problems, such as the simple facts that bacterial genomes do not have introns, or that fungal genomes encode a variety of unique products reflecting biochemical/ biophysical/ morphological/ reproductive/ genetic characteristics distinct from humans and plants, or that plant genomes can be enormous (up to 40 times larger than the human genome and very repetitive owing to polyploidy).

AllBio will organize in March 2012 an Initial Ontology Workshop for 25-40 participants to ensure that the project partners and the external collaborators get access to the information needed to make their facilities operate within the framework of the EDAM ontology. This workshop will also function to make the EDAM team aware of aspects from the bacterial and plant worlds they might have missed and will need to incorporate in EDAM.


The combination of web services and workflow managers such as Taverna, Chipster and Galaxy have proven to be a powerful combination for prototyping bioinformatics programs and pipelines. Often, a workflow is all that is needed to get the job done permanently. The AllBio partners have extensive experience both with workflow-management software (in particular, Taverna, Galaxy and CHIPSTER) and with the creation of web service enabled tools. A programme of activities towards the use of workflow-management software in the bioinformatics activities in the target areas is provided in WP3. Software from within the consortium will be made available as Web services that can be used by workflow-management software; workflow-management training courses are being organised routinely by UNIMAN; examples of workflows that include AllBio produced Web services will be placed on the AllBio portal by individual partners as the tools become available. Many international projects, today, are directed towards systems biology or other holistic approaches.

For the AllBio communities with less experience of developing and deploying web service enabled tools, an initial workshop will be organised by RUNMC in May 2012, and a complementary advanced version of the workshop in month September 2013 offering training for 25-40 participants. These workshops will provide seminars on web service technology, ‘hands on’ practice on deploying web services, and also ‘clinics’ to help those with existing services to use the appropriate ontologies and interchange schemas.

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